https://launchpad.net/ubuntu/+source/python-biopython/1.80+dfsg-4ubuntu1/+build/26341718 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux riscv64-qemu-lgw01-087 5.13.0-1019-generic #21~20.04.1-Ubuntu SMP Thu Mar 24 22:36:01 UTC 2022 riscv64 Buildd toolchain package versions: launchpad-buildd_233~634~ubuntu20.04.1 python3-lpbuildd_233~634~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git_1:2.25.1-1ubuntu3.2 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 27 Jun 09:21:53 ntpdate[2631449]: adjust time server 10.211.37.1 offset -0.000281 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=mantic --arch=riscv64 PACKAGEBUILD-26341718 --image-type chroot /home/buildd/filecache-default/859743d4aa431be74cb50b11ddbd51d0d1ab094f Creating target for build PACKAGEBUILD-26341718 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=mantic --arch=riscv64 PACKAGEBUILD-26341718 Starting target for build PACKAGEBUILD-26341718 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=mantic --arch=riscv64 PACKAGEBUILD-26341718 'deb http://ftpmaster.internal/ubuntu mantic main universe' 'deb http://ftpmaster.internal/ubuntu mantic-security main universe' 'deb http://ftpmaster.internal/ubuntu mantic-updates main universe' 'deb http://ftpmaster.internal/ubuntu mantic-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-26341718 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=mantic --arch=riscv64 PACKAGEBUILD-26341718 Updating target for build PACKAGEBUILD-26341718 Get:1 http://ftpmaster.internal/ubuntu mantic InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu mantic-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu mantic-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu mantic-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu mantic/main riscv64 Packages [1320 kB] Get:6 http://ftpmaster.internal/ubuntu mantic/main Translation-en [515 kB] Get:7 http://ftpmaster.internal/ubuntu mantic/universe riscv64 Packages [13.9 MB] Get:8 http://ftpmaster.internal/ubuntu mantic/universe Translation-en [5937 kB] Get:9 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 Packages [64.8 kB] Get:10 http://ftpmaster.internal/ubuntu mantic-proposed/main Translation-en [29.9 kB] Get:11 http://ftpmaster.internal/ubuntu mantic-proposed/universe riscv64 Packages [571 kB] Get:12 http://ftpmaster.internal/ubuntu mantic-proposed/universe Translation-en [222 kB] Fetched 23.1 MB in 27s (843 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: gcc-13-base libproc2-0 The following packages will be upgraded: adduser advancecomp apt base-files bash binutils binutils-common binutils-riscv64-linux-gnu bsdutils ca-certificates coreutils cpp cpp-12 dash debconf diffutils dpkg dpkg-dev e2fsprogs fakeroot findutils g++ g++-12 gcc gcc-12 gcc-12-base gpg gpg-agent gpgconf gpgv grep hostname libacl1 libapparmor1 libapt-pkg6.0 libargon2-1 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdb5.3 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libext2fs2 libfakeroot libfdisk1 libgcc-12-dev libgcc-s1 libgcrypt20 libgnutls30 libgomp1 libgssapi-krb5-2 libisl23 libk5crypto3 libkmod2 libkrb5-3 libkrb5support0 liblzma5 libmd0 libmount1 libmpfr6 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libperl5.36 libpng16-16 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsmartcols1 libsqlite3-0 libss2 libssl3 libstdc++-12-dev libstdc++6 libsystemd-shared libsystemd0 libtinfo6 libudev1 libuuid1 libzstd1 linux-libc-dev logsave lsb-base lto-disabled-list mawk mount ncurses-base ncurses-bin openssl perl perl-base perl-modules-5.36 pkgbinarymangler procps readline-common sed sensible-utils systemd systemd-sysv sysvinit-utils tar tzdata usrmerge util-linux util-linux-extra xz-utils zlib1g 133 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 93.5 MB of archives. After this operation, 2797 kB disk space will be freed. Get:1 http://ftpmaster.internal/ubuntu mantic/main riscv64 libcrypt-dev riscv64 1:4.4.35-1 [235 kB] Get:2 http://ftpmaster.internal/ubuntu mantic/main riscv64 libc6-dev riscv64 2.37-0ubuntu2 [3134 kB] Get:3 http://ftpmaster.internal/ubuntu mantic/main riscv64 libc-dev-bin riscv64 2.37-0ubuntu2 [18.8 kB] Get:4 http://ftpmaster.internal/ubuntu mantic/main riscv64 libcrypt1 riscv64 1:4.4.35-1 [94.6 kB] Get:5 http://ftpmaster.internal/ubuntu mantic/main riscv64 linux-libc-dev riscv64 6.3.0-7.7 [1512 kB] Get:6 http://ftpmaster.internal/ubuntu mantic/main riscv64 libc6 riscv64 2.37-0ubuntu2 [2609 kB] Get:7 http://ftpmaster.internal/ubuntu mantic/main riscv64 libc-bin riscv64 2.37-0ubuntu2 [551 kB] Get:8 http://ftpmaster.internal/ubuntu mantic/main riscv64 gcc-13-base riscv64 13.1.0-6ubuntu1 [42.0 kB] Get:9 http://ftpmaster.internal/ubuntu mantic/main riscv64 libgcc-s1 riscv64 13.1.0-6ubuntu1 [57.2 kB] Get:10 http://ftpmaster.internal/ubuntu mantic/main riscv64 base-files riscv64 13ubuntu1 [73.7 kB] Get:11 http://ftpmaster.internal/ubuntu mantic/main riscv64 bash riscv64 5.2.15-2ubuntu1 [672 kB] Get:12 http://ftpmaster.internal/ubuntu mantic/main riscv64 bsdutils riscv64 1:2.38.1-5ubuntu2 [101 kB] Get:13 http://ftpmaster.internal/ubuntu mantic/main riscv64 coreutils riscv64 9.1-1ubuntu2 [1309 kB] Get:14 http://ftpmaster.internal/ubuntu mantic/main riscv64 liblzma5 riscv64 5.4.1-0.2 [115 kB] Get:15 http://ftpmaster.internal/ubuntu mantic/main riscv64 libgcrypt20 riscv64 1.10.1-3ubuntu1 [503 kB] Get:16 http://ftpmaster.internal/ubuntu mantic/main riscv64 libstdc++6 riscv64 13.1.0-6ubuntu1 [779 kB] Get:17 http://ftpmaster.internal/ubuntu mantic/main riscv64 libacl1 riscv64 2.3.1-3 [15.7 kB] Get:18 http://ftpmaster.internal/ubuntu mantic/main riscv64 libapparmor1 riscv64 3.0.8-1ubuntu3 [43.1 kB] Get:19 http://ftpmaster.internal/ubuntu mantic/main riscv64 libaudit-common all 1:3.0.9-1 [5142 B] Get:20 http://ftpmaster.internal/ubuntu mantic/main riscv64 libcap-ng0 riscv64 0.8.3-1build2 [13.6 kB] Get:21 http://ftpmaster.internal/ubuntu mantic/main riscv64 libaudit1 riscv64 1:3.0.9-1 [44.0 kB] Get:22 http://ftpmaster.internal/ubuntu mantic/main riscv64 libblkid1 riscv64 2.38.1-5ubuntu2 [155 kB] Get:23 http://ftpmaster.internal/ubuntu mantic/main riscv64 libcap2 riscv64 1:2.66-4ubuntu1 [26.5 kB] Get:24 http://ftpmaster.internal/ubuntu mantic/main riscv64 libperl5.36 riscv64 5.36.0-7ubuntu1 [4203 kB] Get:25 http://ftpmaster.internal/ubuntu mantic/main riscv64 perl riscv64 5.36.0-7ubuntu1 [235 kB] Get:26 http://ftpmaster.internal/ubuntu mantic/main riscv64 perl-base riscv64 5.36.0-7ubuntu1 [1655 kB] Get:27 http://ftpmaster.internal/ubuntu mantic/main riscv64 perl-modules-5.36 all 5.36.0-7ubuntu1 [2984 kB] Get:28 http://ftpmaster.internal/ubuntu mantic/main riscv64 libdb5.3 riscv64 5.3.28+dfsg2-1 [691 kB] Get:29 http://ftpmaster.internal/ubuntu mantic/main riscv64 zlib1g riscv64 1:1.2.13.dfsg-1ubuntu4 [54.0 kB] Get:30 http://ftpmaster.internal/ubuntu mantic/main riscv64 debconf all 1.5.82 [125 kB] Get:31 http://ftpmaster.internal/ubuntu mantic/main riscv64 libssl3 riscv64 3.0.9-1ubuntu1 [1453 kB] Get:32 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 libzstd1 riscv64 1.5.5+dfsg2-1 [314 kB] Get:33 http://ftpmaster.internal/ubuntu mantic/main riscv64 libkmod2 riscv64 30+20221128-1ubuntu1 [43.5 kB] Get:34 http://ftpmaster.internal/ubuntu mantic/main riscv64 libpcre2-8-0 riscv64 10.42-1 [142 kB] Get:35 http://ftpmaster.internal/ubuntu mantic/main riscv64 libselinux1 riscv64 3.4-1build4 [71.6 kB] Get:36 http://ftpmaster.internal/ubuntu mantic/main riscv64 libmount1 riscv64 2.38.1-5ubuntu2 [155 kB] Get:37 http://ftpmaster.internal/ubuntu mantic/main riscv64 libpam0g riscv64 1.5.2-6ubuntu1 [61.6 kB] Get:38 http://ftpmaster.internal/ubuntu mantic/main riscv64 libseccomp2 riscv64 2.5.4-1ubuntu3 [47.0 kB] Get:39 http://ftpmaster.internal/ubuntu mantic/main riscv64 systemd-sysv riscv64 252.5-2ubuntu3 [11.5 kB] Get:40 http://ftpmaster.internal/ubuntu mantic/main riscv64 systemd riscv64 252.5-2ubuntu3 [2815 kB] Get:41 http://ftpmaster.internal/ubuntu mantic/main riscv64 libsystemd-shared riscv64 252.5-2ubuntu3 [1629 kB] Get:42 http://ftpmaster.internal/ubuntu mantic/main riscv64 libatomic1 riscv64 13.1.0-6ubuntu1 [9548 B] Get:43 http://ftpmaster.internal/ubuntu mantic/main riscv64 libargon2-1 riscv64 0~20190702+dfsg-3 [19.9 kB] Get:44 http://ftpmaster.internal/ubuntu mantic/main riscv64 libudev1 riscv64 252.5-2ubuntu3 [143 kB] Get:45 http://ftpmaster.internal/ubuntu mantic/main riscv64 libdevmapper1.02.1 riscv64 2:1.02.185-2ubuntu1 [131 kB] Get:46 http://ftpmaster.internal/ubuntu mantic/main riscv64 libuuid1 riscv64 2.38.1-5ubuntu2 [33.2 kB] Get:47 http://ftpmaster.internal/ubuntu mantic/main riscv64 libcryptsetup12 riscv64 2:2.6.1-4ubuntu1 [210 kB] Get:48 http://ftpmaster.internal/ubuntu mantic/main riscv64 libfdisk1 riscv64 2.38.1-5ubuntu2 [194 kB] Get:49 http://ftpmaster.internal/ubuntu mantic/main riscv64 libp11-kit0 riscv64 0.24.1-2ubuntu1 [196 kB] Get:50 http://ftpmaster.internal/ubuntu mantic/main riscv64 mount riscv64 2.38.1-5ubuntu2 [129 kB] Get:51 http://ftpmaster.internal/ubuntu mantic/main riscv64 libsystemd0 riscv64 252.5-2ubuntu3 [360 kB] Get:52 http://ftpmaster.internal/ubuntu mantic/main riscv64 libapt-pkg6.0 riscv64 2.7.1 [935 kB] Get:53 http://ftpmaster.internal/ubuntu mantic/main riscv64 tar riscv64 1.34+dfsg-1.2ubuntu1 [271 kB] Get:54 http://ftpmaster.internal/ubuntu mantic/main riscv64 dpkg riscv64 1.21.22ubuntu1 [1352 kB] Get:55 http://ftpmaster.internal/ubuntu mantic/main riscv64 dash riscv64 0.5.12-2ubuntu1 [81.8 kB] Get:56 http://ftpmaster.internal/ubuntu mantic/main riscv64 diffutils riscv64 1:3.8-4 [167 kB] Get:57 http://ftpmaster.internal/ubuntu mantic/main riscv64 findutils riscv64 4.9.0-4ubuntu1 [295 kB] Get:58 http://ftpmaster.internal/ubuntu mantic/main riscv64 grep riscv64 3.8-5 [155 kB] Get:59 http://ftpmaster.internal/ubuntu mantic/main riscv64 hostname riscv64 3.23+nmu1ubuntu1 [10.5 kB] Get:60 http://ftpmaster.internal/ubuntu mantic/main riscv64 ncurses-bin riscv64 6.4-4 [177 kB] Get:61 http://ftpmaster.internal/ubuntu mantic/main riscv64 sed riscv64 4.9-1 [191 kB] Get:62 http://ftpmaster.internal/ubuntu mantic/main riscv64 libsmartcols1 riscv64 2.38.1-5ubuntu2 [109 kB] Get:63 http://ftpmaster.internal/ubuntu mantic/main riscv64 util-linux-extra riscv64 2.38.1-5ubuntu2 [104 kB] Get:64 http://ftpmaster.internal/ubuntu mantic/main riscv64 util-linux riscv64 2.38.1-5ubuntu2 [1150 kB] Get:65 http://ftpmaster.internal/ubuntu mantic/main riscv64 ncurses-base all 6.4-4 [23.3 kB] Get:66 http://ftpmaster.internal/ubuntu mantic/main riscv64 sysvinit-utils riscv64 3.06-4ubuntu1 [32.9 kB] Get:67 http://ftpmaster.internal/ubuntu mantic/main riscv64 lsb-base all 11.6 [4606 B] Get:68 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 adduser all 3.134ubuntu1 [136 kB] Get:69 http://ftpmaster.internal/ubuntu mantic/main riscv64 gpgv riscv64 2.2.40-1.1ubuntu1 [205 kB] Get:70 http://ftpmaster.internal/ubuntu mantic/main riscv64 libgnutls30 riscv64 3.7.9-2ubuntu1 [907 kB] Get:71 http://ftpmaster.internal/ubuntu mantic/main riscv64 apt riscv64 2.7.1 [1308 kB] Get:72 http://ftpmaster.internal/ubuntu mantic/main riscv64 libpam-modules-bin riscv64 1.5.2-6ubuntu1 [44.8 kB] Get:73 http://ftpmaster.internal/ubuntu mantic/main riscv64 libpam-modules riscv64 1.5.2-6ubuntu1 [267 kB] Get:74 http://ftpmaster.internal/ubuntu mantic/main riscv64 logsave riscv64 1.47.0-1ubuntu1 [13.7 kB] Get:75 http://ftpmaster.internal/ubuntu mantic/main riscv64 libext2fs2 riscv64 1.47.0-1ubuntu1 [197 kB] Get:76 http://ftpmaster.internal/ubuntu mantic/main riscv64 e2fsprogs riscv64 1.47.0-1ubuntu1 [555 kB] Get:77 http://ftpmaster.internal/ubuntu mantic/main riscv64 libattr1 riscv64 1:2.5.1-4 [11.4 kB] Get:78 http://ftpmaster.internal/ubuntu mantic/main riscv64 libdebconfclient0 riscv64 0.267ubuntu1 [7418 B] Get:79 http://ftpmaster.internal/ubuntu mantic/main riscv64 libmd0 riscv64 1.1.0-1 [28.3 kB] Get:80 http://ftpmaster.internal/ubuntu mantic/main riscv64 libpam-runtime all 1.5.2-6ubuntu1 [41.5 kB] Get:81 http://ftpmaster.internal/ubuntu mantic/main riscv64 libsemanage-common all 3.4-1build4 [9852 B] Get:82 http://ftpmaster.internal/ubuntu mantic/main riscv64 libsepol2 riscv64 3.4-2.1 [258 kB] Get:83 http://ftpmaster.internal/ubuntu mantic/main riscv64 libsemanage2 riscv64 3.4-1build4 [83.5 kB] Get:84 http://ftpmaster.internal/ubuntu mantic/main riscv64 libncurses6 riscv64 6.4-4 [93.2 kB] Get:85 http://ftpmaster.internal/ubuntu mantic/main riscv64 libncursesw6 riscv64 6.4-4 [126 kB] Get:86 http://ftpmaster.internal/ubuntu mantic/main riscv64 libtinfo6 riscv64 6.4-4 [92.6 kB] Get:87 http://ftpmaster.internal/ubuntu mantic/main riscv64 usrmerge all 35ubuntu1 [58.2 kB] Get:88 http://ftpmaster.internal/ubuntu mantic/main riscv64 libcom-err2 riscv64 1.47.0-1ubuntu1 [13.5 kB] Get:89 http://ftpmaster.internal/ubuntu mantic/main riscv64 libproc2-0 riscv64 2:4.0.3-1ubuntu1 [45.2 kB] Get:90 http://ftpmaster.internal/ubuntu mantic/main riscv64 libss2 riscv64 1.47.0-1ubuntu1 [15.2 kB] Get:91 http://ftpmaster.internal/ubuntu mantic/main riscv64 mawk riscv64 1.3.4.20230525-1 [103 kB] Get:92 http://ftpmaster.internal/ubuntu mantic/main riscv64 procps riscv64 2:4.0.3-1ubuntu1 [598 kB] Get:93 http://ftpmaster.internal/ubuntu mantic/main riscv64 sensible-utils all 0.0.20 [19.6 kB] Get:94 http://ftpmaster.internal/ubuntu mantic/main riscv64 openssl riscv64 3.0.9-1ubuntu1 [1149 kB] Get:95 http://ftpmaster.internal/ubuntu mantic/main riscv64 ca-certificates all 20230311ubuntu1 [152 kB] Get:96 http://ftpmaster.internal/ubuntu mantic/main riscv64 libgssapi-krb5-2 riscv64 1.20.1-2 [125 kB] Get:97 http://ftpmaster.internal/ubuntu mantic/main riscv64 libkrb5-3 riscv64 1.20.1-2 [329 kB] Get:98 http://ftpmaster.internal/ubuntu mantic/main riscv64 libkrb5support0 riscv64 1.20.1-2 [31.3 kB] Get:99 http://ftpmaster.internal/ubuntu mantic/main riscv64 libk5crypto3 riscv64 1.20.1-2 [96.5 kB] Get:100 http://ftpmaster.internal/ubuntu mantic/main riscv64 readline-common all 8.2-1.3 [55.7 kB] Get:101 http://ftpmaster.internal/ubuntu mantic/main riscv64 libreadline8 riscv64 8.2-1.3 [131 kB] Get:102 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 libsqlite3-0 riscv64 3.42.0-1 [586 kB] Get:103 http://ftpmaster.internal/ubuntu mantic/main riscv64 tzdata all 2023c-4exp1ubuntu1 [271 kB] Get:104 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 libpng16-16 riscv64 1.6.40-1 [174 kB] Get:105 http://ftpmaster.internal/ubuntu mantic/main riscv64 xz-utils riscv64 5.4.1-0.2 [266 kB] Get:106 http://ftpmaster.internal/ubuntu mantic/main riscv64 advancecomp riscv64 2.5-1 [216 kB] Get:107 http://ftpmaster.internal/ubuntu mantic/main riscv64 libctf0 riscv64 2.40.50.20230622-1ubuntu1 [87.5 kB] Get:108 http://ftpmaster.internal/ubuntu mantic/main riscv64 libctf-nobfd0 riscv64 2.40.50.20230622-1ubuntu1 [89.0 kB] Get:109 http://ftpmaster.internal/ubuntu mantic/main riscv64 binutils-riscv64-linux-gnu riscv64 2.40.50.20230622-1ubuntu1 [827 kB] Get:110 http://ftpmaster.internal/ubuntu mantic/main riscv64 libbinutils riscv64 2.40.50.20230622-1ubuntu1 [460 kB] Get:111 http://ftpmaster.internal/ubuntu mantic/main riscv64 binutils riscv64 2.40.50.20230622-1ubuntu1 [2992 B] Get:112 http://ftpmaster.internal/ubuntu mantic/main riscv64 binutils-common riscv64 2.40.50.20230622-1ubuntu1 [219 kB] Get:113 http://ftpmaster.internal/ubuntu mantic/main riscv64 libisl23 riscv64 0.26-3 [604 kB] Get:114 http://ftpmaster.internal/ubuntu mantic/main riscv64 libmpfr6 riscv64 4.2.0-1 [260 kB] Get:115 http://ftpmaster.internal/ubuntu mantic/main riscv64 g++-12 riscv64 12.3.0-3ubuntu1 [9551 kB] Get:116 http://ftpmaster.internal/ubuntu mantic/main riscv64 gcc-12 riscv64 12.3.0-3ubuntu1 [16.3 MB] Get:117 http://ftpmaster.internal/ubuntu mantic/main riscv64 cpp-12 riscv64 12.3.0-3ubuntu1 [8279 kB] Get:118 http://ftpmaster.internal/ubuntu mantic/main riscv64 libgomp1 riscv64 13.1.0-6ubuntu1 [140 kB] Get:119 http://ftpmaster.internal/ubuntu mantic/main riscv64 libasan8 riscv64 13.1.0-6ubuntu1 [2500 kB] Get:120 http://ftpmaster.internal/ubuntu mantic/main riscv64 libstdc++-12-dev riscv64 12.3.0-3ubuntu1 [4916 kB] Get:121 http://ftpmaster.internal/ubuntu mantic/main riscv64 libgcc-12-dev riscv64 12.3.0-3ubuntu1 [2637 kB] Get:122 http://ftpmaster.internal/ubuntu mantic/main riscv64 libcc1-0 riscv64 13.1.0-6ubuntu1 [45.4 kB] Get:123 http://ftpmaster.internal/ubuntu mantic/main riscv64 gcc-12-base riscv64 12.3.0-3ubuntu1 [42.8 kB] Get:124 http://ftpmaster.internal/ubuntu mantic/main riscv64 g++ riscv64 4:12.2.0-3ubuntu1 [1108 B] Get:125 http://ftpmaster.internal/ubuntu mantic/main riscv64 gcc riscv64 4:12.2.0-3ubuntu1 [5178 B] Get:126 http://ftpmaster.internal/ubuntu mantic/main riscv64 cpp riscv64 4:12.2.0-3ubuntu1 [27.8 kB] Get:127 http://ftpmaster.internal/ubuntu mantic/main riscv64 dpkg-dev all 1.21.22ubuntu1 [1118 kB] Get:128 http://ftpmaster.internal/ubuntu mantic/main riscv64 libdpkg-perl all 1.21.22ubuntu1 [247 kB] Get:129 http://ftpmaster.internal/ubuntu mantic/main riscv64 lto-disabled-list all 41 [12.4 kB] Get:130 http://ftpmaster.internal/ubuntu mantic/main riscv64 libfakeroot riscv64 1.31-1.2 [27.6 kB] Get:131 http://ftpmaster.internal/ubuntu mantic/main riscv64 fakeroot riscv64 1.31-1.2 [67.9 kB] Get:132 http://ftpmaster.internal/ubuntu mantic/main riscv64 gpg riscv64 2.2.40-1.1ubuntu1 [491 kB] Get:133 http://ftpmaster.internal/ubuntu mantic/main riscv64 gpgconf riscv64 2.2.40-1.1ubuntu1 [121 kB] Get:134 http://ftpmaster.internal/ubuntu mantic/main riscv64 gpg-agent riscv64 2.2.40-1.1ubuntu1 [239 kB] Get:135 http://ftpmaster.internal/ubuntu mantic/main riscv64 pkgbinarymangler all 153 [16.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 93.5 MB in 15s (6351 kB/s) (Reading database ... 13011 files and directories currently installed.) Preparing to unpack .../libcrypt-dev_1%3a4.4.35-1_riscv64.deb ... Unpacking libcrypt-dev:riscv64 (1:4.4.35-1) over (1:4.4.33-1) ... Preparing to unpack .../libc6-dev_2.37-0ubuntu2_riscv64.deb ... Unpacking libc6-dev:riscv64 (2.37-0ubuntu2) over (2.36-0ubuntu4) ... Preparing to unpack .../libc-dev-bin_2.37-0ubuntu2_riscv64.deb ... Unpacking libc-dev-bin (2.37-0ubuntu2) over (2.36-0ubuntu4) ... Preparing to unpack .../libcrypt1_1%3a4.4.35-1_riscv64.deb ... Unpacking libcrypt1:riscv64 (1:4.4.35-1) over (1:4.4.33-1) ... Setting up libcrypt1:riscv64 (1:4.4.35-1) ... (Reading database ... 13011 files and directories currently installed.) Preparing to unpack .../linux-libc-dev_6.3.0-7.7_riscv64.deb ... Unpacking linux-libc-dev:riscv64 (6.3.0-7.7) over (5.19.0-21.21) ... Preparing to unpack .../libc6_2.37-0ubuntu2_riscv64.deb ... Unpacking libc6:riscv64 (2.37-0ubuntu2) over (2.36-0ubuntu4) ... Setting up libc6:riscv64 (2.37-0ubuntu2) ... (Reading database ... 13015 files and directories currently installed.) Preparing to unpack .../libc-bin_2.37-0ubuntu2_riscv64.deb ... Unpacking libc-bin (2.37-0ubuntu2) over (2.36-0ubuntu4) ... Setting up libc-bin (2.37-0ubuntu2) ... Selecting previously unselected package gcc-13-base:riscv64. (Reading database ... 13015 files and directories currently installed.) Preparing to unpack .../gcc-13-base_13.1.0-6ubuntu1_riscv64.deb ... Unpacking gcc-13-base:riscv64 (13.1.0-6ubuntu1) ... Setting up gcc-13-base:riscv64 (13.1.0-6ubuntu1) ... (Reading database ... 13020 files and directories currently installed.) Preparing to unpack .../libgcc-s1_13.1.0-6ubuntu1_riscv64.deb ... Unpacking libgcc-s1:riscv64 (13.1.0-6ubuntu1) over (12.2.0-10ubuntu1) ... Setting up libgcc-s1:riscv64 (13.1.0-6ubuntu1) ... (Reading database ... 13020 files and directories currently installed.) Preparing to unpack .../base-files_13ubuntu1_riscv64.deb ... Unpacking base-files (13ubuntu1) over (12.3ubuntu1) ... Setting up base-files (13ubuntu1) ... Installing new version of config file /etc/debian_version ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... (Reading database ... 13020 files and directories currently installed.) Preparing to unpack .../bash_5.2.15-2ubuntu1_riscv64.deb ... Unpacking bash (5.2.15-2ubuntu1) over (5.2-1ubuntu2) ... Setting up bash (5.2.15-2ubuntu1) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... 13020 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.38.1-5ubuntu2_riscv64.deb ... Unpacking bsdutils (1:2.38.1-5ubuntu2) over (1:2.38.1-4ubuntu1) ... Setting up bsdutils (1:2.38.1-5ubuntu2) ... (Reading database ... 13020 files and directories currently installed.) Preparing to unpack .../coreutils_9.1-1ubuntu2_riscv64.deb ... Unpacking coreutils (9.1-1ubuntu2) over (8.32-4.1ubuntu1) ... Setting up coreutils (9.1-1ubuntu2) ... (Reading database ... 13020 files and directories currently installed.) Preparing to unpack .../liblzma5_5.4.1-0.2_riscv64.deb ... Unpacking liblzma5:riscv64 (5.4.1-0.2) over (5.2.9-0.0) ... Setting up liblzma5:riscv64 (5.4.1-0.2) ... (Reading database ... 13020 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.10.1-3ubuntu1_riscv64.deb ... Unpacking libgcrypt20:riscv64 (1.10.1-3ubuntu1) over (1.10.1-2ubuntu1) ... Setting up libgcrypt20:riscv64 (1.10.1-3ubuntu1) ... (Reading database ... 13020 files and directories currently installed.) Preparing to unpack .../libstdc++6_13.1.0-6ubuntu1_riscv64.deb ... Unpacking libstdc++6:riscv64 (13.1.0-6ubuntu1) over (12.2.0-10ubuntu1) ... Setting up libstdc++6:riscv64 (13.1.0-6ubuntu1) ... (Reading database ... 13020 files and directories currently installed.) Preparing to unpack .../libacl1_2.3.1-3_riscv64.deb ... Unpacking libacl1:riscv64 (2.3.1-3) over (2.3.1-2) ... Setting up libacl1:riscv64 (2.3.1-3) ... (Reading database ... 13020 files and directories currently installed.) Preparing to unpack .../libapparmor1_3.0.8-1ubuntu3_riscv64.deb ... Unpacking libapparmor1:riscv64 (3.0.8-1ubuntu3) over (3.0.8-1ubuntu1) ... Preparing to unpack .../libaudit-common_1%3a3.0.9-1_all.deb ... Unpacking libaudit-common (1:3.0.9-1) over (1:3.0.7-1ubuntu3) ... Setting up libaudit-common (1:3.0.9-1) ... (Reading database ... 13020 files and directories currently installed.) Preparing to unpack .../libcap-ng0_0.8.3-1build2_riscv64.deb ... Unpacking libcap-ng0:riscv64 (0.8.3-1build2) over (0.8.3-1build1) ... Setting up libcap-ng0:riscv64 (0.8.3-1build2) ... (Reading database ... 13020 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a3.0.9-1_riscv64.deb ... Unpacking libaudit1:riscv64 (1:3.0.9-1) over (1:3.0.7-1ubuntu3) ... Setting up libaudit1:riscv64 (1:3.0.9-1) ... (Reading database ... 13020 files and directories currently installed.) Preparing to unpack .../libblkid1_2.38.1-5ubuntu2_riscv64.deb ... Unpacking libblkid1:riscv64 (2.38.1-5ubuntu2) over (2.38.1-4ubuntu1) ... Setting up libblkid1:riscv64 (2.38.1-5ubuntu2) ... (Reading database ... 13020 files and directories currently installed.) Preparing to unpack .../libcap2_1%3a2.66-4ubuntu1_riscv64.deb ... Unpacking libcap2:riscv64 (1:2.66-4ubuntu1) over (1:2.44-1build3) ... Setting up libcap2:riscv64 (1:2.66-4ubuntu1) ... (Reading database ... 13022 files and directories currently installed.) Preparing to unpack .../libperl5.36_5.36.0-7ubuntu1_riscv64.deb ... Unpacking libperl5.36:riscv64 (5.36.0-7ubuntu1) over (5.36.0-4ubuntu2) ... Preparing to unpack .../perl_5.36.0-7ubuntu1_riscv64.deb ... Unpacking perl (5.36.0-7ubuntu1) over (5.36.0-4ubuntu2) ... Preparing to unpack .../perl-base_5.36.0-7ubuntu1_riscv64.deb ... Unpacking perl-base (5.36.0-7ubuntu1) over (5.36.0-4ubuntu2) ... Setting up perl-base (5.36.0-7ubuntu1) ... (Reading database ... 13022 files and directories currently installed.) Preparing to unpack .../perl-modules-5.36_5.36.0-7ubuntu1_all.deb ... Unpacking perl-modules-5.36 (5.36.0-7ubuntu1) over (5.36.0-4ubuntu2) ... Preparing to unpack .../libdb5.3_5.3.28+dfsg2-1_riscv64.deb ... Unpacking libdb5.3:riscv64 (5.3.28+dfsg2-1) over (5.3.28+dfsg1-0.10) ... Setting up libdb5.3:riscv64 (5.3.28+dfsg2-1) ... (Reading database ... 13022 files and directories currently installed.) Preparing to unpack .../zlib1g_1%3a1.2.13.dfsg-1ubuntu4_riscv64.deb ... Unpacking zlib1g:riscv64 (1:1.2.13.dfsg-1ubuntu4) over (1:1.2.11.dfsg-4.1ubuntu1) ... Setting up zlib1g:riscv64 (1:1.2.13.dfsg-1ubuntu4) ... (Reading database ... 13022 files and directories currently installed.) Preparing to unpack .../debconf_1.5.82_all.deb ... Unpacking debconf (1.5.82) over (1.5.79ubuntu1) ... Setting up debconf (1.5.82) ... (Reading database ... 13022 files and directories currently installed.) Preparing to unpack .../libssl3_3.0.9-1ubuntu1_riscv64.deb ... Unpacking libssl3:riscv64 (3.0.9-1ubuntu1) over (3.0.5-2ubuntu2) ... Preparing to unpack .../libzstd1_1.5.5+dfsg2-1_riscv64.deb ... Unpacking libzstd1:riscv64 (1.5.5+dfsg2-1) over (1.5.2+dfsg-1) ... Setting up libzstd1:riscv64 (1.5.5+dfsg2-1) ... (Reading database ... 13022 files and directories currently installed.) Preparing to unpack .../libkmod2_30+20221128-1ubuntu1_riscv64.deb ... Unpacking libkmod2:riscv64 (30+20221128-1ubuntu1) over (30+20220905-1ubuntu1) ... Preparing to unpack .../libpcre2-8-0_10.42-1_riscv64.deb ... Unpacking libpcre2-8-0:riscv64 (10.42-1) over (10.40-1ubuntu1) ... Setting up libpcre2-8-0:riscv64 (10.42-1) ... (Reading database ... 13022 files and directories currently installed.) Preparing to unpack .../libselinux1_3.4-1build4_riscv64.deb ... Unpacking libselinux1:riscv64 (3.4-1build4) over (3.4-1build1) ... Setting up libselinux1:riscv64 (3.4-1build4) ... (Reading database ... 13022 files and directories currently installed.) Preparing to unpack .../libmount1_2.38.1-5ubuntu2_riscv64.deb ... Unpacking libmount1:riscv64 (2.38.1-5ubuntu2) over (2.38.1-4ubuntu1) ... Setting up libmount1:riscv64 (2.38.1-5ubuntu2) ... (Reading database ... 13022 files and directories currently installed.) Preparing to unpack .../libpam0g_1.5.2-6ubuntu1_riscv64.deb ... Unpacking libpam0g:riscv64 (1.5.2-6ubuntu1) over (1.5.2-5ubuntu1) ... Setting up libpam0g:riscv64 (1.5.2-6ubuntu1) ... (Reading database ... 13022 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.5.4-1ubuntu3_riscv64.deb ... Unpacking libseccomp2:riscv64 (2.5.4-1ubuntu3) over (2.5.4-1ubuntu2) ... Preparing to unpack .../systemd-sysv_252.5-2ubuntu3_riscv64.deb ... Unpacking systemd-sysv (252.5-2ubuntu3) over (251.4-1ubuntu7) ... Setting up libssl3:riscv64 (3.0.9-1ubuntu1) ... (Reading database ... 13023 files and directories currently installed.) Preparing to unpack .../systemd_252.5-2ubuntu3_riscv64.deb ... Unpacking systemd (252.5-2ubuntu3) over (251.4-1ubuntu7) ... Preparing to unpack .../libsystemd-shared_252.5-2ubuntu3_riscv64.deb ... Unpacking libsystemd-shared:riscv64 (252.5-2ubuntu3) over (251.4-1ubuntu7) ... Preparing to unpack .../libatomic1_13.1.0-6ubuntu1_riscv64.deb ... Unpacking libatomic1:riscv64 (13.1.0-6ubuntu1) over (12.2.0-10ubuntu1) ... Preparing to unpack .../libargon2-1_0~20190702+dfsg-3_riscv64.deb ... Unpacking libargon2-1:riscv64 (0~20190702+dfsg-3) over (0~20171227-0.3) ... Preparing to unpack .../libudev1_252.5-2ubuntu3_riscv64.deb ... Unpacking libudev1:riscv64 (252.5-2ubuntu3) over (251.4-1ubuntu7) ... Setting up libudev1:riscv64 (252.5-2ubuntu3) ... (Reading database ... 13054 files and directories currently installed.) Preparing to unpack .../libdevmapper1.02.1_2%3a1.02.185-2ubuntu1_riscv64.deb ... Unpacking libdevmapper1.02.1:riscv64 (2:1.02.185-2ubuntu1) over (2:1.02.185-1ubuntu1) ... Preparing to unpack .../libuuid1_2.38.1-5ubuntu2_riscv64.deb ... Unpacking libuuid1:riscv64 (2.38.1-5ubuntu2) over (2.38.1-4ubuntu1) ... Setting up libuuid1:riscv64 (2.38.1-5ubuntu2) ... (Reading database ... 13054 files and directories currently installed.) Preparing to unpack .../libcryptsetup12_2%3a2.6.1-4ubuntu1_riscv64.deb ... Unpacking libcryptsetup12:riscv64 (2:2.6.1-4ubuntu1) over (2:2.5.0-6ubuntu3) ... Preparing to unpack .../libfdisk1_2.38.1-5ubuntu2_riscv64.deb ... Unpacking libfdisk1:riscv64 (2.38.1-5ubuntu2) over (2.38.1-4ubuntu1) ... Preparing to unpack .../libp11-kit0_0.24.1-2ubuntu1_riscv64.deb ... Unpacking libp11-kit0:riscv64 (0.24.1-2ubuntu1) over (0.24.1-1ubuntu2) ... Setting up libp11-kit0:riscv64 (0.24.1-2ubuntu1) ... (Reading database ... 13054 files and directories currently installed.) Preparing to unpack .../mount_2.38.1-5ubuntu2_riscv64.deb ... Unpacking mount (2.38.1-5ubuntu2) over (2.38.1-4ubuntu1) ... Preparing to unpack .../libsystemd0_252.5-2ubuntu3_riscv64.deb ... Unpacking libsystemd0:riscv64 (252.5-2ubuntu3) over (251.4-1ubuntu7) ... Setting up libsystemd0:riscv64 (252.5-2ubuntu3) ... (Reading database ... 13055 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0_2.7.1_riscv64.deb ... Unpacking libapt-pkg6.0:riscv64 (2.7.1) over (2.5.4) ... Setting up libapt-pkg6.0:riscv64 (2.7.1) ... (Reading database ... 13055 files and directories currently installed.) Preparing to unpack .../tar_1.34+dfsg-1.2ubuntu1_riscv64.deb ... Unpacking tar (1.34+dfsg-1.2ubuntu1) over (1.34+dfsg-1.1) ... Setting up tar (1.34+dfsg-1.2ubuntu1) ... (Reading database ... 13055 files and directories currently installed.) Preparing to unpack .../dpkg_1.21.22ubuntu1_riscv64.deb ... Unpacking dpkg (1.21.22ubuntu1) over (1.21.11ubuntu2) ... Setting up dpkg (1.21.22ubuntu1) ... (Reading database ... 13058 files and directories currently installed.) Preparing to unpack .../dash_0.5.12-2ubuntu1_riscv64.deb ... Unpacking dash (0.5.12-2ubuntu1) over (0.5.11+git20210903+057cd650a4ed-9ubuntu1) ... Setting up dash (0.5.12-2ubuntu1) ... (Reading database ... 13058 files and directories currently installed.) Preparing to unpack .../diffutils_1%3a3.8-4_riscv64.deb ... Unpacking diffutils (1:3.8-4) over (1:3.8-1) ... Setting up diffutils (1:3.8-4) ... (Reading database ... 13058 files and directories currently installed.) Preparing to unpack .../findutils_4.9.0-4ubuntu1_riscv64.deb ... Unpacking findutils (4.9.0-4ubuntu1) over (4.9.0-3ubuntu1) ... Setting up findutils (4.9.0-4ubuntu1) ... (Reading database ... 13058 files and directories currently installed.) Preparing to unpack .../grep_3.8-5_riscv64.deb ... Unpacking grep (3.8-5) over (3.8-3) ... Setting up grep (3.8-5) ... (Reading database ... 13058 files and directories currently installed.) Preparing to unpack .../hostname_3.23+nmu1ubuntu1_riscv64.deb ... Unpacking hostname (3.23+nmu1ubuntu1) over (3.23ubuntu2) ... Setting up hostname (3.23+nmu1ubuntu1) ... (Reading database ... 13058 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.4-4_riscv64.deb ... Unpacking ncurses-bin (6.4-4) over (6.3+20220423-2) ... Setting up ncurses-bin (6.4-4) ... (Reading database ... 13058 files and directories currently installed.) Preparing to unpack .../archives/sed_4.9-1_riscv64.deb ... Unpacking sed (4.9-1) over (4.8-1ubuntu2) ... Setting up sed (4.9-1) ... (Reading database ... 13058 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.38.1-5ubuntu2_riscv64.deb ... Unpacking libsmartcols1:riscv64 (2.38.1-5ubuntu2) over (2.38.1-4ubuntu1) ... Setting up libsmartcols1:riscv64 (2.38.1-5ubuntu2) ... (Reading database ... 13058 files and directories currently installed.) Preparing to unpack .../util-linux-extra_2.38.1-5ubuntu2_riscv64.deb ... Unpacking util-linux-extra (2.38.1-5ubuntu2) over (2.38.1-4ubuntu1) ... Setting up util-linux-extra (2.38.1-5ubuntu2) ... (Reading database ... 13058 files and directories currently installed.) Preparing to unpack .../util-linux_2.38.1-5ubuntu2_riscv64.deb ... Unpacking util-linux (2.38.1-5ubuntu2) over (2.38.1-4ubuntu1) ... Setting up util-linux (2.38.1-5ubuntu2) ... (Reading database ... 13058 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.4-4_all.deb ... Unpacking ncurses-base (6.4-4) over (6.3+20220423-2) ... Setting up ncurses-base (6.4-4) ... (Reading database ... 13058 files and directories currently installed.) Preparing to unpack .../archives/lsb-base_11.6_all.deb ... Unpacking lsb-base (11.6) over (11.2ubuntu1) ... Preparing to unpack .../sysvinit-utils_3.06-4ubuntu1_riscv64.deb ... Unpacking sysvinit-utils (3.06-4ubuntu1) over (3.04-1ubuntu1) ... Setting up sysvinit-utils (3.06-4ubuntu1) ... (Reading database ... 13058 files and directories currently installed.) Preparing to unpack .../adduser_3.134ubuntu1_all.deb ... moving unchanged adduser.conf to adduser.conf.update-old. New dpkg-conffile will come from the package. Unpacking adduser (3.134ubuntu1) over (3.121ubuntu1) ... Setting up adduser (3.134ubuntu1) ... Installing new version of config file /etc/deluser.conf ... (Reading database ... 13028 files and directories currently installed.) Preparing to unpack .../gpgv_2.2.40-1.1ubuntu1_riscv64.deb ... Unpacking gpgv (2.2.40-1.1ubuntu1) over (2.2.40-1ubuntu1) ... Setting up gpgv (2.2.40-1.1ubuntu1) ... (Reading database ... 13028 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.7.9-2ubuntu1_riscv64.deb ... Unpacking libgnutls30:riscv64 (3.7.9-2ubuntu1) over (3.7.7-2ubuntu2) ... Setting up libgnutls30:riscv64 (3.7.9-2ubuntu1) ... (Reading database ... 13028 files and directories currently installed.) Preparing to unpack .../archives/apt_2.7.1_riscv64.deb ... Unpacking apt (2.7.1) over (2.5.4) ... Setting up apt (2.7.1) ... Installing new version of config file /etc/apt/apt.conf.d/01autoremove ... (Reading database ... 13025 files and directories currently installed.) Preparing to unpack .../libpam-modules-bin_1.5.2-6ubuntu1_riscv64.deb ... Unpacking libpam-modules-bin (1.5.2-6ubuntu1) over (1.5.2-5ubuntu1) ... Setting up libpam-modules-bin (1.5.2-6ubuntu1) ... (Reading database ... 13025 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.5.2-6ubuntu1_riscv64.deb ... Unpacking libpam-modules:riscv64 (1.5.2-6ubuntu1) over (1.5.2-5ubuntu1) ... Setting up libpam-modules:riscv64 (1.5.2-6ubuntu1) ... (Reading database ... 13025 files and directories currently installed.) Preparing to unpack .../logsave_1.47.0-1ubuntu1_riscv64.deb ... Unpacking logsave (1.47.0-1ubuntu1) over (1.46.6~rc1-1ubuntu1) ... Preparing to unpack .../libext2fs2_1.47.0-1ubuntu1_riscv64.deb ... Unpacking libext2fs2:riscv64 (1.47.0-1ubuntu1) over (1.46.6~rc1-1ubuntu1) ... Setting up libext2fs2:riscv64 (1.47.0-1ubuntu1) ... (Reading database ... 13025 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.47.0-1ubuntu1_riscv64.deb ... Unpacking e2fsprogs (1.47.0-1ubuntu1) over (1.46.6~rc1-1ubuntu1) ... Preparing to unpack .../libattr1_1%3a2.5.1-4_riscv64.deb ... Unpacking libattr1:riscv64 (1:2.5.1-4) over (1:2.5.1-3) ... Setting up libattr1:riscv64 (1:2.5.1-4) ... (Reading database ... 13025 files and directories currently installed.) Preparing to unpack .../libdebconfclient0_0.267ubuntu1_riscv64.deb ... Unpacking libdebconfclient0:riscv64 (0.267ubuntu1) over (0.264ubuntu1) ... Setting up libdebconfclient0:riscv64 (0.267ubuntu1) ... (Reading database ... 13025 files and directories currently installed.) Preparing to unpack .../libmd0_1.1.0-1_riscv64.deb ... Unpacking libmd0:riscv64 (1.1.0-1) over (1.0.4-2) ... Setting up libmd0:riscv64 (1.1.0-1) ... (Reading database ... 13025 files and directories currently installed.) Preparing to unpack .../libpam-runtime_1.5.2-6ubuntu1_all.deb ... Unpacking libpam-runtime (1.5.2-6ubuntu1) over (1.5.2-5ubuntu1) ... Setting up libpam-runtime (1.5.2-6ubuntu1) ... (Reading database ... 13025 files and directories currently installed.) Preparing to unpack .../libsemanage-common_3.4-1build4_all.deb ... Unpacking libsemanage-common (3.4-1build4) over (3.4-1build1) ... Setting up libsemanage-common (3.4-1build4) ... (Reading database ... 13025 files and directories currently installed.) Preparing to unpack .../libsepol2_3.4-2.1_riscv64.deb ... Unpacking libsepol2:riscv64 (3.4-2.1) over (3.4-2) ... Setting up libsepol2:riscv64 (3.4-2.1) ... (Reading database ... 13025 files and directories currently installed.) Preparing to unpack .../libsemanage2_3.4-1build4_riscv64.deb ... Unpacking libsemanage2:riscv64 (3.4-1build4) over (3.4-1build1) ... Setting up libsemanage2:riscv64 (3.4-1build4) ... (Reading database ... 13025 files and directories currently installed.) Preparing to unpack .../libncurses6_6.4-4_riscv64.deb ... Unpacking libncurses6:riscv64 (6.4-4) over (6.3+20220423-2) ... Preparing to unpack .../libncursesw6_6.4-4_riscv64.deb ... Unpacking libncursesw6:riscv64 (6.4-4) over (6.3+20220423-2) ... Preparing to unpack .../libtinfo6_6.4-4_riscv64.deb ... Unpacking libtinfo6:riscv64 (6.4-4) over (6.3+20220423-2) ... Setting up libtinfo6:riscv64 (6.4-4) ... (Reading database ... 13025 files and directories currently installed.) Preparing to unpack .../usrmerge_35ubuntu1_all.deb ... Unpacking usrmerge (35ubuntu1) over (33ubuntu1) ... Setting up usrmerge (35ubuntu1) ... (Reading database ... 13025 files and directories currently installed.) Preparing to unpack .../00-libcom-err2_1.47.0-1ubuntu1_riscv64.deb ... Unpacking libcom-err2:riscv64 (1.47.0-1ubuntu1) over (1.46.6~rc1-1ubuntu1) ... Selecting previously unselected package libproc2-0:riscv64. Preparing to unpack .../01-libproc2-0_2%3a4.0.3-1ubuntu1_riscv64.deb ... Unpacking libproc2-0:riscv64 (2:4.0.3-1ubuntu1) ... Preparing to unpack .../02-libss2_1.47.0-1ubuntu1_riscv64.deb ... Unpacking libss2:riscv64 (1.47.0-1ubuntu1) over (1.46.6~rc1-1ubuntu1) ... Preparing to unpack .../03-mawk_1.3.4.20230525-1_riscv64.deb ... Unpacking mawk (1.3.4.20230525-1) over (1.3.4.20200120-3.1) ... Preparing to unpack .../04-procps_2%3a4.0.3-1ubuntu1_riscv64.deb ... Unpacking procps (2:4.0.3-1ubuntu1) over (2:3.3.17-7ubuntu1) ... Preparing to unpack .../05-sensible-utils_0.0.20_all.deb ... Unpacking sensible-utils (0.0.20) over (0.0.17) ... Preparing to unpack .../06-openssl_3.0.9-1ubuntu1_riscv64.deb ... Unpacking openssl (3.0.9-1ubuntu1) over (3.0.5-2ubuntu2) ... Preparing to unpack .../07-ca-certificates_20230311ubuntu1_all.deb ... Unpacking ca-certificates (20230311ubuntu1) over (20211016ubuntu1) ... Preparing to unpack .../08-libgssapi-krb5-2_1.20.1-2_riscv64.deb ... Unpacking libgssapi-krb5-2:riscv64 (1.20.1-2) over (1.20.1-1build1) ... Preparing to unpack .../09-libkrb5-3_1.20.1-2_riscv64.deb ... Unpacking libkrb5-3:riscv64 (1.20.1-2) over (1.20.1-1build1) ... Preparing to unpack .../10-libkrb5support0_1.20.1-2_riscv64.deb ... Unpacking libkrb5support0:riscv64 (1.20.1-2) over (1.20.1-1build1) ... Preparing to unpack .../11-libk5crypto3_1.20.1-2_riscv64.deb ... Unpacking libk5crypto3:riscv64 (1.20.1-2) over (1.20.1-1build1) ... Preparing to unpack .../12-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) over (8.2-1.2) ... Preparing to unpack .../13-libreadline8_8.2-1.3_riscv64.deb ... Unpacking libreadline8:riscv64 (8.2-1.3) over (8.2-1.2) ... Preparing to unpack .../14-libsqlite3-0_3.42.0-1_riscv64.deb ... Unpacking libsqlite3-0:riscv64 (3.42.0-1) over (3.40.0-1) ... Preparing to unpack .../15-tzdata_2023c-4exp1ubuntu1_all.deb ... Unpacking tzdata (2023c-4exp1ubuntu1) over (2022g-1ubuntu1) ... Preparing to unpack .../16-libpng16-16_1.6.40-1_riscv64.deb ... Unpacking libpng16-16:riscv64 (1.6.40-1) over (1.6.39-2) ... Preparing to unpack .../17-xz-utils_5.4.1-0.2_riscv64.deb ... Unpacking xz-utils (5.4.1-0.2) over (5.2.9-0.0) ... Preparing to unpack .../18-advancecomp_2.5-1_riscv64.deb ... Unpacking advancecomp (2.5-1) over (2.4-1) ... Preparing to unpack .../19-libctf0_2.40.50.20230622-1ubuntu1_riscv64.deb ... Unpacking libctf0:riscv64 (2.40.50.20230622-1ubuntu1) over (2.39.50.20221224-1ubuntu1) ... Preparing to unpack .../20-libctf-nobfd0_2.40.50.20230622-1ubuntu1_riscv64.deb ... Unpacking libctf-nobfd0:riscv64 (2.40.50.20230622-1ubuntu1) over (2.39.50.20221224-1ubuntu1) ... Preparing to unpack .../21-binutils-riscv64-linux-gnu_2.40.50.20230622-1ubuntu1_riscv64.deb ... Unpacking binutils-riscv64-linux-gnu (2.40.50.20230622-1ubuntu1) over (2.39.50.20221224-1ubuntu1) ... Preparing to unpack .../22-libbinutils_2.40.50.20230622-1ubuntu1_riscv64.deb ... Unpacking libbinutils:riscv64 (2.40.50.20230622-1ubuntu1) over (2.39.50.20221224-1ubuntu1) ... Preparing to unpack .../23-binutils_2.40.50.20230622-1ubuntu1_riscv64.deb ... Unpacking binutils (2.40.50.20230622-1ubuntu1) over (2.39.50.20221224-1ubuntu1) ... Preparing to unpack .../24-binutils-common_2.40.50.20230622-1ubuntu1_riscv64.deb ... Unpacking binutils-common:riscv64 (2.40.50.20230622-1ubuntu1) over (2.39.50.20221224-1ubuntu1) ... Preparing to unpack .../25-libisl23_0.26-3_riscv64.deb ... Unpacking libisl23:riscv64 (0.26-3) over (0.25-1) ... Preparing to unpack .../26-libmpfr6_4.2.0-1_riscv64.deb ... Unpacking libmpfr6:riscv64 (4.2.0-1) over (4.1.0-3build3) ... Preparing to unpack .../27-g++-12_12.3.0-3ubuntu1_riscv64.deb ... Unpacking g++-12 (12.3.0-3ubuntu1) over (12.2.0-10ubuntu1) ... Preparing to unpack .../28-gcc-12_12.3.0-3ubuntu1_riscv64.deb ... Unpacking gcc-12 (12.3.0-3ubuntu1) over (12.2.0-10ubuntu1) ... Preparing to unpack .../29-cpp-12_12.3.0-3ubuntu1_riscv64.deb ... Unpacking cpp-12 (12.3.0-3ubuntu1) over (12.2.0-10ubuntu1) ... Preparing to unpack .../30-libgomp1_13.1.0-6ubuntu1_riscv64.deb ... Unpacking libgomp1:riscv64 (13.1.0-6ubuntu1) over (12.2.0-10ubuntu1) ... Preparing to unpack .../31-libasan8_13.1.0-6ubuntu1_riscv64.deb ... Unpacking libasan8:riscv64 (13.1.0-6ubuntu1) over (12.2.0-10ubuntu1) ... Preparing to unpack .../32-libstdc++-12-dev_12.3.0-3ubuntu1_riscv64.deb ... Unpacking libstdc++-12-dev:riscv64 (12.3.0-3ubuntu1) over (12.2.0-10ubuntu1) ... Preparing to unpack .../33-libgcc-12-dev_12.3.0-3ubuntu1_riscv64.deb ... Unpacking libgcc-12-dev:riscv64 (12.3.0-3ubuntu1) over (12.2.0-10ubuntu1) ... Preparing to unpack .../34-libcc1-0_13.1.0-6ubuntu1_riscv64.deb ... Unpacking libcc1-0:riscv64 (13.1.0-6ubuntu1) over (12.2.0-10ubuntu1) ... Preparing to unpack .../35-gcc-12-base_12.3.0-3ubuntu1_riscv64.deb ... Unpacking gcc-12-base:riscv64 (12.3.0-3ubuntu1) over (12.2.0-10ubuntu1) ... Preparing to unpack .../36-g++_4%3a12.2.0-3ubuntu1_riscv64.deb ... Unpacking g++ (4:12.2.0-3ubuntu1) over (4:12.2.0-1ubuntu1) ... Preparing to unpack .../37-gcc_4%3a12.2.0-3ubuntu1_riscv64.deb ... Unpacking gcc (4:12.2.0-3ubuntu1) over (4:12.2.0-1ubuntu1) ... Preparing to unpack .../38-cpp_4%3a12.2.0-3ubuntu1_riscv64.deb ... Unpacking cpp (4:12.2.0-3ubuntu1) over (4:12.2.0-1ubuntu1) ... Preparing to unpack .../39-dpkg-dev_1.21.22ubuntu1_all.deb ... Unpacking dpkg-dev (1.21.22ubuntu1) over (1.21.11ubuntu2) ... Preparing to unpack .../40-libdpkg-perl_1.21.22ubuntu1_all.deb ... Unpacking libdpkg-perl (1.21.22ubuntu1) over (1.21.11ubuntu2) ... Preparing to unpack .../41-lto-disabled-list_41_all.deb ... Unpacking lto-disabled-list (41) over (37) ... Preparing to unpack .../42-libfakeroot_1.31-1.2_riscv64.deb ... Unpacking libfakeroot:riscv64 (1.31-1.2) over (1.30.1-1ubuntu1) ... Preparing to unpack .../43-fakeroot_1.31-1.2_riscv64.deb ... Unpacking fakeroot (1.31-1.2) over (1.30.1-1ubuntu1) ... Preparing to unpack .../44-gpg_2.2.40-1.1ubuntu1_riscv64.deb ... Unpacking gpg (2.2.40-1.1ubuntu1) over (2.2.40-1ubuntu1) ... Preparing to unpack .../45-gpgconf_2.2.40-1.1ubuntu1_riscv64.deb ... Unpacking gpgconf (2.2.40-1.1ubuntu1) over (2.2.40-1ubuntu1) ... Preparing to unpack .../46-gpg-agent_2.2.40-1.1ubuntu1_riscv64.deb ... Unpacking gpg-agent (2.2.40-1.1ubuntu1) over (2.2.40-1ubuntu1) ... Preparing to unpack .../47-pkgbinarymangler_153_all.deb ... Unpacking pkgbinarymangler (153) over (149) ... Setting up lsb-base (11.6) ... Setting up lto-disabled-list (41) ... Setting up libapparmor1:riscv64 (3.0.8-1ubuntu3) ... Setting up libargon2-1:riscv64 (0~20190702+dfsg-3) ... Setting up libsqlite3-0:riscv64 (3.42.0-1) ... Setting up binutils-common:riscv64 (2.40.50.20230622-1ubuntu1) ... Setting up linux-libc-dev:riscv64 (6.3.0-7.7) ... Setting up libctf-nobfd0:riscv64 (2.40.50.20230622-1ubuntu1) ... Setting up libcom-err2:riscv64 (1.47.0-1ubuntu1) ... Setting up libgomp1:riscv64 (13.1.0-6ubuntu1) ... Setting up libseccomp2:riscv64 (2.5.4-1ubuntu3) ... Setting up libfakeroot:riscv64 (1.31-1.2) ... Setting up libkrb5support0:riscv64 (1.20.1-2) ... Setting up gcc-12-base:riscv64 (12.3.0-3ubuntu1) ... Setting up tzdata (2023c-4exp1ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Jun 27 09:28:01 UTC 2023. Universal Time is now: Tue Jun 27 09:28:01 UTC 2023. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.31-1.2) ... Setting up perl-modules-5.36 (5.36.0-7ubuntu1) ... Setting up libmpfr6:riscv64 (4.2.0-1) ... Setting up libncurses6:riscv64 (6.4-4) ... Setting up xz-utils (5.4.1-0.2) ... Setting up libproc2-0:riscv64 (2:4.0.3-1ubuntu1) ... Setting up libpng16-16:riscv64 (1.6.40-1) ... Setting up libatomic1:riscv64 (13.1.0-6ubuntu1) ... Setting up libss2:riscv64 (1.47.0-1ubuntu1) ... Setting up libncursesw6:riscv64 (6.4-4) ... Setting up libk5crypto3:riscv64 (1.20.1-2) ... Setting up logsave (1.47.0-1ubuntu1) ... Setting up libfdisk1:riscv64 (2.38.1-5ubuntu2) ... Setting up advancecomp (2.5-1) ... Setting up libdevmapper1.02.1:riscv64 (2:1.02.185-2ubuntu1) ... Setting up mount (2.38.1-5ubuntu2) ... Setting up sensible-utils (0.0.20) ... Setting up libcrypt-dev:riscv64 (1:4.4.35-1) ... Setting up libasan8:riscv64 (13.1.0-6ubuntu1) ... Setting up procps (2:4.0.3-1ubuntu1) ... Setting up libcryptsetup12:riscv64 (2:2.6.1-4ubuntu1) ... Setting up mawk (1.3.4.20230525-1) ... Setting up libkrb5-3:riscv64 (1.20.1-2) ... Setting up libbinutils:riscv64 (2.40.50.20230622-1ubuntu1) ... Setting up libisl23:riscv64 (0.26-3) ... Setting up libc-dev-bin (2.37-0ubuntu2) ... Setting up openssl (3.0.9-1ubuntu1) ... Installing new version of config file /etc/ssl/openssl.cnf ... Setting up readline-common (8.2-1.3) ... Setting up libcc1-0:riscv64 (13.1.0-6ubuntu1) ... Setting up libperl5.36:riscv64 (5.36.0-7ubuntu1) ... Setting up libkmod2:riscv64 (30+20221128-1ubuntu1) ... Setting up libctf0:riscv64 (2.40.50.20230622-1ubuntu1) ... Setting up cpp-12 (12.3.0-3ubuntu1) ... Setting up pkgbinarymangler (153) ... Setting up libreadline8:riscv64 (8.2-1.3) ... Setting up binutils-riscv64-linux-gnu (2.40.50.20230622-1ubuntu1) ... Setting up e2fsprogs (1.47.0-1ubuntu1) ... Installing new version of config file /etc/mke2fs.conf ... Setting up binutils (2.40.50.20230622-1ubuntu1) ... Setting up ca-certificates (20230311ubuntu1) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 19 added, 6 removed; done. Setting up perl (5.36.0-7ubuntu1) ... Setting up libgcc-12-dev:riscv64 (12.3.0-3ubuntu1) ... Setting up libgssapi-krb5-2:riscv64 (1.20.1-2) ... Setting up libsystemd-shared:riscv64 (252.5-2ubuntu3) ... Setting up libdpkg-perl (1.21.22ubuntu1) ... Setting up cpp (4:12.2.0-3ubuntu1) ... Setting up gpgconf (2.2.40-1.1ubuntu1) ... Setting up libc6-dev:riscv64 (2.37-0ubuntu2) ... Setting up gpg (2.2.40-1.1ubuntu1) ... Setting up gpg-agent (2.2.40-1.1ubuntu1) ... Setting up libstdc++-12-dev:riscv64 (12.3.0-3ubuntu1) ... Setting up systemd (252.5-2ubuntu3) ... Installing new version of config file /etc/systemd/logind.conf ... Installing new version of config file /etc/systemd/system.conf ... Installing new version of config file /etc/systemd/user.conf ... Initializing machine ID from random generator. Setting up dpkg-dev (1.21.22ubuntu1) ... Setting up gcc-12 (12.3.0-3ubuntu1) ... Setting up g++-12 (12.3.0-3ubuntu1) ... Setting up systemd-sysv (252.5-2ubuntu3) ... Setting up gcc (4:12.2.0-3ubuntu1) ... Setting up g++ (4:12.2.0-3ubuntu1) ... Processing triggers for libc-bin (2.37-0ubuntu2) ... Processing triggers for debianutils (5.7-0.4) ... Processing triggers for ca-certificates (20230311ubuntu1) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-26341718 riscv64 mantic-proposed -c chroot:build-PACKAGEBUILD-26341718 --arch=riscv64 --dist=mantic-proposed --nolog python-biopython_1.80+dfsg-4ubuntu1.dsc Initiating build PACKAGEBUILD-26341718 with 8 jobs across 8 processor cores. Kernel reported to sbuild: 5.13.0-1019-generic #21~20.04.1-Ubuntu SMP Thu Mar 24 22:36:01 UTC 2022 riscv64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on riscv64-qemu-lgw01-087.buildd +===============================================================================+ | python-biopython 1.80+dfsg-4ubuntu1 (riscv64) Tue, 27 Jun 2023 09:29:33 +0000 | +===============================================================================+ Package: python-biopython Version: 1.80+dfsg-4ubuntu1 Source Version: 1.80+dfsg-4ubuntu1 Distribution: mantic-proposed Machine Architecture: riscv64 Host Architecture: riscv64 Build Architecture: riscv64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-26341718/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/python-biopython-ogJEuU/resolver-Tg4v8N' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- python-biopython_1.80+dfsg-4ubuntu1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/python-biopython-ogJEuU/python-biopython-1.80+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/python-biopython-ogJEuU' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-python, python3-all-dev, python3-numpy, flex, python3-reportlab, hevea, texlive-latex-base, texlive-latex-extra, texlive-fonts-recommended, bwa, clustalo, clustalw, dialign, dssp, emboss, fasttree, mafft, ncbi-blast+, phylip, prank, probcons, python3-networkx, python3-mysqldb, python3-matplotlib, python3-mmtf, python3-pil, python3-rdflib, python3-psycopg2, python3-pygments, python3-scipy, python3-setuptools, python3-unittest2, samtools, t-coffee, wise, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), dh-python, python3-all-dev, python3-numpy, flex, python3-reportlab, hevea, texlive-latex-base, texlive-latex-extra, texlive-fonts-recommended, bwa, clustalo, clustalw, dialign, dssp, emboss, fasttree, mafft, ncbi-blast+, phylip, prank, probcons, python3-networkx, python3-mysqldb, python3-matplotlib, python3-mmtf, python3-pil, python3-rdflib, python3-psycopg2, python3-pygments, python3-scipy, python3-setuptools, python3-unittest2, samtools, t-coffee, wise, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [963 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [648 B] Get:5 copy:/<>/apt_archive ./ Packages [669 B] Fetched 2280 B in 0s (5147 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev blt bsdextrautils bwa clustalo clustalw debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dialign dssp dwz emboss emboss-data emboss-lib fasttree file flex fontconfig-config fonts-dejavu-core fonts-lmodern fonts-lyx fonts-urw-base35 gettext gettext-base ghostscript groff-base hevea hicolor-icon-theme imagemagick imagemagick-6-common imagemagick-6.q16 intltool-debian libaom3 libapache-pom-java libarchive-zip-perl libargtable2-0 libavahi-client3 libavahi-common-data libavahi-common3 libblas3 libboost-dev libboost-regex1.74.0 libboost1.74-dev libbrotli1 libbsd0 libcairo2 libcifpp-data libcifpp5 libcommons-logging-java libcommons-parent-java libcups2 libcurl3-gnutls libdav1d6 libdbus-1-3 libde265-0 libdebhelper-perl libdeflate0 libdw1 libelf1 libexpat1 libexpat1-dev libfftw3-double3 libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgd3 libgfortran5 libglib2.0-0 libgraphite2-3 libgs-common libgs10 libgs10-common libharfbuzz0b libheif1 libhpdf-2.3.0 libhts3 libhtscodecs2 libice6 libicu72 libidn12 libijs-0.35 libimagequant0 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libkpathsea6 liblapack3 liblbfgsb0 liblcms2-2 libldap2 liblerc4 liblmdb0 liblqr-1-0 libltdl7 libmagic-mgc libmagic1 libmagickcore-6.q16-6 libmagickwand-6.q16-6 libmbedcrypto7 libmbedtls14 libmbedx509-1 libmysqlclient21 libnetpbm11 libnghttp2-14 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libopenjp2-7 libpaper-utils libpaper1 libpcre3 libpdfbox-java libpipeline1 libpixman-1-0 libpq5 libpsl5 libptexenc1 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.11 libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib libqhull-r8.0 libraqm0 librtmp1 libsasl2-2 libsasl2-modules-db libsm6 libssh-4 libsub-override-perl libsynctex2 libtcl8.6 libteckit0 libtexlua53-5 libtiff6 libtk8.6 libtool libuchardet0 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libx265-199 libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxsimd-dev libxslt1.1 libxss1 libxt6 libzzip-0-13 m4 mafft mailcap man-db media-types mime-support mysql-common ncbi-blast+ ncbi-data netpbm phylip po-debconf poppler-data prank preview-latex-style probcons python-matplotlib-data python3 python3-all python3-all-dev python3-appdirs python3-attr python3-beniget python3-brotli python3-contourpy python3-cycler python3-dateutil python3-decorator python3-dev python3-distutils python3-fonttools python3-fs python3-gast python3-isodate python3-kiwisolver python3-lib2to3 python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-mmtf python3-mpmath python3-msgpack python3-mysqldb python3-networkx python3-numpy python3-packaging python3-pil python3-pil.imagetk python3-pkg-resources python3-ply python3-psycopg2 python3-pygments python3-pyparsing python3-pythran python3-rdflib python3-reportlab python3-scipy python3-setuptools python3-six python3-sympy python3-tk python3-tz python3-ufolib2 python3-unittest2 python3.11 python3.11-dev python3.11-minimal samtools t-coffee t1utils tex-common texlive-base texlive-binaries texlive-fonts-recommended texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures tk8.6-blt2.5 ucf unicode-data wise wise-data x11-common xdg-utils xfonts-encodings xfonts-utils zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc blt-demo clustalx seaview dh-make flit python3-build python3-installer python3-wheel emboss-doc emboss-test embassy bison flex-doc fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre gettext-doc libasprintf-dev libgettextpo-dev groff hevea-doc imagemagick-doc autotrace cups-bsd | lpr | lprng curl enscript ffmpeg gimp gnuplot grads graphviz hp2xx html2ps libwmf-bin mplayer povray radiance sane-utils transfig ufraw-batch libboost-doc libboost1.74-doc libboost-atomic1.74-dev libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev libboost-contract1.74-dev libboost-coroutine1.74-dev libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev libboost-filesystem1.74-dev libboost-graph1.74-dev libboost-graph-parallel1.74-dev libboost-iostreams1.74-dev libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev libboost-program-options1.74-dev libboost-python1.74-dev libboost-random1.74-dev libboost-regex1.74-dev libboost-serialization1.74-dev libboost-stacktrace1.74-dev libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev libavalon-framework-java libcommons-logging-java-doc libexcalibur-logkit-java liblog4j1.2-java cups-common libfftw3-bin libfftw3-dev libgd-tools low-memory-monitor libjs-jquery-ui-docs liblcms2-utils libmagickcore-6.q16-6-extra tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk libxsimd-doc m4-doc apparmor less www-browser phylip-doc libmail-box-perl poppler-utils fonts-japanese-mincho | fonts-ipafont-mincho fonts-japanese-gothic | fonts-ipafont-gothic fonts-arphic-ukai fonts-arphic-uming fonts-nanum probcons-extra python3-doc python3-venv python-attr-doc python-cycler-doc python-lxml-doc cm-super-minimal dvipng fonts-staypuft gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip python3-tornado texlive-extra-utils python-mpmath-doc python3-gmpy2 default-mysql-server | virtual-mysql-server python-networkx-doc python3-gdal python3-pydot python3-pygraphviz gfortran python3-pytest python-pil-doc python-ply-doc python-psycopg2-doc python-pygments-doc ttf-bitstream-vera python-pyparsing-doc python-rdflib-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc python-scipy-doc python-setuptools-doc texlive-fonts-extra python-sympy-doc tix python3-tk-dbg python3.11-venv python3.11-doc binfmt-support cwltool boxshade t-coffee-examples perl-tk xpdf | pdf-viewer xzdec texlive-fonts-recommended-doc texlive-latex-base-doc wp2latex icc-profiles libfile-which-perl texlive-latex-extra-doc texlive-science texlive-latex-recommended-doc texlive-luatex texlive-pstricks dot2tex prerex texlive-pictures-doc vprerex wise-doc Recommended packages: primer3 libfl-dev curl | wget | lynx libmagickcore-6.q16-6-extra dbus libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs fonts-droid-fallback javascript-common libldap-common gsfonts publicsuffix libsasl2-modules libltdl-dev blast2 libwww-perl lynx ruby libmail-sendmail-perl python3-bs4 python3-html5lib python3-yaml python3-olefile python3-sparqlwrapper isympy-common amap-align dialign-tx fsa kalign libsoap-lite-perl libxml-simple-perl muscle mustang poa proda tm-align lmodern dvisvgm tex-gyre tipa default-jre libspreadsheet-parseexcel-perl texlive-plain-generic tk libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: autoconf automake autopoint autotools-dev blt bsdextrautils bwa clustalo clustalw debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dialign dssp dwz emboss emboss-data emboss-lib fasttree file flex fontconfig-config fonts-dejavu-core fonts-lmodern fonts-lyx fonts-urw-base35 gettext gettext-base ghostscript groff-base hevea hicolor-icon-theme imagemagick imagemagick-6-common imagemagick-6.q16 intltool-debian libaom3 libapache-pom-java libarchive-zip-perl libargtable2-0 libavahi-client3 libavahi-common-data libavahi-common3 libblas3 libboost-dev libboost-regex1.74.0 libboost1.74-dev libbrotli1 libbsd0 libcairo2 libcifpp-data libcifpp5 libcommons-logging-java libcommons-parent-java libcups2 libcurl3-gnutls libdav1d6 libdbus-1-3 libde265-0 libdebhelper-perl libdeflate0 libdw1 libelf1 libexpat1 libexpat1-dev libfftw3-double3 libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgd3 libgfortran5 libglib2.0-0 libgraphite2-3 libgs-common libgs10 libgs10-common libharfbuzz0b libheif1 libhpdf-2.3.0 libhts3 libhtscodecs2 libice6 libicu72 libidn12 libijs-0.35 libimagequant0 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libkpathsea6 liblapack3 liblbfgsb0 liblcms2-2 libldap2 liblerc4 liblmdb0 liblqr-1-0 libltdl7 libmagic-mgc libmagic1 libmagickcore-6.q16-6 libmagickwand-6.q16-6 libmbedcrypto7 libmbedtls14 libmbedx509-1 libmysqlclient21 libnetpbm11 libnghttp2-14 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libopenjp2-7 libpaper-utils libpaper1 libpcre3 libpdfbox-java libpipeline1 libpixman-1-0 libpq5 libpsl5 libptexenc1 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.11 libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib libqhull-r8.0 libraqm0 librtmp1 libsasl2-2 libsasl2-modules-db libsm6 libssh-4 libsub-override-perl libsynctex2 libtcl8.6 libteckit0 libtexlua53-5 libtiff6 libtk8.6 libtool libuchardet0 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libx265-199 libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxsimd-dev libxslt1.1 libxss1 libxt6 libzzip-0-13 m4 mafft mailcap man-db media-types mime-support mysql-common ncbi-blast+ ncbi-data netpbm phylip po-debconf poppler-data prank preview-latex-style probcons python-matplotlib-data python3 python3-all python3-all-dev python3-appdirs python3-attr python3-beniget python3-brotli python3-contourpy python3-cycler python3-dateutil python3-decorator python3-dev python3-distutils python3-fonttools python3-fs python3-gast python3-isodate python3-kiwisolver python3-lib2to3 python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-mmtf python3-mpmath python3-msgpack python3-mysqldb python3-networkx python3-numpy python3-packaging python3-pil python3-pil.imagetk python3-pkg-resources python3-ply python3-psycopg2 python3-pygments python3-pyparsing python3-pythran python3-rdflib python3-reportlab python3-scipy python3-setuptools python3-six python3-sympy python3-tk python3-tz python3-ufolib2 python3-unittest2 python3.11 python3.11-dev python3.11-minimal samtools sbuild-build-depends-main-dummy t-coffee t1utils tex-common texlive-base texlive-binaries texlive-fonts-recommended texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures tk8.6-blt2.5 ucf unicode-data wise wise-data x11-common xdg-utils xfonts-encodings xfonts-utils zlib1g-dev 0 upgraded, 269 newly installed, 0 to remove and 0 not upgraded. Need to get 340 MB of archives. After this operation, 1731 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [880 B] Get:2 http://ftpmaster.internal/ubuntu mantic/main riscv64 libpython3.11-minimal riscv64 3.11.4-1 [825 kB] Get:3 http://ftpmaster.internal/ubuntu mantic/main riscv64 libexpat1 riscv64 2.5.0-2 [78.2 kB] Get:4 http://ftpmaster.internal/ubuntu mantic/main riscv64 python3.11-minimal riscv64 3.11.4-1 [1872 kB] Get:5 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 python3-minimal riscv64 3.11.4-1 [26.6 kB] Get:6 http://ftpmaster.internal/ubuntu mantic/main riscv64 media-types all 10.0.0 [25.8 kB] Get:7 http://ftpmaster.internal/ubuntu mantic/main riscv64 mailcap all 3.70+nmu1ubuntu1 [23.8 kB] Get:8 http://ftpmaster.internal/ubuntu mantic/main riscv64 mime-support all 3.66 [3696 B] Get:9 http://ftpmaster.internal/ubuntu mantic/main riscv64 libpython3.11-stdlib riscv64 3.11.4-1 [1815 kB] Get:10 http://ftpmaster.internal/ubuntu mantic/main riscv64 python3.11 riscv64 3.11.4-1 [572 kB] Get:11 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 libpython3-stdlib riscv64 3.11.4-1 [9338 B] Get:12 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 python3 riscv64 3.11.4-1 [22.9 kB] Get:13 http://ftpmaster.internal/ubuntu mantic/main riscv64 m4 riscv64 1.4.19-3 [243 kB] Get:14 http://ftpmaster.internal/ubuntu mantic/main riscv64 flex riscv64 2.6.4-8.2 [295 kB] Get:15 http://ftpmaster.internal/ubuntu mantic/main riscv64 libfftw3-double3 riscv64 3.3.10-1ubuntu1 [382 kB] Get:16 http://ftpmaster.internal/ubuntu mantic/main riscv64 libbrotli1 riscv64 1.0.9-2build8 [324 kB] Get:17 http://ftpmaster.internal/ubuntu mantic/main riscv64 libfreetype6 riscv64 2.12.1+dfsg-5 [363 kB] Get:18 http://ftpmaster.internal/ubuntu mantic/main riscv64 fonts-dejavu-core all 2.37-6 [1137 kB] Get:19 http://ftpmaster.internal/ubuntu mantic/main riscv64 libfontenc1 riscv64 1:1.1.4-1build3 [13.2 kB] Get:20 http://ftpmaster.internal/ubuntu mantic/main riscv64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] Get:21 http://ftpmaster.internal/ubuntu mantic/main riscv64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] Get:22 http://ftpmaster.internal/ubuntu mantic/main riscv64 xfonts-utils riscv64 1:7.7+6build2 [92.1 kB] Get:23 http://ftpmaster.internal/ubuntu mantic/main riscv64 fonts-urw-base35 all 20200910-7 [11.0 MB] Get:24 http://ftpmaster.internal/ubuntu mantic/main riscv64 fontconfig-config riscv64 2.14.1-4ubuntu1 [35.0 kB] Get:25 http://ftpmaster.internal/ubuntu mantic/main riscv64 libfontconfig1 riscv64 2.14.1-4ubuntu1 [119 kB] Get:26 http://ftpmaster.internal/ubuntu mantic-proposed/universe riscv64 libaom3 riscv64 3.6.1-1 [1291 kB] Get:27 http://ftpmaster.internal/ubuntu mantic/universe riscv64 libdav1d6 riscv64 1.2.1-2 [262 kB] Get:28 http://ftpmaster.internal/ubuntu mantic/universe riscv64 libde265-0 riscv64 1.0.12-1 [178 kB] Get:29 http://ftpmaster.internal/ubuntu mantic/universe riscv64 libx265-199 riscv64 3.5-2 [688 kB] Get:30 http://ftpmaster.internal/ubuntu mantic/universe riscv64 libheif1 riscv64 1.15.1-1 [224 kB] Get:31 http://ftpmaster.internal/ubuntu mantic/main riscv64 libjbig0 riscv64 2.1-6.1ubuntu1 [28.0 kB] Get:32 http://ftpmaster.internal/ubuntu mantic/main riscv64 libjpeg-turbo8 riscv64 2.1.5-2ubuntu1 [119 kB] Get:33 http://ftpmaster.internal/ubuntu mantic/main riscv64 libjpeg8 riscv64 8c-2ubuntu11 [2150 B] Get:34 http://ftpmaster.internal/ubuntu mantic/main riscv64 liblcms2-2 riscv64 2.14-2 [145 kB] Get:35 http://ftpmaster.internal/ubuntu mantic/main riscv64 libglib2.0-0 riscv64 2.76.3-1ubuntu1 [1365 kB] Get:36 http://ftpmaster.internal/ubuntu mantic/universe riscv64 liblqr-1-0 riscv64 0.4.2-2.1 [24.5 kB] Get:37 http://ftpmaster.internal/ubuntu mantic/main riscv64 libltdl7 riscv64 2.4.7-5 [37.2 kB] Get:38 http://ftpmaster.internal/ubuntu mantic/main riscv64 libopenjp2-7 riscv64 2.5.0-2 [175 kB] Get:39 http://ftpmaster.internal/ubuntu mantic/main riscv64 libdeflate0 riscv64 1.15-1 [36.8 kB] Get:40 http://ftpmaster.internal/ubuntu mantic/main riscv64 liblerc4 riscv64 4.0.0+ds-2ubuntu2 [172 kB] Get:41 http://ftpmaster.internal/ubuntu mantic/main riscv64 libwebp7 riscv64 1.2.4-0.2 [166 kB] Get:42 http://ftpmaster.internal/ubuntu mantic/main riscv64 libtiff6 riscv64 4.5.0-6ubuntu1 [176 kB] Get:43 http://ftpmaster.internal/ubuntu mantic/main riscv64 libwebpdemux2 riscv64 1.2.4-0.2 [9024 B] Get:44 http://ftpmaster.internal/ubuntu mantic/main riscv64 libwebpmux3 riscv64 1.2.4-0.2 [18.4 kB] Get:45 http://ftpmaster.internal/ubuntu mantic/main riscv64 libxau6 riscv64 1:1.0.9-1build5 [6836 B] Get:46 http://ftpmaster.internal/ubuntu mantic/main riscv64 libbsd0 riscv64 0.11.7-4 [38.2 kB] Get:47 http://ftpmaster.internal/ubuntu mantic/main riscv64 libxdmcp6 riscv64 1:1.1.3-0ubuntu5 [10.3 kB] Get:48 http://ftpmaster.internal/ubuntu mantic/main riscv64 libxcb1 riscv64 1.15-1 [42.1 kB] Get:49 http://ftpmaster.internal/ubuntu mantic/main riscv64 libx11-data all 2:1.8.6-1 [115 kB] Get:50 http://ftpmaster.internal/ubuntu mantic/main riscv64 libx11-6 riscv64 2:1.8.6-1 [599 kB] Get:51 http://ftpmaster.internal/ubuntu mantic/main riscv64 libxext6 riscv64 2:1.3.4-1build1 [27.8 kB] Get:52 http://ftpmaster.internal/ubuntu mantic/main riscv64 libicu72 riscv64 72.1-3ubuntu2 [10.7 MB] Get:53 http://ftpmaster.internal/ubuntu mantic/main riscv64 libxml2 riscv64 2.9.14+dfsg-1.2 [600 kB] Get:54 http://ftpmaster.internal/ubuntu mantic/universe riscv64 imagemagick-6-common all 8:6.9.11.60+dfsg-1.6 [64.6 kB] Get:55 http://ftpmaster.internal/ubuntu mantic/universe riscv64 libmagickcore-6.q16-6 riscv64 8:6.9.11.60+dfsg-1.6 [1776 kB] Get:56 http://ftpmaster.internal/ubuntu mantic/universe riscv64 libmagickwand-6.q16-6 riscv64 8:6.9.11.60+dfsg-1.6 [338 kB] Get:57 http://ftpmaster.internal/ubuntu mantic/main riscv64 poppler-data all 0.4.12-1 [2060 kB] Get:58 http://ftpmaster.internal/ubuntu mantic/main riscv64 libdbus-1-3 riscv64 1.14.6-1ubuntu1 [189 kB] Get:59 http://ftpmaster.internal/ubuntu mantic/main riscv64 libelf1 riscv64 0.188-2.1 [49.1 kB] Get:60 http://ftpmaster.internal/ubuntu mantic/main riscv64 libfribidi0 riscv64 1.0.13-3 [26.1 kB] Get:61 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 python3-pkg-resources all 67.8.0-1 [161 kB] Get:62 http://ftpmaster.internal/ubuntu mantic/main riscv64 python3-pygments all 2.15.1+dfsg-1 [820 kB] Get:63 http://ftpmaster.internal/ubuntu mantic/main riscv64 ucf all 3.0043+nmu1 [56.5 kB] Get:64 http://ftpmaster.internal/ubuntu mantic/main riscv64 bsdextrautils riscv64 2.38.1-5ubuntu2 [81.4 kB] Get:65 http://ftpmaster.internal/ubuntu mantic/main riscv64 libmagic-mgc riscv64 1:5.44-3 [293 kB] Get:66 http://ftpmaster.internal/ubuntu mantic/main riscv64 libmagic1 riscv64 1:5.44-3 [85.1 kB] Get:67 http://ftpmaster.internal/ubuntu mantic/main riscv64 file riscv64 1:5.44-3 [21.0 kB] Get:68 http://ftpmaster.internal/ubuntu mantic/main riscv64 gettext-base riscv64 0.21-12 [38.9 kB] Get:69 http://ftpmaster.internal/ubuntu mantic/main riscv64 libuchardet0 riscv64 0.0.7-1build2 [78.9 kB] Get:70 http://ftpmaster.internal/ubuntu mantic/main riscv64 groff-base riscv64 1.22.4-10 [906 kB] Get:71 http://ftpmaster.internal/ubuntu mantic/main riscv64 liblmdb0 riscv64 0.9.24-1build2 [46.0 kB] Get:72 http://ftpmaster.internal/ubuntu mantic/main riscv64 libnghttp2-14 riscv64 1.54.0-1 [70.9 kB] Get:73 http://ftpmaster.internal/ubuntu mantic/main riscv64 libpipeline1 riscv64 1.5.7-1 [26.8 kB] Get:74 http://ftpmaster.internal/ubuntu mantic/main riscv64 libpsl5 riscv64 0.21.2-1 [57.9 kB] Get:75 http://ftpmaster.internal/ubuntu mantic/main riscv64 man-db riscv64 2.11.2-2 [1180 kB] Get:76 http://ftpmaster.internal/ubuntu mantic/main riscv64 autoconf all 2.71-3 [339 kB] Get:77 http://ftpmaster.internal/ubuntu mantic/main riscv64 autotools-dev all 20220109.1 [44.9 kB] Get:78 http://ftpmaster.internal/ubuntu mantic/main riscv64 automake all 1:1.16.5-1.3 [558 kB] Get:79 http://ftpmaster.internal/ubuntu mantic/main riscv64 autopoint all 0.21-12 [422 kB] Get:80 http://ftpmaster.internal/ubuntu mantic/main riscv64 libtcl8.6 riscv64 8.6.13+dfsg-2 [944 kB] Get:81 http://ftpmaster.internal/ubuntu mantic/main riscv64 libxrender1 riscv64 1:0.9.10-1.1 [17.5 kB] Get:82 http://ftpmaster.internal/ubuntu mantic/main riscv64 libxft2 riscv64 2.3.6-1 [39.0 kB] Get:83 http://ftpmaster.internal/ubuntu mantic/main riscv64 libxss1 riscv64 1:1.2.3-1build2 [7676 B] Get:84 http://ftpmaster.internal/ubuntu mantic/main riscv64 libtk8.6 riscv64 8.6.13-2 [698 kB] Get:85 http://ftpmaster.internal/ubuntu mantic/main riscv64 tk8.6-blt2.5 riscv64 2.5.3+dfsg-4.1build2 [549 kB] Get:86 http://ftpmaster.internal/ubuntu mantic/main riscv64 blt riscv64 2.5.3+dfsg-4.1build2 [4838 B] Get:87 http://ftpmaster.internal/ubuntu mantic/universe riscv64 bwa riscv64 0.7.17-7 [205 kB] Get:88 http://ftpmaster.internal/ubuntu mantic/universe riscv64 libargtable2-0 riscv64 13-1.1 [12.1 kB] Get:89 http://ftpmaster.internal/ubuntu mantic/universe riscv64 clustalo riscv64 1.2.4-7 [255 kB] Get:90 http://ftpmaster.internal/ubuntu mantic/universe riscv64 clustalw riscv64 2.1+lgpl-7 [265 kB] Get:91 http://ftpmaster.internal/ubuntu mantic/main riscv64 libdebhelper-perl all 13.11.4ubuntu3 [66.1 kB] Get:92 http://ftpmaster.internal/ubuntu mantic/main riscv64 libtool all 2.4.7-5 [166 kB] Get:93 http://ftpmaster.internal/ubuntu mantic/main riscv64 dh-autoreconf all 20 [16.1 kB] Get:94 http://ftpmaster.internal/ubuntu mantic/main riscv64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:95 http://ftpmaster.internal/ubuntu mantic/main riscv64 libsub-override-perl all 0.09-4 [8706 B] Get:96 http://ftpmaster.internal/ubuntu mantic/main riscv64 libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:97 http://ftpmaster.internal/ubuntu mantic/main riscv64 dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:98 http://ftpmaster.internal/ubuntu mantic/main riscv64 libdw1 riscv64 0.188-2.1 [229 kB] Get:99 http://ftpmaster.internal/ubuntu mantic/main riscv64 debugedit riscv64 1:5.0-5 [48.8 kB] Get:100 http://ftpmaster.internal/ubuntu mantic/main riscv64 dwz riscv64 0.15-1 [115 kB] Get:101 http://ftpmaster.internal/ubuntu mantic/main riscv64 gettext riscv64 0.21-12 [811 kB] Get:102 http://ftpmaster.internal/ubuntu mantic/main riscv64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:103 http://ftpmaster.internal/ubuntu mantic/main riscv64 po-debconf all 1.0.21+nmu1 [233 kB] Get:104 http://ftpmaster.internal/ubuntu mantic/main riscv64 debhelper all 13.11.4ubuntu3 [925 kB] Get:105 http://ftpmaster.internal/ubuntu mantic/main riscv64 python3-lib2to3 all 3.11.4-1 [79.0 kB] Get:106 http://ftpmaster.internal/ubuntu mantic/main riscv64 python3-distutils all 3.11.4-1 [131 kB] Get:107 http://ftpmaster.internal/ubuntu mantic-proposed/universe riscv64 dh-python all 6.20230603 [107 kB] Get:108 http://ftpmaster.internal/ubuntu mantic/universe riscv64 dialign riscv64 2.2.1-11 [141 kB] Get:109 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 libboost-regex1.74.0 riscv64 1.74.0+ds1-21.1ubuntu1 [491 kB] Get:110 http://ftpmaster.internal/ubuntu mantic/universe riscv64 libcifpp-data all 5.0.7.1-1build1 [450 kB] Get:111 http://ftpmaster.internal/ubuntu mantic/universe riscv64 libcifpp5 riscv64 5.0.7.1-1build1 [883 kB] Get:112 http://ftpmaster.internal/ubuntu mantic/universe riscv64 dssp riscv64 4.2.2-2 [996 kB] Get:113 http://ftpmaster.internal/ubuntu mantic/main riscv64 libxpm4 riscv64 1:3.5.12-1.1 [33.2 kB] Get:114 http://ftpmaster.internal/ubuntu mantic/main riscv64 libgd3 riscv64 2.3.3-9ubuntu1 [115 kB] Get:115 http://ftpmaster.internal/ubuntu mantic/universe riscv64 libhpdf-2.3.0 riscv64 2.3.0+dfsg-1build1 [348 kB] Get:116 http://ftpmaster.internal/ubuntu mantic/main riscv64 mysql-common all 5.8+1.1.0 [6626 B] Get:117 http://ftpmaster.internal/ubuntu mantic/main riscv64 libmysqlclient21 riscv64 8.0.33-2 [1327 kB] Get:118 http://ftpmaster.internal/ubuntu mantic/main riscv64 libsasl2-modules-db riscv64 2.1.28+dfsg1-1 [19.2 kB] Get:119 http://ftpmaster.internal/ubuntu mantic/main riscv64 libsasl2-2 riscv64 2.1.28+dfsg1-1 [54.0 kB] Get:120 http://ftpmaster.internal/ubuntu mantic/main riscv64 libldap2 riscv64 2.6.3+dfsg-1~exp1ubuntu2 [163 kB] Get:121 http://ftpmaster.internal/ubuntu mantic/main riscv64 libpq5 riscv64 15.3-1 [121 kB] Get:122 http://ftpmaster.internal/ubuntu mantic/universe riscv64 emboss-lib riscv64 6.6.0+dfsg-12ubuntu1 [5091 kB] Get:123 http://ftpmaster.internal/ubuntu mantic/universe riscv64 emboss-data all 6.6.0+dfsg-12ubuntu1 [61.0 MB] Get:124 http://ftpmaster.internal/ubuntu mantic/universe riscv64 emboss riscv64 6.6.0+dfsg-12ubuntu1 [932 kB] Get:125 http://ftpmaster.internal/ubuntu mantic/universe riscv64 fonts-lmodern all 2.005-1 [4799 kB] Get:126 http://ftpmaster.internal/ubuntu mantic/universe riscv64 fonts-lyx all 2.3.7-1 [167 kB] Get:127 http://ftpmaster.internal/ubuntu mantic/main riscv64 libgs-common all 10.0.0~dfsg1-0ubuntu1.1 [174 kB] Get:128 http://ftpmaster.internal/ubuntu mantic/main riscv64 libgs10-common all 10.0.0~dfsg1-0ubuntu1.1 [601 kB] Get:129 http://ftpmaster.internal/ubuntu mantic/main riscv64 libavahi-common-data riscv64 0.8-10ubuntu1 [27.7 kB] Get:130 http://ftpmaster.internal/ubuntu mantic/main riscv64 libavahi-common3 riscv64 0.8-10ubuntu1 [20.1 kB] Get:131 http://ftpmaster.internal/ubuntu mantic/main riscv64 libavahi-client3 riscv64 0.8-10ubuntu1 [24.1 kB] Get:132 http://ftpmaster.internal/ubuntu mantic/main riscv64 libcups2 riscv64 2.4.5-0ubuntu2 [251 kB] Get:133 http://ftpmaster.internal/ubuntu mantic/main riscv64 libidn12 riscv64 1.41-1 [57.1 kB] Get:134 http://ftpmaster.internal/ubuntu mantic/main riscv64 libijs-0.35 riscv64 0.35-15.1 [14.3 kB] Get:135 http://ftpmaster.internal/ubuntu mantic/main riscv64 libjbig2dec0 riscv64 0.19-3build2 [60.4 kB] Get:136 http://ftpmaster.internal/ubuntu mantic/main riscv64 libpaper1 riscv64 1.1.29 [12.6 kB] Get:137 http://ftpmaster.internal/ubuntu mantic/main riscv64 libice6 riscv64 2:1.0.10-1build2 [37.3 kB] Get:138 http://ftpmaster.internal/ubuntu mantic/main riscv64 libsm6 riscv64 2:1.2.3-1build2 [15.3 kB] Get:139 http://ftpmaster.internal/ubuntu mantic/main riscv64 libxt6 riscv64 1:1.2.1-1.1 [146 kB] Get:140 http://ftpmaster.internal/ubuntu mantic/main riscv64 libgs10 riscv64 10.0.0~dfsg1-0ubuntu1.1 [4496 kB] Get:141 http://ftpmaster.internal/ubuntu mantic/main riscv64 ghostscript riscv64 10.0.0~dfsg1-0ubuntu1.1 [49.2 kB] Get:142 http://ftpmaster.internal/ubuntu mantic/universe riscv64 libnetpbm11 riscv64 2:11.01.00-2build1 [98.9 kB] Get:143 http://ftpmaster.internal/ubuntu mantic/universe riscv64 netpbm riscv64 2:11.01.00-2build1 [1928 kB] Get:144 http://ftpmaster.internal/ubuntu mantic/universe riscv64 tex-common all 6.18 [32.8 kB] Get:145 http://ftpmaster.internal/ubuntu mantic/main riscv64 libpaper-utils riscv64 1.1.29 [8248 B] Get:146 http://ftpmaster.internal/ubuntu mantic/main riscv64 libkpathsea6 riscv64 2022.20220321.62855-5.1 [57.3 kB] Get:147 http://ftpmaster.internal/ubuntu mantic/main riscv64 libptexenc1 riscv64 2022.20220321.62855-5.1 [36.2 kB] Get:148 http://ftpmaster.internal/ubuntu mantic/main riscv64 libsynctex2 riscv64 2022.20220321.62855-5.1 [51.3 kB] Get:149 http://ftpmaster.internal/ubuntu mantic/main riscv64 libtexlua53-5 riscv64 2022.20220321.62855-5.1 [104 kB] Get:150 http://ftpmaster.internal/ubuntu mantic/main riscv64 t1utils riscv64 1.41-4build2 [55.5 kB] Get:151 http://ftpmaster.internal/ubuntu mantic/main riscv64 libpixman-1-0 riscv64 0.42.2-1 [165 kB] Get:152 http://ftpmaster.internal/ubuntu mantic/main riscv64 libxcb-render0 riscv64 1.15-1 [13.8 kB] Get:153 http://ftpmaster.internal/ubuntu mantic/main riscv64 libxcb-shm0 riscv64 1.15-1 [5326 B] Get:154 http://ftpmaster.internal/ubuntu mantic/main riscv64 libcairo2 riscv64 1.16.0-7 [463 kB] Get:155 http://ftpmaster.internal/ubuntu mantic/main riscv64 libgraphite2-3 riscv64 1.3.14-1build2 [71.5 kB] Get:156 http://ftpmaster.internal/ubuntu mantic/main riscv64 libharfbuzz0b riscv64 6.0.0+dfsg-3build1 [443 kB] Get:157 http://ftpmaster.internal/ubuntu mantic/universe riscv64 libteckit0 riscv64 2.5.11+ds1-1 [352 kB] Get:158 http://ftpmaster.internal/ubuntu mantic/main riscv64 libxmu6 riscv64 2:1.1.3-3 [43.7 kB] Get:159 http://ftpmaster.internal/ubuntu mantic/main riscv64 libxaw7 riscv64 2:1.0.14-1 [163 kB] Get:160 http://ftpmaster.internal/ubuntu mantic/main riscv64 libxi6 riscv64 2:1.8-1build1 [29.7 kB] Get:161 http://ftpmaster.internal/ubuntu mantic/universe riscv64 libzzip-0-13 riscv64 0.13.72+dfsg.1-1.1 [23.7 kB] Get:162 http://ftpmaster.internal/ubuntu mantic/universe riscv64 texlive-binaries riscv64 2022.20220321.62855-5.1 [8258 kB] Get:163 http://ftpmaster.internal/ubuntu mantic/main riscv64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] Get:164 http://ftpmaster.internal/ubuntu mantic/universe riscv64 texlive-base all 2022.20230122-3 [21.7 MB] Get:165 http://ftpmaster.internal/ubuntu mantic/main riscv64 hicolor-icon-theme all 0.17-2 [9976 B] Get:166 http://ftpmaster.internal/ubuntu mantic/universe riscv64 imagemagick-6.q16 riscv64 8:6.9.11.60+dfsg-1.6 [222 kB] Get:167 http://ftpmaster.internal/ubuntu mantic/universe riscv64 imagemagick riscv64 8:6.9.11.60+dfsg-1.6 [14.5 kB] Get:168 http://ftpmaster.internal/ubuntu mantic/universe riscv64 hevea riscv64 2.36-1build1 [1947 kB] Get:169 http://ftpmaster.internal/ubuntu mantic/universe riscv64 libapache-pom-java all 29-2 [5284 B] Get:170 http://ftpmaster.internal/ubuntu mantic/main riscv64 libblas3 riscv64 3.11.0-2 [123 kB] Get:171 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 libboost1.74-dev riscv64 1.74.0+ds1-21.1ubuntu1 [9586 kB] Get:172 http://ftpmaster.internal/ubuntu mantic/main riscv64 libboost-dev riscv64 1.74.0.3ubuntu7 [3492 B] Get:173 http://ftpmaster.internal/ubuntu mantic/universe riscv64 libcommons-parent-java all 56-1 [10.7 kB] Get:174 http://ftpmaster.internal/ubuntu mantic/universe riscv64 libcommons-logging-java all 1.2-3 [59.9 kB] Get:175 http://ftpmaster.internal/ubuntu mantic/main riscv64 librtmp1 riscv64 2.4+20151223.gitfa8646d.1-2build4 [54.6 kB] Get:176 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 libssh-4 riscv64 0.10.5-2 [163 kB] Get:177 http://ftpmaster.internal/ubuntu mantic/main riscv64 libcurl3-gnutls riscv64 7.88.1-10ubuntu1 [265 kB] Get:178 http://ftpmaster.internal/ubuntu mantic/main riscv64 libexpat1-dev riscv64 2.5.0-2 [292 kB] Get:179 http://ftpmaster.internal/ubuntu mantic/main riscv64 libgfortran5 riscv64 13.1.0-6ubuntu1 [456 kB] Get:180 http://ftpmaster.internal/ubuntu mantic/universe riscv64 libhtscodecs2 riscv64 1.5.0-1 [80.7 kB] Get:181 http://ftpmaster.internal/ubuntu mantic-proposed/universe riscv64 libhts3 riscv64 1.17+ds-1 [390 kB] Get:182 http://ftpmaster.internal/ubuntu mantic/main riscv64 libimagequant0 riscv64 2.17.0-1 [32.1 kB] Get:183 http://ftpmaster.internal/ubuntu mantic/main riscv64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] Get:184 http://ftpmaster.internal/ubuntu mantic/universe riscv64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] Get:185 http://ftpmaster.internal/ubuntu mantic/main riscv64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] Get:186 http://ftpmaster.internal/ubuntu mantic/main riscv64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get:187 http://ftpmaster.internal/ubuntu mantic/universe riscv64 libopenblas0-pthread riscv64 0.3.23+ds-2 [2875 kB] Get:188 http://ftpmaster.internal/ubuntu mantic/main riscv64 liblapack3 riscv64 3.11.0-2 [1962 kB] Get:189 http://ftpmaster.internal/ubuntu mantic/universe riscv64 liblbfgsb0 riscv64 3.0+dfsg.4-1 [27.6 kB] Get:190 http://ftpmaster.internal/ubuntu mantic/universe riscv64 libmbedcrypto7 riscv64 2.28.3-1 [196 kB] Get:191 http://ftpmaster.internal/ubuntu mantic/universe riscv64 libmbedx509-1 riscv64 2.28.3-1 [42.3 kB] Get:192 http://ftpmaster.internal/ubuntu mantic/universe riscv64 libmbedtls14 riscv64 2.28.3-1 [75.4 kB] Get:193 http://ftpmaster.internal/ubuntu mantic/universe riscv64 libopenblas0 riscv64 0.3.23+ds-2 [6126 B] Get:194 http://ftpmaster.internal/ubuntu mantic/universe riscv64 libopenblas-pthread-dev riscv64 0.3.23+ds-2 [7054 kB] Get:195 http://ftpmaster.internal/ubuntu mantic/universe riscv64 libopenblas-dev riscv64 0.3.23+ds-2 [19.0 kB] Get:196 http://ftpmaster.internal/ubuntu mantic/main riscv64 libpcre3 riscv64 2:8.39-15 [176 kB] Get:197 http://ftpmaster.internal/ubuntu mantic/main riscv64 libpython3.11 riscv64 3.11.4-1 [1932 kB] Get:198 http://ftpmaster.internal/ubuntu mantic/main riscv64 zlib1g-dev riscv64 1:1.2.13.dfsg-1ubuntu4 [957 kB] Get:199 http://ftpmaster.internal/ubuntu mantic/main riscv64 libpython3.11-dev riscv64 3.11.4-1 [13.8 MB] Get:200 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 libpython3-dev riscv64 3.11.4-1 [9600 B] Get:201 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 libpython3-all-dev riscv64 3.11.4-1 [908 B] Get:202 http://ftpmaster.internal/ubuntu mantic/universe riscv64 libqhull-r8.0 riscv64 2020.2-5 [180 kB] Get:203 http://ftpmaster.internal/ubuntu mantic/main riscv64 libraqm0 riscv64 0.10.1-1 [13.2 kB] Get:204 http://ftpmaster.internal/ubuntu mantic/universe riscv64 libxsimd-dev riscv64 8.1.0-7 [90.7 kB] Get:205 http://ftpmaster.internal/ubuntu mantic/main riscv64 libxslt1.1 riscv64 1.1.35-1 [146 kB] Get:206 http://ftpmaster.internal/ubuntu mantic/universe riscv64 mafft riscv64 7.505-1 [1101 kB] Get:207 http://ftpmaster.internal/ubuntu mantic/universe riscv64 ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB] Get:208 http://ftpmaster.internal/ubuntu mantic/universe riscv64 ncbi-blast+ riscv64 2.12.0+ds-3build1 [12.4 MB] Get:209 http://ftpmaster.internal/ubuntu mantic/universe riscv64 phylip riscv64 1:3.697+dfsg-2 [815 kB] Get:210 http://ftpmaster.internal/ubuntu mantic/universe riscv64 prank riscv64 0.0.170427+dfsg-3 [366 kB] Get:211 http://ftpmaster.internal/ubuntu mantic/universe riscv64 preview-latex-style all 12.2-1ubuntu1 [185 kB] Get:212 http://ftpmaster.internal/ubuntu mantic/universe riscv64 probcons riscv64 1.12-14 [142 kB] Get:213 http://ftpmaster.internal/ubuntu mantic/universe riscv64 python-matplotlib-data all 3.6.3-1ubuntu2 [2939 kB] Get:214 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 python3-all riscv64 3.11.4-1 [900 B] Get:215 http://ftpmaster.internal/ubuntu mantic/main riscv64 python3.11-dev riscv64 3.11.4-1 [500 kB] Get:216 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 python3-dev riscv64 3.11.4-1 [26.8 kB] Get:217 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 python3-all-dev riscv64 3.11.4-1 [908 B] Get:218 http://ftpmaster.internal/ubuntu mantic/main riscv64 python3-appdirs all 1.4.4-3 [10.8 kB] Get:219 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 python3-attr all 23.1.0-1 [50.4 kB] Get:220 http://ftpmaster.internal/ubuntu mantic/universe riscv64 python3-gast all 0.5.2-2 [9394 B] Get:221 http://ftpmaster.internal/ubuntu mantic/universe riscv64 python3-beniget all 0.4.1-3 [10.0 kB] Get:222 http://ftpmaster.internal/ubuntu mantic/universe riscv64 python3-brotli riscv64 1.0.9-2build8 [325 kB] Get:223 http://ftpmaster.internal/ubuntu mantic/main riscv64 python3-numpy riscv64 1:1.24.2-1 [3499 kB] Get:224 http://ftpmaster.internal/ubuntu mantic/universe riscv64 python3-contourpy riscv64 1.0.7-1build1 [176 kB] Get:225 http://ftpmaster.internal/ubuntu mantic/universe riscv64 python3-cycler all 0.11.0-1 [8156 B] Get:226 http://ftpmaster.internal/ubuntu mantic/main riscv64 python3-six all 1.16.0-4 [12.4 kB] Get:227 http://ftpmaster.internal/ubuntu mantic/main riscv64 python3-dateutil all 2.8.2-2 [79.2 kB] Get:228 http://ftpmaster.internal/ubuntu mantic/main riscv64 python3-decorator all 5.1.1-3 [9938 B] Get:229 http://ftpmaster.internal/ubuntu mantic/main riscv64 python3-ply all 3.11-5 [47.5 kB] Get:230 http://ftpmaster.internal/ubuntu mantic/universe riscv64 python3-pythran riscv64 0.11.0+ds-7 [427 kB] Get:231 http://ftpmaster.internal/ubuntu mantic/universe riscv64 python3-scipy riscv64 1.10.1-2 [15.4 MB] Get:232 http://ftpmaster.internal/ubuntu mantic/universe riscv64 python3-ufolib2 all 0.14.0+dfsg1-1 [34.4 kB] Get:233 http://ftpmaster.internal/ubuntu mantic/universe riscv64 python3-mpmath all 1.2.1-2 [419 kB] Get:234 http://ftpmaster.internal/ubuntu mantic-proposed/universe riscv64 python3-sympy all 1.12-2 [3967 kB] Get:235 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 python3-tz all 2023.3-3 [31.2 kB] Get:236 http://ftpmaster.internal/ubuntu mantic/universe riscv64 python3-fs all 2.4.16-2 [91.0 kB] Get:237 http://ftpmaster.internal/ubuntu mantic/main riscv64 python3-lxml riscv64 4.9.2-1build1 [1119 kB] Get:238 http://ftpmaster.internal/ubuntu mantic/universe riscv64 python3-lz4 riscv64 4.0.2+dfsg-1build1 [24.6 kB] Get:239 http://ftpmaster.internal/ubuntu mantic/universe riscv64 unicode-data all 15.0.0-1 [8262 kB] Get:240 http://ftpmaster.internal/ubuntu mantic/universe riscv64 python3-fonttools riscv64 4.38.0-1build1 [1029 kB] Get:241 http://ftpmaster.internal/ubuntu mantic/universe riscv64 python3-isodate all 0.6.1-1 [24.7 kB] Get:242 http://ftpmaster.internal/ubuntu mantic/universe riscv64 python3-kiwisolver riscv64 1.4.4-1build1 [61.6 kB] Get:243 http://ftpmaster.internal/ubuntu mantic/main riscv64 python3-pil riscv64 9.5.0-1 [419 kB] Get:244 http://ftpmaster.internal/ubuntu mantic/main riscv64 python3-tk riscv64 3.11.4-1 [108 kB] Get:245 http://ftpmaster.internal/ubuntu mantic/universe riscv64 python3-pil.imagetk riscv64 9.5.0-1 [8782 B] Get:246 http://ftpmaster.internal/ubuntu mantic/main riscv64 python3-pyparsing all 3.0.9-1 [83.1 kB] Get:247 http://ftpmaster.internal/ubuntu mantic/main riscv64 python3-packaging all 23.1-1 [38.1 kB] Get:248 http://ftpmaster.internal/ubuntu mantic/universe riscv64 python3-matplotlib riscv64 3.6.3-1ubuntu2 [5806 kB] Get:249 http://ftpmaster.internal/ubuntu mantic/main riscv64 python3-msgpack riscv64 1.0.3-2build1 [65.6 kB] Get:250 http://ftpmaster.internal/ubuntu mantic/universe riscv64 python3-mmtf all 1.1.3-1 [16.2 kB] Get:251 http://ftpmaster.internal/ubuntu mantic/main riscv64 python3-mysqldb riscv64 1.4.6-2build1 [44.2 kB] Get:252 http://ftpmaster.internal/ubuntu mantic/main riscv64 python3-networkx all 2.8.8-1ubuntu1 [1468 kB] Get:253 http://ftpmaster.internal/ubuntu mantic/main riscv64 python3-psycopg2 riscv64 2.9.5-1build1 [116 kB] Get:254 http://ftpmaster.internal/ubuntu mantic/universe riscv64 python3-rdflib all 6.1.1-1 [363 kB] Get:255 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 python3-reportlab all 4.0.4-1 [566 kB] Get:256 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 python3-setuptools all 67.8.0-1 [392 kB] Get:257 http://ftpmaster.internal/ubuntu mantic/main riscv64 python3-unittest2 all 1.1.0-9 [76.3 kB] Get:258 http://ftpmaster.internal/ubuntu mantic-proposed/universe riscv64 samtools riscv64 1.17-1 [600 kB] Get:259 http://ftpmaster.internal/ubuntu mantic/universe riscv64 t-coffee riscv64 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 [1047 kB] Get:260 http://ftpmaster.internal/ubuntu mantic/universe riscv64 texlive-fonts-recommended all 2022.20230122-3 [4973 kB] Get:261 http://ftpmaster.internal/ubuntu mantic/universe riscv64 texlive-latex-base all 2022.20230122-3 [1165 kB] Get:262 http://ftpmaster.internal/ubuntu mantic/universe riscv64 libfontbox-java all 1:1.8.16-2 [207 kB] Get:263 http://ftpmaster.internal/ubuntu mantic/universe riscv64 libpdfbox-java all 1:1.8.16-2 [5199 kB] Get:264 http://ftpmaster.internal/ubuntu mantic/universe riscv64 texlive-latex-recommended all 2022.20230122-3 [8864 kB] Get:265 http://ftpmaster.internal/ubuntu mantic/universe riscv64 texlive-pictures all 2022.20230122-3 [15.8 MB] Get:266 http://ftpmaster.internal/ubuntu mantic/universe riscv64 texlive-latex-extra all 2022.20230122-4 [18.8 MB] Get:267 http://ftpmaster.internal/ubuntu mantic/universe riscv64 wise-data all 2.4.1-23 [76.8 kB] Get:268 http://ftpmaster.internal/ubuntu mantic/universe riscv64 wise riscv64 2.4.1-23 [859 kB] Get:269 http://ftpmaster.internal/ubuntu mantic/universe riscv64 fasttree riscv64 2.1.11-2 [165 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 340 MB in 47s (7165 kB/s) Selecting previously unselected package libpython3.11-minimal:riscv64. (Reading database ... 12511 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.4-1_riscv64.deb ... Unpacking libpython3.11-minimal:riscv64 (3.11.4-1) ... Selecting previously unselected package libexpat1:riscv64. Preparing to unpack .../libexpat1_2.5.0-2_riscv64.deb ... Unpacking libexpat1:riscv64 (2.5.0-2) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.4-1_riscv64.deb ... Unpacking python3.11-minimal (3.11.4-1) ... Setting up libpython3.11-minimal:riscv64 (3.11.4-1) ... Setting up libexpat1:riscv64 (2.5.0-2) ... Setting up python3.11-minimal (3.11.4-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 12825 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.4-1_riscv64.deb ... Unpacking python3-minimal (3.11.4-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package mailcap. Preparing to unpack .../2-mailcap_3.70+nmu1ubuntu1_all.deb ... Unpacking mailcap (3.70+nmu1ubuntu1) ... Selecting previously unselected package mime-support. Preparing to unpack .../3-mime-support_3.66_all.deb ... Unpacking mime-support (3.66) ... Selecting previously unselected package libpython3.11-stdlib:riscv64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.4-1_riscv64.deb ... Unpacking libpython3.11-stdlib:riscv64 (3.11.4-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.4-1_riscv64.deb ... Unpacking python3.11 (3.11.4-1) ... Selecting previously unselected package libpython3-stdlib:riscv64. Preparing to unpack .../6-libpython3-stdlib_3.11.4-1_riscv64.deb ... Unpacking libpython3-stdlib:riscv64 (3.11.4-1) ... Setting up python3-minimal (3.11.4-1) ... Selecting previously unselected package python3. (Reading database ... 13258 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.4-1_riscv64.deb ... Unpacking python3 (3.11.4-1) ... Selecting previously unselected package m4. Preparing to unpack .../001-m4_1.4.19-3_riscv64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package flex. Preparing to unpack .../002-flex_2.6.4-8.2_riscv64.deb ... Unpacking flex (2.6.4-8.2) ... Selecting previously unselected package libfftw3-double3:riscv64. Preparing to unpack .../003-libfftw3-double3_3.3.10-1ubuntu1_riscv64.deb ... Unpacking libfftw3-double3:riscv64 (3.3.10-1ubuntu1) ... Selecting previously unselected package libbrotli1:riscv64. Preparing to unpack .../004-libbrotli1_1.0.9-2build8_riscv64.deb ... Unpacking libbrotli1:riscv64 (1.0.9-2build8) ... Selecting previously unselected package libfreetype6:riscv64. Preparing to unpack .../005-libfreetype6_2.12.1+dfsg-5_riscv64.deb ... Unpacking libfreetype6:riscv64 (2.12.1+dfsg-5) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../006-fonts-dejavu-core_2.37-6_all.deb ... Unpacking fonts-dejavu-core (2.37-6) ... Selecting previously unselected package libfontenc1:riscv64. Preparing to unpack .../007-libfontenc1_1%3a1.1.4-1build3_riscv64.deb ... Unpacking libfontenc1:riscv64 (1:1.1.4-1build3) ... Selecting previously unselected package x11-common. Preparing to unpack .../008-x11-common_1%3a7.7+23ubuntu2_all.deb ... Unpacking x11-common (1:7.7+23ubuntu2) ... Selecting previously unselected package xfonts-encodings. Preparing to unpack .../009-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... Selecting previously unselected package xfonts-utils. Preparing to unpack .../010-xfonts-utils_1%3a7.7+6build2_riscv64.deb ... Unpacking xfonts-utils (1:7.7+6build2) ... Selecting previously unselected package fonts-urw-base35. Preparing to unpack .../011-fonts-urw-base35_20200910-7_all.deb ... Unpacking fonts-urw-base35 (20200910-7) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../012-fontconfig-config_2.14.1-4ubuntu1_riscv64.deb ... Unpacking fontconfig-config (2.14.1-4ubuntu1) ... Selecting previously unselected package libfontconfig1:riscv64. Preparing to unpack .../013-libfontconfig1_2.14.1-4ubuntu1_riscv64.deb ... Unpacking libfontconfig1:riscv64 (2.14.1-4ubuntu1) ... Selecting previously unselected package libaom3:riscv64. Preparing to unpack .../014-libaom3_3.6.1-1_riscv64.deb ... Unpacking libaom3:riscv64 (3.6.1-1) ... Selecting previously unselected package libdav1d6:riscv64. Preparing to unpack .../015-libdav1d6_1.2.1-2_riscv64.deb ... Unpacking libdav1d6:riscv64 (1.2.1-2) ... Selecting previously unselected package libde265-0:riscv64. Preparing to unpack .../016-libde265-0_1.0.12-1_riscv64.deb ... Unpacking libde265-0:riscv64 (1.0.12-1) ... Selecting previously unselected package libx265-199:riscv64. Preparing to unpack .../017-libx265-199_3.5-2_riscv64.deb ... Unpacking libx265-199:riscv64 (3.5-2) ... Selecting previously unselected package libheif1:riscv64. Preparing to unpack .../018-libheif1_1.15.1-1_riscv64.deb ... Unpacking libheif1:riscv64 (1.15.1-1) ... Selecting previously unselected package libjbig0:riscv64. Preparing to unpack .../019-libjbig0_2.1-6.1ubuntu1_riscv64.deb ... Unpacking libjbig0:riscv64 (2.1-6.1ubuntu1) ... Selecting previously unselected package libjpeg-turbo8:riscv64. Preparing to unpack .../020-libjpeg-turbo8_2.1.5-2ubuntu1_riscv64.deb ... Unpacking libjpeg-turbo8:riscv64 (2.1.5-2ubuntu1) ... Selecting previously unselected package libjpeg8:riscv64. Preparing to unpack .../021-libjpeg8_8c-2ubuntu11_riscv64.deb ... Unpacking libjpeg8:riscv64 (8c-2ubuntu11) ... Selecting previously unselected package liblcms2-2:riscv64. Preparing to unpack .../022-liblcms2-2_2.14-2_riscv64.deb ... Unpacking liblcms2-2:riscv64 (2.14-2) ... Selecting previously unselected package libglib2.0-0:riscv64. Preparing to unpack .../023-libglib2.0-0_2.76.3-1ubuntu1_riscv64.deb ... Unpacking libglib2.0-0:riscv64 (2.76.3-1ubuntu1) ... Selecting previously unselected package liblqr-1-0:riscv64. Preparing to unpack .../024-liblqr-1-0_0.4.2-2.1_riscv64.deb ... Unpacking liblqr-1-0:riscv64 (0.4.2-2.1) ... Selecting previously unselected package libltdl7:riscv64. Preparing to unpack .../025-libltdl7_2.4.7-5_riscv64.deb ... Unpacking libltdl7:riscv64 (2.4.7-5) ... Selecting previously unselected package libopenjp2-7:riscv64. Preparing to unpack .../026-libopenjp2-7_2.5.0-2_riscv64.deb ... Unpacking libopenjp2-7:riscv64 (2.5.0-2) ... Selecting previously unselected package libdeflate0:riscv64. Preparing to unpack .../027-libdeflate0_1.15-1_riscv64.deb ... Unpacking libdeflate0:riscv64 (1.15-1) ... Selecting previously unselected package liblerc4:riscv64. Preparing to unpack .../028-liblerc4_4.0.0+ds-2ubuntu2_riscv64.deb ... Unpacking liblerc4:riscv64 (4.0.0+ds-2ubuntu2) ... Selecting previously unselected package libwebp7:riscv64. Preparing to unpack .../029-libwebp7_1.2.4-0.2_riscv64.deb ... Unpacking libwebp7:riscv64 (1.2.4-0.2) ... Selecting previously unselected package libtiff6:riscv64. Preparing to unpack .../030-libtiff6_4.5.0-6ubuntu1_riscv64.deb ... Unpacking libtiff6:riscv64 (4.5.0-6ubuntu1) ... Selecting previously unselected package libwebpdemux2:riscv64. Preparing to unpack .../031-libwebpdemux2_1.2.4-0.2_riscv64.deb ... Unpacking libwebpdemux2:riscv64 (1.2.4-0.2) ... Selecting previously unselected package libwebpmux3:riscv64. Preparing to unpack .../032-libwebpmux3_1.2.4-0.2_riscv64.deb ... Unpacking libwebpmux3:riscv64 (1.2.4-0.2) ... Selecting previously unselected package libxau6:riscv64. Preparing to unpack .../033-libxau6_1%3a1.0.9-1build5_riscv64.deb ... Unpacking libxau6:riscv64 (1:1.0.9-1build5) ... Selecting previously unselected package libbsd0:riscv64. Preparing to unpack .../034-libbsd0_0.11.7-4_riscv64.deb ... Unpacking libbsd0:riscv64 (0.11.7-4) ... Selecting previously unselected package libxdmcp6:riscv64. Preparing to unpack .../035-libxdmcp6_1%3a1.1.3-0ubuntu5_riscv64.deb ... Unpacking libxdmcp6:riscv64 (1:1.1.3-0ubuntu5) ... Selecting previously unselected package libxcb1:riscv64. Preparing to unpack .../036-libxcb1_1.15-1_riscv64.deb ... Unpacking libxcb1:riscv64 (1.15-1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../037-libx11-data_2%3a1.8.6-1_all.deb ... Unpacking libx11-data (2:1.8.6-1) ... Selecting previously unselected package libx11-6:riscv64. Preparing to unpack .../038-libx11-6_2%3a1.8.6-1_riscv64.deb ... Unpacking libx11-6:riscv64 (2:1.8.6-1) ... Selecting previously unselected package libxext6:riscv64. Preparing to unpack .../039-libxext6_2%3a1.3.4-1build1_riscv64.deb ... Unpacking libxext6:riscv64 (2:1.3.4-1build1) ... Selecting previously unselected package libicu72:riscv64. Preparing to unpack .../040-libicu72_72.1-3ubuntu2_riscv64.deb ... Unpacking libicu72:riscv64 (72.1-3ubuntu2) ... Selecting previously unselected package libxml2:riscv64. Preparing to unpack .../041-libxml2_2.9.14+dfsg-1.2_riscv64.deb ... Unpacking libxml2:riscv64 (2.9.14+dfsg-1.2) ... Selecting previously unselected package imagemagick-6-common. Preparing to unpack .../042-imagemagick-6-common_8%3a6.9.11.60+dfsg-1.6_all.deb ... Unpacking imagemagick-6-common (8:6.9.11.60+dfsg-1.6) ... Selecting previously unselected package libmagickcore-6.q16-6:riscv64. Preparing to unpack .../043-libmagickcore-6.q16-6_8%3a6.9.11.60+dfsg-1.6_riscv64.deb ... Unpacking libmagickcore-6.q16-6:riscv64 (8:6.9.11.60+dfsg-1.6) ... Selecting previously unselected package libmagickwand-6.q16-6:riscv64. Preparing to unpack .../044-libmagickwand-6.q16-6_8%3a6.9.11.60+dfsg-1.6_riscv64.deb ... Unpacking libmagickwand-6.q16-6:riscv64 (8:6.9.11.60+dfsg-1.6) ... Selecting previously unselected package poppler-data. Preparing to unpack .../045-poppler-data_0.4.12-1_all.deb ... Unpacking poppler-data (0.4.12-1) ... Selecting previously unselected package libdbus-1-3:riscv64. Preparing to unpack .../046-libdbus-1-3_1.14.6-1ubuntu1_riscv64.deb ... Unpacking libdbus-1-3:riscv64 (1.14.6-1ubuntu1) ... Selecting previously unselected package libelf1:riscv64. Preparing to unpack .../047-libelf1_0.188-2.1_riscv64.deb ... Unpacking libelf1:riscv64 (0.188-2.1) ... Selecting previously unselected package libfribidi0:riscv64. Preparing to unpack .../048-libfribidi0_1.0.13-3_riscv64.deb ... Unpacking libfribidi0:riscv64 (1.0.13-3) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../049-python3-pkg-resources_67.8.0-1_all.deb ... Unpacking python3-pkg-resources (67.8.0-1) ... Selecting previously unselected package python3-pygments. Preparing to unpack .../050-python3-pygments_2.15.1+dfsg-1_all.deb ... Unpacking python3-pygments (2.15.1+dfsg-1) ... Selecting previously unselected package ucf. Preparing to unpack .../051-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../052-bsdextrautils_2.38.1-5ubuntu2_riscv64.deb ... Unpacking bsdextrautils (2.38.1-5ubuntu2) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../053-libmagic-mgc_1%3a5.44-3_riscv64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:riscv64. Preparing to unpack .../054-libmagic1_1%3a5.44-3_riscv64.deb ... Unpacking libmagic1:riscv64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../055-file_1%3a5.44-3_riscv64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../056-gettext-base_0.21-12_riscv64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:riscv64. Preparing to unpack .../057-libuchardet0_0.0.7-1build2_riscv64.deb ... Unpacking libuchardet0:riscv64 (0.0.7-1build2) ... Selecting previously unselected package groff-base. Preparing to unpack .../058-groff-base_1.22.4-10_riscv64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package liblmdb0:riscv64. Preparing to unpack .../059-liblmdb0_0.9.24-1build2_riscv64.deb ... Unpacking liblmdb0:riscv64 (0.9.24-1build2) ... Selecting previously unselected package libnghttp2-14:riscv64. Preparing to unpack .../060-libnghttp2-14_1.54.0-1_riscv64.deb ... Unpacking libnghttp2-14:riscv64 (1.54.0-1) ... Selecting previously unselected package libpipeline1:riscv64. Preparing to unpack .../061-libpipeline1_1.5.7-1_riscv64.deb ... Unpacking libpipeline1:riscv64 (1.5.7-1) ... Selecting previously unselected package libpsl5:riscv64. Preparing to unpack .../062-libpsl5_0.21.2-1_riscv64.deb ... Unpacking libpsl5:riscv64 (0.21.2-1) ... Selecting previously unselected package man-db. Preparing to unpack .../063-man-db_2.11.2-2_riscv64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../064-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../065-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../066-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../067-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libtcl8.6:riscv64. Preparing to unpack .../068-libtcl8.6_8.6.13+dfsg-2_riscv64.deb ... Unpacking libtcl8.6:riscv64 (8.6.13+dfsg-2) ... Selecting previously unselected package libxrender1:riscv64. Preparing to unpack .../069-libxrender1_1%3a0.9.10-1.1_riscv64.deb ... Unpacking libxrender1:riscv64 (1:0.9.10-1.1) ... Selecting previously unselected package libxft2:riscv64. Preparing to unpack .../070-libxft2_2.3.6-1_riscv64.deb ... Unpacking libxft2:riscv64 (2.3.6-1) ... Selecting previously unselected package libxss1:riscv64. Preparing to unpack .../071-libxss1_1%3a1.2.3-1build2_riscv64.deb ... Unpacking libxss1:riscv64 (1:1.2.3-1build2) ... Selecting previously unselected package libtk8.6:riscv64. Preparing to unpack .../072-libtk8.6_8.6.13-2_riscv64.deb ... Unpacking libtk8.6:riscv64 (8.6.13-2) ... Selecting previously unselected package tk8.6-blt2.5. Preparing to unpack .../073-tk8.6-blt2.5_2.5.3+dfsg-4.1build2_riscv64.deb ... Unpacking tk8.6-blt2.5 (2.5.3+dfsg-4.1build2) ... Selecting previously unselected package blt. Preparing to unpack .../074-blt_2.5.3+dfsg-4.1build2_riscv64.deb ... Unpacking blt (2.5.3+dfsg-4.1build2) ... Selecting previously unselected package bwa. Preparing to unpack .../075-bwa_0.7.17-7_riscv64.deb ... Unpacking bwa (0.7.17-7) ... Selecting previously unselected package libargtable2-0. Preparing to unpack .../076-libargtable2-0_13-1.1_riscv64.deb ... Unpacking libargtable2-0 (13-1.1) ... Selecting previously unselected package clustalo. Preparing to unpack .../077-clustalo_1.2.4-7_riscv64.deb ... Unpacking clustalo (1.2.4-7) ... Selecting previously unselected package clustalw. Preparing to unpack .../078-clustalw_2.1+lgpl-7_riscv64.deb ... Unpacking clustalw (2.1+lgpl-7) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../079-libdebhelper-perl_13.11.4ubuntu3_all.deb ... Unpacking libdebhelper-perl (13.11.4ubuntu3) ... Selecting previously unselected package libtool. Preparing to unpack .../080-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../081-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../082-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../083-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../084-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../085-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libdw1:riscv64. Preparing to unpack .../086-libdw1_0.188-2.1_riscv64.deb ... Unpacking libdw1:riscv64 (0.188-2.1) ... Selecting previously unselected package debugedit. Preparing to unpack .../087-debugedit_1%3a5.0-5_riscv64.deb ... Unpacking debugedit (1:5.0-5) ... Selecting previously unselected package dwz. Preparing to unpack .../088-dwz_0.15-1_riscv64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package gettext. Preparing to unpack .../089-gettext_0.21-12_riscv64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../090-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../091-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../092-debhelper_13.11.4ubuntu3_all.deb ... Unpacking debhelper (13.11.4ubuntu3) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../093-python3-lib2to3_3.11.4-1_all.deb ... Unpacking python3-lib2to3 (3.11.4-1) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../094-python3-distutils_3.11.4-1_all.deb ... Unpacking python3-distutils (3.11.4-1) ... Selecting previously unselected package dh-python. Preparing to unpack .../095-dh-python_6.20230603_all.deb ... Unpacking dh-python (6.20230603) ... Selecting previously unselected package dialign. Preparing to unpack .../096-dialign_2.2.1-11_riscv64.deb ... Unpacking dialign (2.2.1-11) ... Selecting previously unselected package libboost-regex1.74.0:riscv64. Preparing to unpack .../097-libboost-regex1.74.0_1.74.0+ds1-21.1ubuntu1_riscv64.deb ... Unpacking libboost-regex1.74.0:riscv64 (1.74.0+ds1-21.1ubuntu1) ... Selecting previously unselected package libcifpp-data. Preparing to unpack .../098-libcifpp-data_5.0.7.1-1build1_all.deb ... Unpacking libcifpp-data (5.0.7.1-1build1) ... Selecting previously unselected package libcifpp5:riscv64. Preparing to unpack .../099-libcifpp5_5.0.7.1-1build1_riscv64.deb ... Unpacking libcifpp5:riscv64 (5.0.7.1-1build1) ... Selecting previously unselected package dssp. Preparing to unpack .../100-dssp_4.2.2-2_riscv64.deb ... Unpacking dssp (4.2.2-2) ... Selecting previously unselected package libxpm4:riscv64. Preparing to unpack .../101-libxpm4_1%3a3.5.12-1.1_riscv64.deb ... Unpacking libxpm4:riscv64 (1:3.5.12-1.1) ... Selecting previously unselected package libgd3:riscv64. Preparing to unpack .../102-libgd3_2.3.3-9ubuntu1_riscv64.deb ... Unpacking libgd3:riscv64 (2.3.3-9ubuntu1) ... Selecting previously unselected package libhpdf-2.3.0:riscv64. Preparing to unpack .../103-libhpdf-2.3.0_2.3.0+dfsg-1build1_riscv64.deb ... Unpacking libhpdf-2.3.0:riscv64 (2.3.0+dfsg-1build1) ... Selecting previously unselected package mysql-common. Preparing to unpack .../104-mysql-common_5.8+1.1.0_all.deb ... Unpacking mysql-common (5.8+1.1.0) ... Selecting previously unselected package libmysqlclient21:riscv64. Preparing to unpack .../105-libmysqlclient21_8.0.33-2_riscv64.deb ... Unpacking libmysqlclient21:riscv64 (8.0.33-2) ... Selecting previously unselected package libsasl2-modules-db:riscv64. Preparing to unpack .../106-libsasl2-modules-db_2.1.28+dfsg1-1_riscv64.deb ... Unpacking libsasl2-modules-db:riscv64 (2.1.28+dfsg1-1) ... Selecting previously unselected package libsasl2-2:riscv64. Preparing to unpack .../107-libsasl2-2_2.1.28+dfsg1-1_riscv64.deb ... Unpacking libsasl2-2:riscv64 (2.1.28+dfsg1-1) ... Selecting previously unselected package libldap2:riscv64. Preparing to unpack .../108-libldap2_2.6.3+dfsg-1~exp1ubuntu2_riscv64.deb ... Unpacking libldap2:riscv64 (2.6.3+dfsg-1~exp1ubuntu2) ... Selecting previously unselected package libpq5:riscv64. Preparing to unpack .../109-libpq5_15.3-1_riscv64.deb ... Unpacking libpq5:riscv64 (15.3-1) ... Selecting previously unselected package emboss-lib. Preparing to unpack .../110-emboss-lib_6.6.0+dfsg-12ubuntu1_riscv64.deb ... Unpacking emboss-lib (6.6.0+dfsg-12ubuntu1) ... Selecting previously unselected package emboss-data. Preparing to unpack .../111-emboss-data_6.6.0+dfsg-12ubuntu1_all.deb ... Unpacking emboss-data (6.6.0+dfsg-12ubuntu1) ... Selecting previously unselected package emboss. Preparing to unpack .../112-emboss_6.6.0+dfsg-12ubuntu1_riscv64.deb ... Unpacking emboss (6.6.0+dfsg-12ubuntu1) ... Selecting previously unselected package fonts-lmodern. Preparing to unpack .../113-fonts-lmodern_2.005-1_all.deb ... Unpacking fonts-lmodern (2.005-1) ... Selecting previously unselected package fonts-lyx. Preparing to unpack .../114-fonts-lyx_2.3.7-1_all.deb ... Unpacking fonts-lyx (2.3.7-1) ... Selecting previously unselected package libgs-common. Preparing to unpack .../115-libgs-common_10.0.0~dfsg1-0ubuntu1.1_all.deb ... Unpacking libgs-common (10.0.0~dfsg1-0ubuntu1.1) ... Selecting previously unselected package libgs10-common. Preparing to unpack .../116-libgs10-common_10.0.0~dfsg1-0ubuntu1.1_all.deb ... Unpacking libgs10-common (10.0.0~dfsg1-0ubuntu1.1) ... Selecting previously unselected package libavahi-common-data:riscv64. Preparing to unpack .../117-libavahi-common-data_0.8-10ubuntu1_riscv64.deb ... Unpacking libavahi-common-data:riscv64 (0.8-10ubuntu1) ... Selecting previously unselected package libavahi-common3:riscv64. Preparing to unpack .../118-libavahi-common3_0.8-10ubuntu1_riscv64.deb ... Unpacking libavahi-common3:riscv64 (0.8-10ubuntu1) ... Selecting previously unselected package libavahi-client3:riscv64. Preparing to unpack .../119-libavahi-client3_0.8-10ubuntu1_riscv64.deb ... Unpacking libavahi-client3:riscv64 (0.8-10ubuntu1) ... Selecting previously unselected package libcups2:riscv64. Preparing to unpack .../120-libcups2_2.4.5-0ubuntu2_riscv64.deb ... Unpacking libcups2:riscv64 (2.4.5-0ubuntu2) ... Selecting previously unselected package libidn12:riscv64. Preparing to unpack .../121-libidn12_1.41-1_riscv64.deb ... Unpacking libidn12:riscv64 (1.41-1) ... Selecting previously unselected package libijs-0.35:riscv64. Preparing to unpack .../122-libijs-0.35_0.35-15.1_riscv64.deb ... Unpacking libijs-0.35:riscv64 (0.35-15.1) ... Selecting previously unselected package libjbig2dec0:riscv64. Preparing to unpack .../123-libjbig2dec0_0.19-3build2_riscv64.deb ... Unpacking libjbig2dec0:riscv64 (0.19-3build2) ... Selecting previously unselected package libpaper1:riscv64. Preparing to unpack .../124-libpaper1_1.1.29_riscv64.deb ... Unpacking libpaper1:riscv64 (1.1.29) ... Selecting previously unselected package libice6:riscv64. Preparing to unpack .../125-libice6_2%3a1.0.10-1build2_riscv64.deb ... Unpacking libice6:riscv64 (2:1.0.10-1build2) ... Selecting previously unselected package libsm6:riscv64. Preparing to unpack .../126-libsm6_2%3a1.2.3-1build2_riscv64.deb ... Unpacking libsm6:riscv64 (2:1.2.3-1build2) ... Selecting previously unselected package libxt6:riscv64. Preparing to unpack .../127-libxt6_1%3a1.2.1-1.1_riscv64.deb ... Unpacking libxt6:riscv64 (1:1.2.1-1.1) ... Selecting previously unselected package libgs10:riscv64. Preparing to unpack .../128-libgs10_10.0.0~dfsg1-0ubuntu1.1_riscv64.deb ... Unpacking libgs10:riscv64 (10.0.0~dfsg1-0ubuntu1.1) ... Selecting previously unselected package ghostscript. Preparing to unpack .../129-ghostscript_10.0.0~dfsg1-0ubuntu1.1_riscv64.deb ... Unpacking ghostscript (10.0.0~dfsg1-0ubuntu1.1) ... Selecting previously unselected package libnetpbm11:riscv64. Preparing to unpack .../130-libnetpbm11_2%3a11.01.00-2build1_riscv64.deb ... Unpacking libnetpbm11:riscv64 (2:11.01.00-2build1) ... Selecting previously unselected package netpbm. Preparing to unpack .../131-netpbm_2%3a11.01.00-2build1_riscv64.deb ... Unpacking netpbm (2:11.01.00-2build1) ... Selecting previously unselected package tex-common. Preparing to unpack .../132-tex-common_6.18_all.deb ... Unpacking tex-common (6.18) ... Selecting previously unselected package libpaper-utils. Preparing to unpack .../133-libpaper-utils_1.1.29_riscv64.deb ... Unpacking libpaper-utils (1.1.29) ... Selecting previously unselected package libkpathsea6:riscv64. Preparing to unpack .../134-libkpathsea6_2022.20220321.62855-5.1_riscv64.deb ... Unpacking libkpathsea6:riscv64 (2022.20220321.62855-5.1) ... Selecting previously unselected package libptexenc1:riscv64. Preparing to unpack .../135-libptexenc1_2022.20220321.62855-5.1_riscv64.deb ... Unpacking libptexenc1:riscv64 (2022.20220321.62855-5.1) ... Selecting previously unselected package libsynctex2:riscv64. Preparing to unpack .../136-libsynctex2_2022.20220321.62855-5.1_riscv64.deb ... Unpacking libsynctex2:riscv64 (2022.20220321.62855-5.1) ... Selecting previously unselected package libtexlua53-5:riscv64. Preparing to unpack .../137-libtexlua53-5_2022.20220321.62855-5.1_riscv64.deb ... Unpacking libtexlua53-5:riscv64 (2022.20220321.62855-5.1) ... Selecting previously unselected package t1utils. Preparing to unpack .../138-t1utils_1.41-4build2_riscv64.deb ... Unpacking t1utils (1.41-4build2) ... Selecting previously unselected package libpixman-1-0:riscv64. Preparing to unpack .../139-libpixman-1-0_0.42.2-1_riscv64.deb ... Unpacking libpixman-1-0:riscv64 (0.42.2-1) ... Selecting previously unselected package libxcb-render0:riscv64. Preparing to unpack .../140-libxcb-render0_1.15-1_riscv64.deb ... Unpacking libxcb-render0:riscv64 (1.15-1) ... Selecting previously unselected package libxcb-shm0:riscv64. Preparing to unpack .../141-libxcb-shm0_1.15-1_riscv64.deb ... Unpacking libxcb-shm0:riscv64 (1.15-1) ... Selecting previously unselected package libcairo2:riscv64. Preparing to unpack .../142-libcairo2_1.16.0-7_riscv64.deb ... Unpacking libcairo2:riscv64 (1.16.0-7) ... Selecting previously unselected package libgraphite2-3:riscv64. Preparing to unpack .../143-libgraphite2-3_1.3.14-1build2_riscv64.deb ... Unpacking libgraphite2-3:riscv64 (1.3.14-1build2) ... Selecting previously unselected package libharfbuzz0b:riscv64. Preparing to unpack .../144-libharfbuzz0b_6.0.0+dfsg-3build1_riscv64.deb ... Unpacking libharfbuzz0b:riscv64 (6.0.0+dfsg-3build1) ... Selecting previously unselected package libteckit0:riscv64. Preparing to unpack .../145-libteckit0_2.5.11+ds1-1_riscv64.deb ... Unpacking libteckit0:riscv64 (2.5.11+ds1-1) ... Selecting previously unselected package libxmu6:riscv64. Preparing to unpack .../146-libxmu6_2%3a1.1.3-3_riscv64.deb ... Unpacking libxmu6:riscv64 (2:1.1.3-3) ... Selecting previously unselected package libxaw7:riscv64. Preparing to unpack .../147-libxaw7_2%3a1.0.14-1_riscv64.deb ... Unpacking libxaw7:riscv64 (2:1.0.14-1) ... Selecting previously unselected package libxi6:riscv64. Preparing to unpack .../148-libxi6_2%3a1.8-1build1_riscv64.deb ... Unpacking libxi6:riscv64 (2:1.8-1build1) ... Selecting previously unselected package libzzip-0-13:riscv64. Preparing to unpack .../149-libzzip-0-13_0.13.72+dfsg.1-1.1_riscv64.deb ... Unpacking libzzip-0-13:riscv64 (0.13.72+dfsg.1-1.1) ... Selecting previously unselected package texlive-binaries. Preparing to unpack .../150-texlive-binaries_2022.20220321.62855-5.1_riscv64.deb ... Unpacking texlive-binaries (2022.20220321.62855-5.1) ... Selecting previously unselected package xdg-utils. Preparing to unpack .../151-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... Selecting previously unselected package texlive-base. Preparing to unpack .../152-texlive-base_2022.20230122-3_all.deb ... Unpacking texlive-base (2022.20230122-3) ... Selecting previously unselected package hicolor-icon-theme. Preparing to unpack .../153-hicolor-icon-theme_0.17-2_all.deb ... Unpacking hicolor-icon-theme (0.17-2) ... Selecting previously unselected package imagemagick-6.q16. Preparing to unpack .../154-imagemagick-6.q16_8%3a6.9.11.60+dfsg-1.6_riscv64.deb ... Unpacking imagemagick-6.q16 (8:6.9.11.60+dfsg-1.6) ... Selecting previously unselected package imagemagick. Preparing to unpack .../155-imagemagick_8%3a6.9.11.60+dfsg-1.6_riscv64.deb ... Unpacking imagemagick (8:6.9.11.60+dfsg-1.6) ... Selecting previously unselected package hevea. Preparing to unpack .../156-hevea_2.36-1build1_riscv64.deb ... Unpacking hevea (2.36-1build1) ... Selecting previously unselected package libapache-pom-java. Preparing to unpack .../157-libapache-pom-java_29-2_all.deb ... Unpacking libapache-pom-java (29-2) ... Selecting previously unselected package libblas3:riscv64. Preparing to unpack .../158-libblas3_3.11.0-2_riscv64.deb ... Unpacking libblas3:riscv64 (3.11.0-2) ... Selecting previously unselected package libboost1.74-dev:riscv64. Preparing to unpack .../159-libboost1.74-dev_1.74.0+ds1-21.1ubuntu1_riscv64.deb ... Unpacking libboost1.74-dev:riscv64 (1.74.0+ds1-21.1ubuntu1) ... Selecting previously unselected package libboost-dev:riscv64. Preparing to unpack .../160-libboost-dev_1.74.0.3ubuntu7_riscv64.deb ... Unpacking libboost-dev:riscv64 (1.74.0.3ubuntu7) ... Selecting previously unselected package libcommons-parent-java. Preparing to unpack .../161-libcommons-parent-java_56-1_all.deb ... Unpacking libcommons-parent-java (56-1) ... Selecting previously unselected package libcommons-logging-java. Preparing to unpack .../162-libcommons-logging-java_1.2-3_all.deb ... Unpacking libcommons-logging-java (1.2-3) ... Selecting previously unselected package librtmp1:riscv64. Preparing to unpack .../163-librtmp1_2.4+20151223.gitfa8646d.1-2build4_riscv64.deb ... Unpacking librtmp1:riscv64 (2.4+20151223.gitfa8646d.1-2build4) ... Selecting previously unselected package libssh-4:riscv64. Preparing to unpack .../164-libssh-4_0.10.5-2_riscv64.deb ... Unpacking libssh-4:riscv64 (0.10.5-2) ... Selecting previously unselected package libcurl3-gnutls:riscv64. Preparing to unpack .../165-libcurl3-gnutls_7.88.1-10ubuntu1_riscv64.deb ... Unpacking libcurl3-gnutls:riscv64 (7.88.1-10ubuntu1) ... Selecting previously unselected package libexpat1-dev:riscv64. Preparing to unpack .../166-libexpat1-dev_2.5.0-2_riscv64.deb ... Unpacking libexpat1-dev:riscv64 (2.5.0-2) ... Selecting previously unselected package libgfortran5:riscv64. Preparing to unpack .../167-libgfortran5_13.1.0-6ubuntu1_riscv64.deb ... Unpacking libgfortran5:riscv64 (13.1.0-6ubuntu1) ... Selecting previously unselected package libhtscodecs2:riscv64. Preparing to unpack .../168-libhtscodecs2_1.5.0-1_riscv64.deb ... Unpacking libhtscodecs2:riscv64 (1.5.0-1) ... Selecting previously unselected package libhts3:riscv64. Preparing to unpack .../169-libhts3_1.17+ds-1_riscv64.deb ... Unpacking libhts3:riscv64 (1.17+ds-1) ... Selecting previously unselected package libimagequant0:riscv64. Preparing to unpack .../170-libimagequant0_2.17.0-1_riscv64.deb ... Unpacking libimagequant0:riscv64 (2.17.0-1) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../171-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-jquery-ui. Preparing to unpack .../172-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../173-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../174-libjs-sphinxdoc_5.3.0-4_all.deb ... Unpacking libjs-sphinxdoc (5.3.0-4) ... Selecting previously unselected package libopenblas0-pthread:riscv64. Preparing to unpack .../175-libopenblas0-pthread_0.3.23+ds-2_riscv64.deb ... Unpacking libopenblas0-pthread:riscv64 (0.3.23+ds-2) ... Selecting previously unselected package liblapack3:riscv64. Preparing to unpack .../176-liblapack3_3.11.0-2_riscv64.deb ... Unpacking liblapack3:riscv64 (3.11.0-2) ... Selecting previously unselected package liblbfgsb0:riscv64. Preparing to unpack .../177-liblbfgsb0_3.0+dfsg.4-1_riscv64.deb ... Unpacking liblbfgsb0:riscv64 (3.0+dfsg.4-1) ... Selecting previously unselected package libmbedcrypto7:riscv64. Preparing to unpack .../178-libmbedcrypto7_2.28.3-1_riscv64.deb ... Unpacking libmbedcrypto7:riscv64 (2.28.3-1) ... Selecting previously unselected package libmbedx509-1:riscv64. Preparing to unpack .../179-libmbedx509-1_2.28.3-1_riscv64.deb ... Unpacking libmbedx509-1:riscv64 (2.28.3-1) ... Selecting previously unselected package libmbedtls14:riscv64. Preparing to unpack .../180-libmbedtls14_2.28.3-1_riscv64.deb ... Unpacking libmbedtls14:riscv64 (2.28.3-1) ... Selecting previously unselected package libopenblas0:riscv64. Preparing to unpack .../181-libopenblas0_0.3.23+ds-2_riscv64.deb ... Unpacking libopenblas0:riscv64 (0.3.23+ds-2) ... Selecting previously unselected package libopenblas-pthread-dev:riscv64. Preparing to unpack .../182-libopenblas-pthread-dev_0.3.23+ds-2_riscv64.deb ... Unpacking libopenblas-pthread-dev:riscv64 (0.3.23+ds-2) ... Selecting previously unselected package libopenblas-dev:riscv64. Preparing to unpack .../183-libopenblas-dev_0.3.23+ds-2_riscv64.deb ... Unpacking libopenblas-dev:riscv64 (0.3.23+ds-2) ... Selecting previously unselected package libpcre3:riscv64. Preparing to unpack .../184-libpcre3_2%3a8.39-15_riscv64.deb ... Unpacking libpcre3:riscv64 (2:8.39-15) ... Selecting previously unselected package libpython3.11:riscv64. Preparing to unpack .../185-libpython3.11_3.11.4-1_riscv64.deb ... Unpacking libpython3.11:riscv64 (3.11.4-1) ... Selecting previously unselected package zlib1g-dev:riscv64. Preparing to unpack .../186-zlib1g-dev_1%3a1.2.13.dfsg-1ubuntu4_riscv64.deb ... Unpacking zlib1g-dev:riscv64 (1:1.2.13.dfsg-1ubuntu4) ... Selecting previously unselected package libpython3.11-dev:riscv64. Preparing to unpack .../187-libpython3.11-dev_3.11.4-1_riscv64.deb ... Unpacking libpython3.11-dev:riscv64 (3.11.4-1) ... Selecting previously unselected package libpython3-dev:riscv64. Preparing to unpack .../188-libpython3-dev_3.11.4-1_riscv64.deb ... Unpacking libpython3-dev:riscv64 (3.11.4-1) ... Selecting previously unselected package libpython3-all-dev:riscv64. Preparing to unpack .../189-libpython3-all-dev_3.11.4-1_riscv64.deb ... Unpacking libpython3-all-dev:riscv64 (3.11.4-1) ... Selecting previously unselected package libqhull-r8.0:riscv64. Preparing to unpack .../190-libqhull-r8.0_2020.2-5_riscv64.deb ... Unpacking libqhull-r8.0:riscv64 (2020.2-5) ... Selecting previously unselected package libraqm0:riscv64. Preparing to unpack .../191-libraqm0_0.10.1-1_riscv64.deb ... Unpacking libraqm0:riscv64 (0.10.1-1) ... Selecting previously unselected package libxsimd-dev:riscv64. Preparing to unpack .../192-libxsimd-dev_8.1.0-7_riscv64.deb ... Unpacking libxsimd-dev:riscv64 (8.1.0-7) ... Selecting previously unselected package libxslt1.1:riscv64. Preparing to unpack .../193-libxslt1.1_1.1.35-1_riscv64.deb ... Unpacking libxslt1.1:riscv64 (1.1.35-1) ... Selecting previously unselected package mafft. Preparing to unpack .../194-mafft_7.505-1_riscv64.deb ... Unpacking mafft (7.505-1) ... Selecting previously unselected package ncbi-data. Preparing to unpack .../195-ncbi-data_6.1.20170106+dfsg1-10_all.deb ... Unpacking ncbi-data (6.1.20170106+dfsg1-10) ... Selecting previously unselected package ncbi-blast+. Preparing to unpack .../196-ncbi-blast+_2.12.0+ds-3build1_riscv64.deb ... Unpacking ncbi-blast+ (2.12.0+ds-3build1) ... Selecting previously unselected package phylip. Preparing to unpack .../197-phylip_1%3a3.697+dfsg-2_riscv64.deb ... Unpacking phylip (1:3.697+dfsg-2) ... Selecting previously unselected package prank. Preparing to unpack .../198-prank_0.0.170427+dfsg-3_riscv64.deb ... Unpacking prank (0.0.170427+dfsg-3) ... Selecting previously unselected package preview-latex-style. Preparing to unpack .../199-preview-latex-style_12.2-1ubuntu1_all.deb ... Unpacking preview-latex-style (12.2-1ubuntu1) ... Selecting previously unselected package probcons. Preparing to unpack .../200-probcons_1.12-14_riscv64.deb ... Unpacking probcons (1.12-14) ... Selecting previously unselected package python-matplotlib-data. Preparing to unpack .../201-python-matplotlib-data_3.6.3-1ubuntu2_all.deb ... Unpacking python-matplotlib-data (3.6.3-1ubuntu2) ... Selecting previously unselected package python3-all. Preparing to unpack .../202-python3-all_3.11.4-1_riscv64.deb ... Unpacking python3-all (3.11.4-1) ... Selecting previously unselected package python3.11-dev. Preparing to unpack .../203-python3.11-dev_3.11.4-1_riscv64.deb ... Unpacking python3.11-dev (3.11.4-1) ... Selecting previously unselected package python3-dev. Preparing to unpack .../204-python3-dev_3.11.4-1_riscv64.deb ... Unpacking python3-dev (3.11.4-1) ... Selecting previously unselected package python3-all-dev. Preparing to unpack .../205-python3-all-dev_3.11.4-1_riscv64.deb ... Unpacking python3-all-dev (3.11.4-1) ... Selecting previously unselected package python3-appdirs. Preparing to unpack .../206-python3-appdirs_1.4.4-3_all.deb ... Unpacking python3-appdirs (1.4.4-3) ... Selecting previously unselected package python3-attr. Preparing to unpack .../207-python3-attr_23.1.0-1_all.deb ... Unpacking python3-attr (23.1.0-1) ... Selecting previously unselected package python3-gast. Preparing to unpack .../208-python3-gast_0.5.2-2_all.deb ... Unpacking python3-gast (0.5.2-2) ... Selecting previously unselected package python3-beniget. Preparing to unpack .../209-python3-beniget_0.4.1-3_all.deb ... Unpacking python3-beniget (0.4.1-3) ... Selecting previously unselected package python3-brotli. Preparing to unpack .../210-python3-brotli_1.0.9-2build8_riscv64.deb ... Unpacking python3-brotli (1.0.9-2build8) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../211-python3-numpy_1%3a1.24.2-1_riscv64.deb ... Unpacking python3-numpy (1:1.24.2-1) ... Selecting previously unselected package python3-contourpy. Preparing to unpack .../212-python3-contourpy_1.0.7-1build1_riscv64.deb ... Unpacking python3-contourpy (1.0.7-1build1) ... Selecting previously unselected package python3-cycler. Preparing to unpack .../213-python3-cycler_0.11.0-1_all.deb ... Unpacking python3-cycler (0.11.0-1) ... Selecting previously unselected package python3-six. Preparing to unpack .../214-python3-six_1.16.0-4_all.deb ... Unpacking python3-six (1.16.0-4) ... Selecting previously unselected package python3-dateutil. Preparing to unpack .../215-python3-dateutil_2.8.2-2_all.deb ... Unpacking python3-dateutil (2.8.2-2) ... Selecting previously unselected package python3-decorator. Preparing to unpack .../216-python3-decorator_5.1.1-3_all.deb ... Unpacking python3-decorator (5.1.1-3) ... Selecting previously unselected package python3-ply. Preparing to unpack .../217-python3-ply_3.11-5_all.deb ... Unpacking python3-ply (3.11-5) ... Selecting previously unselected package python3-pythran. Preparing to unpack .../218-python3-pythran_0.11.0+ds-7_riscv64.deb ... Unpacking python3-pythran (0.11.0+ds-7) ... Selecting previously unselected package python3-scipy. Preparing to unpack .../219-python3-scipy_1.10.1-2_riscv64.deb ... Unpacking python3-scipy (1.10.1-2) ... Selecting previously unselected package python3-ufolib2. Preparing to unpack .../220-python3-ufolib2_0.14.0+dfsg1-1_all.deb ... Unpacking python3-ufolib2 (0.14.0+dfsg1-1) ... Selecting previously unselected package python3-mpmath. Preparing to unpack .../221-python3-mpmath_1.2.1-2_all.deb ... Unpacking python3-mpmath (1.2.1-2) ... Selecting previously unselected package python3-sympy. Preparing to unpack .../222-python3-sympy_1.12-2_all.deb ... Unpacking python3-sympy (1.12-2) ... Selecting previously unselected package python3-tz. Preparing to unpack .../223-python3-tz_2023.3-3_all.deb ... Unpacking python3-tz (2023.3-3) ... Selecting previously unselected package python3-fs. Preparing to unpack .../224-python3-fs_2.4.16-2_all.deb ... Unpacking python3-fs (2.4.16-2) ... Selecting previously unselected package python3-lxml:riscv64. Preparing to unpack .../225-python3-lxml_4.9.2-1build1_riscv64.deb ... Unpacking python3-lxml:riscv64 (4.9.2-1build1) ... Selecting previously unselected package python3-lz4. Preparing to unpack .../226-python3-lz4_4.0.2+dfsg-1build1_riscv64.deb ... Unpacking python3-lz4 (4.0.2+dfsg-1build1) ... Selecting previously unselected package unicode-data. Preparing to unpack .../227-unicode-data_15.0.0-1_all.deb ... Unpacking unicode-data (15.0.0-1) ... Selecting previously unselected package python3-fonttools. Preparing to unpack .../228-python3-fonttools_4.38.0-1build1_riscv64.deb ... Unpacking python3-fonttools (4.38.0-1build1) ... Selecting previously unselected package python3-isodate. Preparing to unpack .../229-python3-isodate_0.6.1-1_all.deb ... Unpacking python3-isodate (0.6.1-1) ... Selecting previously unselected package python3-kiwisolver. Preparing to unpack .../230-python3-kiwisolver_1.4.4-1build1_riscv64.deb ... Unpacking python3-kiwisolver (1.4.4-1build1) ... Selecting previously unselected package python3-pil:riscv64. Preparing to unpack .../231-python3-pil_9.5.0-1_riscv64.deb ... Unpacking python3-pil:riscv64 (9.5.0-1) ... Selecting previously unselected package python3-tk:riscv64. Preparing to unpack .../232-python3-tk_3.11.4-1_riscv64.deb ... Unpacking python3-tk:riscv64 (3.11.4-1) ... Selecting previously unselected package python3-pil.imagetk:riscv64. Preparing to unpack .../233-python3-pil.imagetk_9.5.0-1_riscv64.deb ... Unpacking python3-pil.imagetk:riscv64 (9.5.0-1) ... Selecting previously unselected package python3-pyparsing. Preparing to unpack .../234-python3-pyparsing_3.0.9-1_all.deb ... Unpacking python3-pyparsing (3.0.9-1) ... Selecting previously unselected package python3-packaging. Preparing to unpack .../235-python3-packaging_23.1-1_all.deb ... Unpacking python3-packaging (23.1-1) ... Selecting previously unselected package python3-matplotlib. Preparing to unpack .../236-python3-matplotlib_3.6.3-1ubuntu2_riscv64.deb ... Unpacking python3-matplotlib (3.6.3-1ubuntu2) ... Selecting previously unselected package python3-msgpack. Preparing to unpack .../237-python3-msgpack_1.0.3-2build1_riscv64.deb ... Unpacking python3-msgpack (1.0.3-2build1) ... Selecting previously unselected package python3-mmtf. Preparing to unpack .../238-python3-mmtf_1.1.3-1_all.deb ... Unpacking python3-mmtf (1.1.3-1) ... Selecting previously unselected package python3-mysqldb. Preparing to unpack .../239-python3-mysqldb_1.4.6-2build1_riscv64.deb ... Unpacking python3-mysqldb (1.4.6-2build1) ... Selecting previously unselected package python3-networkx. Preparing to unpack .../240-python3-networkx_2.8.8-1ubuntu1_all.deb ... Unpacking python3-networkx (2.8.8-1ubuntu1) ... Selecting previously unselected package python3-psycopg2. Preparing to unpack .../241-python3-psycopg2_2.9.5-1build1_riscv64.deb ... Unpacking python3-psycopg2 (2.9.5-1build1) ... Selecting previously unselected package python3-rdflib. Preparing to unpack .../242-python3-rdflib_6.1.1-1_all.deb ... Unpacking python3-rdflib (6.1.1-1) ... Selecting previously unselected package python3-reportlab. Preparing to unpack .../243-python3-reportlab_4.0.4-1_all.deb ... Unpacking python3-reportlab (4.0.4-1) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../244-python3-setuptools_67.8.0-1_all.deb ... Unpacking python3-setuptools (67.8.0-1) ... Selecting previously unselected package python3-unittest2. Preparing to unpack .../245-python3-unittest2_1.1.0-9_all.deb ... Unpacking python3-unittest2 (1.1.0-9) ... Selecting previously unselected package samtools. Preparing to unpack .../246-samtools_1.17-1_riscv64.deb ... Unpacking samtools (1.17-1) ... Selecting previously unselected package t-coffee. Preparing to unpack .../247-t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_riscv64.deb ... Unpacking t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) ... Selecting previously unselected package texlive-fonts-recommended. Preparing to unpack .../248-texlive-fonts-recommended_2022.20230122-3_all.deb ... Unpacking texlive-fonts-recommended (2022.20230122-3) ... Selecting previously unselected package texlive-latex-base. Preparing to unpack .../249-texlive-latex-base_2022.20230122-3_all.deb ... Unpacking texlive-latex-base (2022.20230122-3) ... Selecting previously unselected package libfontbox-java. Preparing to unpack .../250-libfontbox-java_1%3a1.8.16-2_all.deb ... Unpacking libfontbox-java (1:1.8.16-2) ... Selecting previously unselected package libpdfbox-java. Preparing to unpack .../251-libpdfbox-java_1%3a1.8.16-2_all.deb ... Unpacking libpdfbox-java (1:1.8.16-2) ... Selecting previously unselected package texlive-latex-recommended. Preparing to unpack .../252-texlive-latex-recommended_2022.20230122-3_all.deb ... Unpacking texlive-latex-recommended (2022.20230122-3) ... Selecting previously unselected package texlive-pictures. Preparing to unpack .../253-texlive-pictures_2022.20230122-3_all.deb ... Unpacking texlive-pictures (2022.20230122-3) ... Selecting previously unselected package texlive-latex-extra. Preparing to unpack .../254-texlive-latex-extra_2022.20230122-4_all.deb ... Unpacking texlive-latex-extra (2022.20230122-4) ... Selecting previously unselected package wise-data. Preparing to unpack .../255-wise-data_2.4.1-23_all.deb ... Unpacking wise-data (2.4.1-23) ... Selecting previously unselected package wise. Preparing to unpack .../256-wise_2.4.1-23_riscv64.deb ... Unpacking wise (2.4.1-23) ... Selecting previously unselected package fasttree. Preparing to unpack .../257-fasttree_2.1.11-2_riscv64.deb ... Unpacking fasttree (2.1.11-2) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../258-sbuild-build-depends-main-dummy_0.invalid.0_riscv64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libhtscodecs2:riscv64 (1.5.0-1) ... Setting up media-types (10.0.0) ... Setting up libpipeline1:riscv64 (1.5.7-1) ... Setting up liblmdb0:riscv64 (0.9.24-1build2) ... Setting up libgraphite2-3:riscv64 (1.3.14-1build2) ... Setting up liblcms2-2:riscv64 (2.14-2) ... Setting up ncbi-data (6.1.20170106+dfsg1-10) ... Setting up libpixman-1-0:riscv64 (0.42.2-1) ... Setting up libaom3:riscv64 (3.6.1-1) ... Setting up mysql-common (5.8+1.1.0) ... update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode Setting up libmysqlclient21:riscv64 (8.0.33-2) ... Setting up libxau6:riscv64 (1:1.0.9-1build5) ... Setting up imagemagick-6-common (8:6.9.11.60+dfsg-1.6) ... Setting up libhpdf-2.3.0:riscv64 (2.3.0+dfsg-1build1) ... Setting up libpsl5:riscv64 (0.21.2-1) ... Setting up libboost1.74-dev:riscv64 (1.74.0+ds1-21.1ubuntu1) ... Setting up libicu72:riscv64 (72.1-3ubuntu2) ... Setting up liblerc4:riscv64 (4.0.0+ds-2ubuntu2) ... Setting up bsdextrautils (2.38.1-5ubuntu2) ... Setting up hicolor-icon-theme (0.17-2) ... Setting up probcons (1.12-14) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up mafft (7.505-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:riscv64 (2.76.3-1ubuntu1) ... No schema files found: doing nothing. Setting up bwa (0.7.17-7) ... Setting up fonts-lyx (2.3.7-1) ... Setting up libijs-0.35:riscv64 (0.35-15.1) ... Setting up libpython3.11-stdlib:riscv64 (3.11.4-1) ... Setting up libdebhelper-perl (13.11.4ubuntu3) ... Setting up libgs-common (10.0.0~dfsg1-0ubuntu1.1) ... Setting up libbrotli1:riscv64 (1.0.9-2build8) ... Setting up libfontbox-java (1:1.8.16-2) ... Setting up phylip (1:3.697+dfsg-2) ... Setting up x11-common (1:7.7+23ubuntu2) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libnghttp2-14:riscv64 (1.54.0-1) ... Setting up libmagic1:riscv64 (1:5.44-3) ... Setting up libnetpbm11:riscv64 (2:11.01.00-2build1) ... Setting up libdeflate0:riscv64 (1.15-1) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up libqhull-r8.0:riscv64 (2020.2-5) ... Setting up libzzip-0-13:riscv64 (0.13.72+dfsg.1-1.1) ... Setting up file (1:5.44-3) ... Setting up emboss-data (6.6.0+dfsg-12ubuntu1) ... Setting up libjbig0:riscv64 (2.1-6.1ubuntu1) ... Setting up t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) ... Setting up poppler-data (0.4.12-1) ... Setting up libsasl2-modules-db:riscv64 (2.1.28+dfsg1-1) ... Setting up unicode-data (15.0.0-1) ... Setting up libxsimd-dev:riscv64 (8.1.0-7) ... Setting up libpcre3:riscv64 (2:8.39-15) ... Setting up libfontenc1:riscv64 (1:1.1.4-1build3) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:riscv64 (3.11.0-2) ... update-alternatives: using /usr/lib/riscv64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/riscv64-linux-gnu/libblas.so.3 (libblas.so.3-riscv64-linux-gnu) in auto mode Setting up libexpat1-dev:riscv64 (2.5.0-2) ... Setting up libfreetype6:riscv64 (2.12.1+dfsg-5) ... Setting up libmbedcrypto7:riscv64 (2.28.3-1) ... Setting up libx11-data (2:1.8.6-1) ... Setting up libjbig2dec0:riscv64 (0.19-3build2) ... Setting up librtmp1:riscv64 (2.4+20151223.gitfa8646d.1-2build4) ... Setting up libteckit0:riscv64 (2.5.11+ds1-1) ... Setting up libapache-pom-java (29-2) ... Setting up libavahi-common-data:riscv64 (0.8-10ubuntu1) ... Setting up libdbus-1-3:riscv64 (1.14.6-1ubuntu1) ... Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... Setting up libfribidi0:riscv64 (1.0.13-3) ... Setting up libboost-regex1.74.0:riscv64 (1.74.0+ds1-21.1ubuntu1) ... Setting up t1utils (1.41-4build2) ... Setting up libtexlua53-5:riscv64 (2022.20220321.62855-5.1) ... Setting up libimagequant0:riscv64 (2.17.0-1) ... Setting up libidn12:riscv64 (1.41-1) ... Setting up libtcl8.6:riscv64 (8.6.13+dfsg-2) ... Setting up autopoint (0.21-12) ... Setting up fonts-dejavu-core (2.37-6) ... Setting up ucf (3.0043+nmu1) ... Setting up wise-data (2.4.1-23) ... Setting up libjpeg-turbo8:riscv64 (2.1.5-2ubuntu1) ... Setting up libdav1d6:riscv64 (1.2.1-2) ... Setting up libltdl7:riscv64 (2.4.7-5) ... Setting up libfftw3-double3:riscv64 (3.3.10-1ubuntu1) ... Setting up libcifpp-data (5.0.7.1-1build1) ... Setting up libkpathsea6:riscv64 (2022.20220321.62855-5.1) ... Setting up libsasl2-2:riscv64 (2.1.28+dfsg1-1) ... Setting up libssh-4:riscv64 (0.10.5-2) ... Setting up libgfortran5:riscv64 (13.1.0-6ubuntu1) ... Setting up autoconf (2.71-3) ... Setting up libx265-199:riscv64 (3.5-2) ... Setting up libwebp7:riscv64 (1.2.4-0.2) ... Setting up zlib1g-dev:riscv64 (1:1.2.13.dfsg-1ubuntu4) ... Setting up liblqr-1-0:riscv64 (0.4.2-2.1) ... Setting up libuchardet0:riscv64 (0.0.7-1build2) ... Setting up clustalw (2.1+lgpl-7) ... Setting up fonts-lmodern (2.005-1) ... Setting up libopenjp2-7:riscv64 (2.5.0-2) ... Setting up libsub-override-perl (0.09-4) ... Setting up libharfbuzz0b:riscv64 (6.0.0+dfsg-3build1) ... Setting up fasttree (2.1.11-2) ... Setting up libboost-dev:riscv64 (1.74.0.3ubuntu7) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libde265-0:riscv64 (1.0.12-1) ... Setting up python-matplotlib-data (3.6.3-1ubuntu2) ... Setting up libwebpmux3:riscv64 (1.2.4-0.2) ... Setting up libbsd0:riscv64 (0.11.7-4) ... Setting up mailcap (3.70+nmu1ubuntu1) ... Setting up libelf1:riscv64 (0.188-2.1) ... Setting up dialign (2.2.1-11) ... Setting up libxml2:riscv64 (2.9.14+dfsg-1.2) ... Setting up xdg-utils (1.1.3-4.1ubuntu3) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libldap2:riscv64 (2.6.3+dfsg-1~exp1ubuntu2) ... Setting up libsynctex2:riscv64 (2022.20220321.62855-5.1) ... Setting up libpython3-stdlib:riscv64 (3.11.4-1) ... Setting up prank (0.0.170427+dfsg-3) ... Setting up libargtable2-0 (13-1.1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libjpeg8:riscv64 (8c-2ubuntu11) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libpaper1:riscv64 (1.1.29) ... Creating config file /etc/papersize with new version Setting up python3.11 (3.11.4-1) ... Setting up libice6:riscv64 (2:1.0.10-1build2) ... Setting up libdw1:riscv64 (0.188-2.1) ... Setting up libxdmcp6:riscv64 (1:1.1.3-0ubuntu5) ... Setting up flex (2.6.4-8.2) ... Setting up liblapack3:riscv64 (3.11.0-2) ... update-alternatives: using /usr/lib/riscv64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/riscv64-linux-gnu/liblapack.so.3 (liblapack.so.3-riscv64-linux-gnu) in auto mode Setting up libxcb1:riscv64 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libopenblas0-pthread:riscv64 (0.3.23+ds-2) ... update-alternatives: using /usr/lib/riscv64-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/riscv64-linux-gnu/libblas.so.3 (libblas.so.3-riscv64-linux-gnu) in auto mode update-alternatives: using /usr/lib/riscv64-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/riscv64-linux-gnu/liblapack.so.3 (liblapack.so.3-riscv64-linux-gnu) in auto mode update-alternatives: using /usr/lib/riscv64-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/riscv64-linux-gnu/libopenblas.so.0 (libopenblas.so.0-riscv64-linux-gnu) in auto mode Setting up libpdfbox-java (1:1.8.16-2) ... Setting up mime-support (3.66) ... Setting up libpython3.11:riscv64 (3.11.4-1) ... Setting up libmbedx509-1:riscv64 (2.28.3-1) ... Setting up libmbedtls14:riscv64 (2.28.3-1) ... Setting up libtool (2.4.7-5) ... Setting up libxcb-render0:riscv64 (1.15-1) ... Setting up fontconfig-config (2.14.1-4ubuntu1) ... Setting up wise (2.4.1-23) ... Setting up libwebpdemux2:riscv64 (1.2.4-0.2) ... Setting up libheif1:riscv64 (1.15.1-1) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:riscv64 (0.8-10ubuntu1) ... Setting up libpq5:riscv64 (15.3-1) ... Setting up libcommons-logging-java (1.2-3) ... Setting up libcurl3-gnutls:riscv64 (7.88.1-10ubuntu1) ... Setting up python3 (3.11.4-1) ... Setting up libxcb-shm0:riscv64 (1.15-1) ... Setting up libpaper-utils (1.1.29) ... Setting up clustalo (1.2.4-7) ... Setting up xfonts-utils (1:7.7+6build2) ... Setting up python3-tz (2023.3-3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up ncbi-blast+ (2.12.0+ds-3build1) ... Setting up libcifpp5:riscv64 (5.0.7.1-1build1) ... Setting up python3-mysqldb (1.4.6-2build1) ... Setting up python3-six (1.16.0-4) ... Setting up dh-autoreconf (20) ... Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up python3-isodate (0.6.1-1) ... Setting up python3-decorator (5.1.1-3) ... Setting up python3-packaging (23.1-1) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libptexenc1:riscv64 (2022.20220321.62855-5.1) ... Setting up python3-pyparsing (3.0.9-1) ... Setting up libpython3.11-dev:riscv64 (3.11.4-1) ... Setting up python3-brotli (1.0.9-2build8) ... Setting up libraqm0:riscv64 (0.10.1-1) ... Setting up python3-cycler (0.11.0-1) ... Setting up python3-kiwisolver (1.4.4-1build1) ... Setting up python3-psycopg2 (2.9.5-1build1) ... Setting up libjs-sphinxdoc (5.3.0-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up libopenblas0:riscv64 (0.3.23+ds-2) ... Setting up groff-base (1.22.4-10) ... Setting up libtiff6:riscv64 (4.5.0-6ubuntu1) ... Setting up libxslt1.1:riscv64 (1.1.35-1) ... Setting up debugedit (1:5.0-5) ... Setting up libx11-6:riscv64 (2:1.8.6-1) ... Setting up python3-dateutil (2.8.2-2) ... Setting up python3-msgpack (1.0.3-2build1) ... Setting up libfontconfig1:riscv64 (2.14.1-4ubuntu1) ... Setting up python3-mpmath (1.2.1-2) ... Setting up python3-lib2to3 (3.11.4-1) ... Setting up python3-appdirs (1.4.4-3) ... Setting up libsm6:riscv64 (2:1.2.3-1build2) ... Setting up libavahi-client3:riscv64 (0.8-10ubuntu1) ... Setting up liblbfgsb0:riscv64 (3.0+dfsg.4-1) ... Setting up python3-pkg-resources (67.8.0-1) ... Setting up python3-distutils (3.11.4-1) ... Setting up libopenblas-pthread-dev:riscv64 (0.3.23+ds-2) ... update-alternatives: using /usr/lib/riscv64-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/riscv64-linux-gnu/libblas.so (libblas.so-riscv64-linux-gnu) in auto mode update-alternatives: using /usr/lib/riscv64-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/riscv64-linux-gnu/liblapack.so (liblapack.so-riscv64-linux-gnu) in auto mode update-alternatives: using /usr/lib/riscv64-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/riscv64-linux-gnu/libopenblas.so (libopenblas.so-riscv64-linux-gnu) in auto mode Setting up dh-python (6.20230603) ... Setting up python3-sympy (1.12-2) ... Setting up python3-attr (23.1.0-1) ... Setting up libhts3:riscv64 (1.17+ds-1) ... Setting up libpython3-dev:riscv64 (3.11.4-1) ... Setting up python3-setuptools (67.8.0-1) ... Setting up libxpm4:riscv64 (1:3.5.12-1.1) ... Setting up libxrender1:riscv64 (1:0.9.10-1.1) ... Setting up python3-lz4 (4.0.2+dfsg-1build1) ... Setting up python3.11-dev (3.11.4-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up preview-latex-style (12.2-1ubuntu1) ... Setting up python3-ply (3.11-5) ... Setting up python3-gast (0.5.2-2) ... Setting up libxext6:riscv64 (2:1.3.4-1build1) ... Setting up python3-all (3.11.4-1) ... Setting up fonts-urw-base35 (20200910-7) ... Setting up dssp (4.2.2-2) ... Setting up python3-networkx (2.8.8-1ubuntu1) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up libcairo2:riscv64 (1.16.0-7) ... Setting up samtools (1.17-1) ... Setting up python3-fs (2.4.16-2) ... Setting up python3-beniget (0.4.1-3) ... Setting up python3-pil:riscv64 (9.5.0-1) ... Setting up libmagickcore-6.q16-6:riscv64 (8:6.9.11.60+dfsg-1.6) ... Setting up libopenblas-dev:riscv64 (0.3.23+ds-2) ... Setting up python3-pygments (2.15.1+dfsg-1) ... Setting up libpython3-all-dev:riscv64 (3.11.4-1) ... Setting up python3-dev (3.11.4-1) ... Setting up libgd3:riscv64 (2.3.3-9ubuntu1) ... Setting up python3-unittest2 (1.1.0-9) ... update-alternatives: using /usr/bin/python3-unit2 to provide /usr/bin/unit2 (unit2) in auto mode Setting up netpbm (2:11.01.00-2build1) ... Setting up libxt6:riscv64 (1:1.2.1-1.1) ... Setting up python3-numpy (1:1.24.2-1) ... Setting up python3-reportlab (4.0.4-1) ... Setting up libcups2:riscv64 (2.4.5-0ubuntu2) ... Setting up python3-lxml:riscv64 (4.9.2-1build1) ... Setting up python3-rdflib (6.1.1-1) ... Setting up libmagickwand-6.q16-6:riscv64 (8:6.9.11.60+dfsg-1.6) ... Setting up python3-contourpy (1.0.7-1build1) ... Setting up emboss-lib (6.6.0+dfsg-12ubuntu1) ... Setting up libxss1:riscv64 (1:1.2.3-1build2) ... Setting up python3-all-dev (3.11.4-1) ... Setting up libgs10-common (10.0.0~dfsg1-0ubuntu1.1) ... Setting up libxft2:riscv64 (2.3.6-1) ... Setting up libxmu6:riscv64 (2:1.1.3-3) ... Setting up emboss (6.6.0+dfsg-12ubuntu1) ... Setting up libxi6:riscv64 (2:1.8-1build1) ... Setting up libtk8.6:riscv64 (8.6.13-2) ... Setting up debhelper (13.11.4ubuntu3) ... Setting up libxaw7:riscv64 (2:1.0.14-1) ... Setting up python3-mmtf (1.1.3-1) ... Setting up imagemagick-6.q16 (8:6.9.11.60+dfsg-1.6) ... update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare (compare) in auto mode update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare-im6 (compare-im6) in auto mode update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate (animate) in auto mode update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate-im6 (animate-im6) in auto mode update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert (convert) in auto mode update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert-im6 (convert-im6) in auto mode update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite (composite) in auto mode update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite-im6 (composite-im6) in auto mode update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure (conjure) in auto mode update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure-im6 (conjure-im6) in auto mode update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import (import) in auto mode update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import-im6 (import-im6) in auto mode update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify (identify) in auto mode update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify-im6 (identify-im6) in auto mode update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream (stream) in auto mode update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream-im6 (stream-im6) in auto mode update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display (display) in auto mode update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display-im6 (display-im6) in auto mode update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage (montage) in auto mode update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage-im6 (montage-im6) in auto mode update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify (mogrify) in auto mode update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify-im6 (mogrify-im6) in auto mode Setting up python3-pythran (0.11.0+ds-7) ... Setting up texlive-binaries (2022.20220321.62855-5.1) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up texlive-base (2022.20230122-3) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up libgs10:riscv64 (10.0.0~dfsg1-0ubuntu1.1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-4.1build2) ... Setting up python3-scipy (1.10.1-2) ... Setting up blt (2.5.3+dfsg-4.1build2) ... Setting up python3-tk:riscv64 (3.11.4-1) ... Setting up ghostscript (10.0.0~dfsg1-0ubuntu1.1) ... Setting up texlive-latex-base (2022.20230122-3) ... Setting up python3-pil.imagetk:riscv64 (9.5.0-1) ... Setting up texlive-latex-recommended (2022.20230122-3) ... Setting up hevea (2.36-1build1) ... Setting up texlive-pictures (2022.20230122-3) ... Setting up imagemagick (8:6.9.11.60+dfsg-1.6) ... Setting up texlive-fonts-recommended (2022.20230122-3) ... Setting up texlive-latex-extra (2022.20230122-4) ... Setting up python3-fonttools (4.38.0-1build1) ... Setting up python3-ufolib2 (0.14.0+dfsg1-1) ... Setting up python3-matplotlib (3.6.3-1ubuntu2) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.37-0ubuntu2) ... Processing triggers for systemd (252.5-2ubuntu3) ... Processing triggers for tex-common (6.18) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (riscv64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.13.0-1019-generic #21~20.04.1-Ubuntu SMP Thu Mar 24 22:36:01 UTC 2022 riscv64 (riscv64) Toolchain package versions: binutils_2.40.50.20230622-1ubuntu1 dpkg-dev_1.21.22ubuntu1 g++-12_12.3.0-3ubuntu1 gcc-12_12.3.0-3ubuntu1 libc6-dev_2.37-0ubuntu2 libstdc++-12-dev_12.3.0-3ubuntu1 libstdc++6_13.1.0-6ubuntu1 linux-libc-dev_6.3.0-7.7 Package versions: adduser_3.134ubuntu1 advancecomp_2.5-1 apt_2.7.1 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-12 autotools-dev_20220109.1 base-files_13ubuntu1 base-passwd_3.6.1 bash_5.2.15-2ubuntu1 binutils_2.40.50.20230622-1ubuntu1 binutils-common_2.40.50.20230622-1ubuntu1 binutils-riscv64-linux-gnu_2.40.50.20230622-1ubuntu1 blt_2.5.3+dfsg-4.1build2 bsdextrautils_2.38.1-5ubuntu2 bsdutils_1:2.38.1-5ubuntu2 build-essential_12.9ubuntu3 bwa_0.7.17-7 bzip2_1.0.8-5build1 ca-certificates_20230311ubuntu1 clustalo_1.2.4-7 clustalw_2.1+lgpl-7 coreutils_9.1-1ubuntu2 cpp_4:12.2.0-3ubuntu1 cpp-12_12.3.0-3ubuntu1 dash_0.5.12-2ubuntu1 debconf_1.5.82 debhelper_13.11.4ubuntu3 debianutils_5.7-0.4 debugedit_1:5.0-5 dh-autoreconf_20 dh-python_6.20230603 dh-strip-nondeterminism_1.13.1-1 dialign_2.2.1-11 diffutils_1:3.8-4 dpkg_1.21.22ubuntu1 dpkg-dev_1.21.22ubuntu1 dssp_4.2.2-2 dwz_0.15-1 e2fsprogs_1.47.0-1ubuntu1 emboss_6.6.0+dfsg-12ubuntu1 emboss-data_6.6.0+dfsg-12ubuntu1 emboss-lib_6.6.0+dfsg-12ubuntu1 fakeroot_1.31-1.2 fasttree_2.1.11-2 file_1:5.44-3 findutils_4.9.0-4ubuntu1 flex_2.6.4-8.2 fontconfig-config_2.14.1-4ubuntu1 fonts-dejavu-core_2.37-6 fonts-lmodern_2.005-1 fonts-lyx_2.3.7-1 fonts-urw-base35_20200910-7 g++_4:12.2.0-3ubuntu1 g++-12_12.3.0-3ubuntu1 gcc_4:12.2.0-3ubuntu1 gcc-12_12.3.0-3ubuntu1 gcc-12-base_12.3.0-3ubuntu1 gcc-13-base_13.1.0-6ubuntu1 gettext_0.21-12 gettext-base_0.21-12 ghostscript_10.0.0~dfsg1-0ubuntu1.1 gpg_2.2.40-1.1ubuntu1 gpg-agent_2.2.40-1.1ubuntu1 gpgconf_2.2.40-1.1ubuntu1 gpgv_2.2.40-1.1ubuntu1 grep_3.8-5 groff-base_1.22.4-10 gzip_1.12-1ubuntu1 hevea_2.36-1build1 hicolor-icon-theme_0.17-2 hostname_3.23+nmu1ubuntu1 imagemagick_8:6.9.11.60+dfsg-1.6 imagemagick-6-common_8:6.9.11.60+dfsg-1.6 imagemagick-6.q16_8:6.9.11.60+dfsg-1.6 init_1.65.2 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 libacl1_2.3.1-3 libaom3_3.6.1-1 libapache-pom-java_29-2 libapparmor1_3.0.8-1ubuntu3 libapt-pkg6.0_2.7.1 libarchive-zip-perl_1.68-1 libargon2-1_0~20190702+dfsg-3 libargtable2-0_13-1.1 libasan8_13.1.0-6ubuntu1 libassuan0_2.5.5-5 libatomic1_13.1.0-6ubuntu1 libattr1_1:2.5.1-4 libaudit-common_1:3.0.9-1 libaudit1_1:3.0.9-1 libavahi-client3_0.8-10ubuntu1 libavahi-common-data_0.8-10ubuntu1 libavahi-common3_0.8-10ubuntu1 libbinutils_2.40.50.20230622-1ubuntu1 libblas3_3.11.0-2 libblkid1_2.38.1-5ubuntu2 libboost-dev_1.74.0.3ubuntu7 libboost-regex1.74.0_1.74.0+ds1-21.1ubuntu1 libboost1.74-dev_1.74.0+ds1-21.1ubuntu1 libbrotli1_1.0.9-2build8 libbsd0_0.11.7-4 libbz2-1.0_1.0.8-5build1 libc-bin_2.37-0ubuntu2 libc-dev-bin_2.37-0ubuntu2 libc6_2.37-0ubuntu2 libc6-dev_2.37-0ubuntu2 libcairo2_1.16.0-7 libcap-ng0_0.8.3-1build2 libcap2_1:2.66-4ubuntu1 libcc1-0_13.1.0-6ubuntu1 libcifpp-data_5.0.7.1-1build1 libcifpp5_5.0.7.1-1build1 libcom-err2_1.47.0-1ubuntu1 libcommons-logging-java_1.2-3 libcommons-parent-java_56-1 libcrypt-dev_1:4.4.35-1 libcrypt1_1:4.4.35-1 libcryptsetup12_2:2.6.1-4ubuntu1 libctf-nobfd0_2.40.50.20230622-1ubuntu1 libctf0_2.40.50.20230622-1ubuntu1 libcups2_2.4.5-0ubuntu2 libcurl3-gnutls_7.88.1-10ubuntu1 libdav1d6_1.2.1-2 libdb5.3_5.3.28+dfsg2-1 libdbus-1-3_1.14.6-1ubuntu1 libde265-0_1.0.12-1 libdebconfclient0_0.267ubuntu1 libdebhelper-perl_13.11.4ubuntu3 libdeflate0_1.15-1 libdevmapper1.02.1_2:1.02.185-2ubuntu1 libdpkg-perl_1.21.22ubuntu1 libdw1_0.188-2.1 libelf1_0.188-2.1 libexpat1_2.5.0-2 libexpat1-dev_2.5.0-2 libext2fs2_1.47.0-1ubuntu1 libfakeroot_1.31-1.2 libfdisk1_2.38.1-5ubuntu2 libffi8_3.4.4-1 libfftw3-double3_3.3.10-1ubuntu1 libfile-stripnondeterminism-perl_1.13.1-1 libfontbox-java_1:1.8.16-2 libfontconfig1_2.14.1-4ubuntu1 libfontenc1_1:1.1.4-1build3 libfreetype6_2.12.1+dfsg-5 libfribidi0_1.0.13-3 libgcc-12-dev_12.3.0-3ubuntu1 libgcc-s1_13.1.0-6ubuntu1 libgcrypt20_1.10.1-3ubuntu1 libgd3_2.3.3-9ubuntu1 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgfortran5_13.1.0-6ubuntu1 libglib2.0-0_2.76.3-1ubuntu1 libgmp10_2:6.2.1+dfsg1-1.1ubuntu1 libgnutls30_3.7.9-2ubuntu1 libgomp1_13.1.0-6ubuntu1 libgpg-error0_1.46-1 libgraphite2-3_1.3.14-1build2 libgs-common_10.0.0~dfsg1-0ubuntu1.1 libgs10_10.0.0~dfsg1-0ubuntu1.1 libgs10-common_10.0.0~dfsg1-0ubuntu1.1 libgssapi-krb5-2_1.20.1-2 libharfbuzz0b_6.0.0+dfsg-3build1 libheif1_1.15.1-1 libhogweed6_3.8.1-2 libhpdf-2.3.0_2.3.0+dfsg-1build1 libhts3_1.17+ds-1 libhtscodecs2_1.5.0-1 libice6_2:1.0.10-1build2 libicu72_72.1-3ubuntu2 libidn12_1.41-1 libidn2-0_2.3.3-1build1 libijs-0.35_0.35-15.1 libimagequant0_2.17.0-1 libip4tc2_1.8.7-1ubuntu7 libisl23_0.26-3 libjansson4_2.14-2 libjbig0_2.1-6.1ubuntu1 libjbig2dec0_0.19-3build2 libjpeg-turbo8_2.1.5-2ubuntu1 libjpeg8_8c-2ubuntu11 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-jquery-ui_1.13.2+dfsg-1 libjs-sphinxdoc_5.3.0-4 libjs-underscore_1.13.4~dfsg+~1.11.4-3 libjson-c5_0.16-2 libk5crypto3_1.20.1-2 libkeyutils1_1.6.3-2 libkmod2_30+20221128-1ubuntu1 libkpathsea6_2022.20220321.62855-5.1 libkrb5-3_1.20.1-2 libkrb5support0_1.20.1-2 liblapack3_3.11.0-2 liblbfgsb0_3.0+dfsg.4-1 liblcms2-2_2.14-2 libldap2_2.6.3+dfsg-1~exp1ubuntu2 liblerc4_4.0.0+ds-2ubuntu2 liblmdb0_0.9.24-1build2 liblockfile-bin_1.17-1build2 liblockfile1_1.17-1build2 liblqr-1-0_0.4.2-2.1 libltdl7_2.4.7-5 liblz4-1_1.9.4-1 liblzma5_5.4.1-0.2 libmagic-mgc_1:5.44-3 libmagic1_1:5.44-3 libmagickcore-6.q16-6_8:6.9.11.60+dfsg-1.6 libmagickwand-6.q16-6_8:6.9.11.60+dfsg-1.6 libmbedcrypto7_2.28.3-1 libmbedtls14_2.28.3-1 libmbedx509-1_2.28.3-1 libmd0_1.1.0-1 libmount1_2.38.1-5ubuntu2 libmpc3_1.3.1-1 libmpfr6_4.2.0-1 libmysqlclient21_8.0.33-2 libncurses6_6.4-4 libncursesw6_6.4-4 libnetpbm11_2:11.01.00-2build1 libnettle8_3.8.1-2 libnghttp2-14_1.54.0-1 libnpth0_1.6-3build2 libnsl-dev_1.3.0-2build2 libnsl2_1.3.0-2build2 libopenblas-dev_0.3.23+ds-2 libopenblas-pthread-dev_0.3.23+ds-2 libopenblas0_0.3.23+ds-2 libopenblas0-pthread_0.3.23+ds-2 libopenjp2-7_2.5.0-2 libp11-kit0_0.24.1-2ubuntu1 libpam-modules_1.5.2-6ubuntu1 libpam-modules-bin_1.5.2-6ubuntu1 libpam-runtime_1.5.2-6ubuntu1 libpam0g_1.5.2-6ubuntu1 libpaper-utils_1.1.29 libpaper1_1.1.29 libpcre2-8-0_10.42-1 libpcre3_2:8.39-15 libpdfbox-java_1:1.8.16-2 libperl5.36_5.36.0-7ubuntu1 libpipeline1_1.5.7-1 libpixman-1-0_0.42.2-1 libpng16-16_1.6.40-1 libpq5_15.3-1 libproc2-0_2:4.0.3-1ubuntu1 libprocps8_2:3.3.17-7ubuntu1 libpsl5_0.21.2-1 libptexenc1_2022.20220321.62855-5.1 libpython3-all-dev_3.11.4-1 libpython3-dev_3.11.4-1 libpython3-stdlib_3.11.4-1 libpython3.11_3.11.4-1 libpython3.11-dev_3.11.4-1 libpython3.11-minimal_3.11.4-1 libpython3.11-stdlib_3.11.4-1 libqhull-r8.0_2020.2-5 libraqm0_0.10.1-1 libreadline8_8.2-1.3 librtmp1_2.4+20151223.gitfa8646d.1-2build4 libsasl2-2_2.1.28+dfsg1-1 libsasl2-modules-db_2.1.28+dfsg1-1 libseccomp2_2.5.4-1ubuntu3 libselinux1_3.4-1build4 libsemanage-common_3.4-1build4 libsemanage2_3.4-1build4 libsepol2_3.4-2.1 libsm6_2:1.2.3-1build2 libsmartcols1_2.38.1-5ubuntu2 libsqlite3-0_3.42.0-1 libss2_1.47.0-1ubuntu1 libssh-4_0.10.5-2 libssl3_3.0.9-1ubuntu1 libstdc++-12-dev_12.3.0-3ubuntu1 libstdc++6_13.1.0-6ubuntu1 libsub-override-perl_0.09-4 libsynctex2_2022.20220321.62855-5.1 libsystemd-shared_252.5-2ubuntu3 libsystemd0_252.5-2ubuntu3 libtasn1-6_4.19.0-2 libtcl8.6_8.6.13+dfsg-2 libteckit0_2.5.11+ds1-1 libtexlua53-5_2022.20220321.62855-5.1 libtiff6_4.5.0-6ubuntu1 libtinfo6_6.4-4 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtk8.6_8.6.13-2 libtool_2.4.7-5 libuchardet0_0.0.7-1build2 libudev1_252.5-2ubuntu3 libunistring2_1.0-2 libuuid1_2.38.1-5ubuntu2 libwebp7_1.2.4-0.2 libwebpdemux2_1.2.4-0.2 libwebpmux3_1.2.4-0.2 libx11-6_2:1.8.6-1 libx11-data_2:1.8.6-1 libx265-199_3.5-2 libxau6_1:1.0.9-1build5 libxaw7_2:1.0.14-1 libxcb-render0_1.15-1 libxcb-shm0_1.15-1 libxcb1_1.15-1 libxdmcp6_1:1.1.3-0ubuntu5 libxext6_2:1.3.4-1build1 libxft2_2.3.6-1 libxi6_2:1.8-1build1 libxml2_2.9.14+dfsg-1.2 libxmu6_2:1.1.3-3 libxpm4_1:3.5.12-1.1 libxrender1_1:0.9.10-1.1 libxsimd-dev_8.1.0-7 libxslt1.1_1.1.35-1 libxss1_1:1.2.3-1build2 libxt6_1:1.2.1-1.1 libxxhash0_0.8.1-1 libzstd1_1.5.5+dfsg2-1 libzzip-0-13_0.13.72+dfsg.1-1.1 linux-libc-dev_6.3.0-7.7 lockfile-progs_0.1.19build1 login_1:4.13+dfsg1-1ubuntu1 logsave_1.47.0-1ubuntu1 lsb-base_11.6 lto-disabled-list_41 m4_1.4.19-3 mafft_7.505-1 mailcap_3.70+nmu1ubuntu1 make_4.3-4.1build1 man-db_2.11.2-2 mawk_1.3.4.20230525-1 media-types_10.0.0 mime-support_3.66 mount_2.38.1-5ubuntu2 mysql-common_5.8+1.1.0 ncbi-blast+_2.12.0+ds-3build1 ncbi-data_6.1.20170106+dfsg1-10 ncurses-base_6.4-4 ncurses-bin_6.4-4 netpbm_2:11.01.00-2build1 openssl_3.0.9-1ubuntu1 optipng_0.7.7-2build1 passwd_1:4.13+dfsg1-1ubuntu1 patch_2.7.6-7build2 perl_5.36.0-7ubuntu1 perl-base_5.36.0-7ubuntu1 perl-modules-5.36_5.36.0-7ubuntu1 phylip_1:3.697+dfsg-2 pinentry-curses_1.2.1-1ubuntu1 pkgbinarymangler_153 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 poppler-data_0.4.12-1 prank_0.0.170427+dfsg-3 preview-latex-style_12.2-1ubuntu1 probcons_1.12-14 procps_2:4.0.3-1ubuntu1 python-matplotlib-data_3.6.3-1ubuntu2 python3_3.11.4-1 python3-all_3.11.4-1 python3-all-dev_3.11.4-1 python3-appdirs_1.4.4-3 python3-attr_23.1.0-1 python3-beniget_0.4.1-3 python3-brotli_1.0.9-2build8 python3-contourpy_1.0.7-1build1 python3-cycler_0.11.0-1 python3-dateutil_2.8.2-2 python3-decorator_5.1.1-3 python3-dev_3.11.4-1 python3-distutils_3.11.4-1 python3-fonttools_4.38.0-1build1 python3-fs_2.4.16-2 python3-gast_0.5.2-2 python3-isodate_0.6.1-1 python3-kiwisolver_1.4.4-1build1 python3-lib2to3_3.11.4-1 python3-lxml_4.9.2-1build1 python3-lz4_4.0.2+dfsg-1build1 python3-matplotlib_3.6.3-1ubuntu2 python3-minimal_3.11.4-1 python3-mmtf_1.1.3-1 python3-mpmath_1.2.1-2 python3-msgpack_1.0.3-2build1 python3-mysqldb_1.4.6-2build1 python3-networkx_2.8.8-1ubuntu1 python3-numpy_1:1.24.2-1 python3-packaging_23.1-1 python3-pil_9.5.0-1 python3-pil.imagetk_9.5.0-1 python3-pkg-resources_67.8.0-1 python3-ply_3.11-5 python3-psycopg2_2.9.5-1build1 python3-pygments_2.15.1+dfsg-1 python3-pyparsing_3.0.9-1 python3-pythran_0.11.0+ds-7 python3-rdflib_6.1.1-1 python3-reportlab_4.0.4-1 python3-scipy_1.10.1-2 python3-setuptools_67.8.0-1 python3-six_1.16.0-4 python3-sympy_1.12-2 python3-tk_3.11.4-1 python3-tz_2023.3-3 python3-ufolib2_0.14.0+dfsg1-1 python3-unittest2_1.1.0-9 python3.11_3.11.4-1 python3.11-dev_3.11.4-1 python3.11-minimal_3.11.4-1 readline-common_8.2-1.3 rpcsvc-proto_1.4.2-0ubuntu6 samtools_1.17-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.20 systemd_252.5-2ubuntu3 systemd-sysv_252.5-2ubuntu3 sysvinit-utils_3.06-4ubuntu1 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 t1utils_1.41-4build2 tar_1.34+dfsg-1.2ubuntu1 tex-common_6.18 texlive-base_2022.20230122-3 texlive-binaries_2022.20220321.62855-5.1 texlive-fonts-recommended_2022.20230122-3 texlive-latex-base_2022.20230122-3 texlive-latex-extra_2022.20230122-4 texlive-latex-recommended_2022.20230122-3 texlive-pictures_2022.20230122-3 tk8.6-blt2.5_2.5.3+dfsg-4.1build2 tzdata_2023c-4exp1ubuntu1 ubuntu-keyring_2021.03.26 ucf_3.0043+nmu1 unicode-data_15.0.0-1 usrmerge_35ubuntu1 util-linux_2.38.1-5ubuntu2 util-linux-extra_2.38.1-5ubuntu2 wise_2.4.1-23 wise-data_2.4.1-23 x11-common_1:7.7+23ubuntu2 xdg-utils_1.1.3-4.1ubuntu3 xfonts-encodings_1:1.0.5-0ubuntu2 xfonts-utils_1:7.7+6build2 xz-utils_5.4.1-0.2 zlib1g_1:1.2.13.dfsg-1ubuntu4 zlib1g-dev_1:1.2.13.dfsg-1ubuntu4 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: python-biopython Binary: python3-biopython, python-biopython-doc, python3-biopython-sql Architecture: any all Version: 1.80+dfsg-4ubuntu1 Maintainer: Ubuntu Developers Uploaders: Charles Plessy , Andreas Tille , Étienne Mollier Homepage: https://biopython.org Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/python-biopython Vcs-Git: https://salsa.debian.org/med-team/python-biopython.git Testsuite: autopkgtest Testsuite-Triggers: @builddeps@, python3-all, python3-setuptools Build-Depends: debhelper-compat (= 13), dh-python, python3-all-dev, python3-numpy , flex, python3-reportlab , hevea , texlive-latex-base, texlive-latex-extra, texlive-fonts-recommended, bwa , clustalo , clustalw , dialign , dssp , emboss , fasttree , mafft , muscle3 [i386 amd64 x32] , ncbi-blast+ , phylip , phyml [any-amd64 any-i386] , prank , probcons , python3-networkx , python3-mysqldb , python3-matplotlib , python3-mmtf , python3-pil , python3-rdflib , python3-psycopg2 , python3-pygments , python3-scipy , python3-setuptools, python3-unittest2 , raxml [any-amd64 any-i386] , samtools , t-coffee , wise Package-List: python-biopython-doc deb doc optional arch=all python3-biopython deb python optional arch=any python3-biopython-sql deb python optional arch=all Checksums-Sha1: c6351b33b1c214687eb27908202c47e9bb607c03 10665048 python-biopython_1.80+dfsg.orig.tar.xz 9b850399bfe353bf1ae1fe42cfdeb7f33ba16bbe 20968 python-biopython_1.80+dfsg-4ubuntu1.debian.tar.xz Checksums-Sha256: 33f55619b952b7ae13539ba898aa4d24a2326b649ad581f185f6f706426fdd02 10665048 python-biopython_1.80+dfsg.orig.tar.xz b5a251ae461e8c658b4cb25241edc7829d5f00db778c494d0e437c3e13cf5615 20968 python-biopython_1.80+dfsg-4ubuntu1.debian.tar.xz Files: 0016b019c8961b2ce17e245a3b44ee9a 10665048 python-biopython_1.80+dfsg.orig.tar.xz ffaa80fcb5311b4669b25f286e6fa2e0 20968 python-biopython_1.80+dfsg-4ubuntu1.debian.tar.xz Original-Maintainer: Debian Med Packaging Team -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEE496GmCL5m2y8NfJ5v322IrMDrIsFAmSaqYYACgkQv322IrMD rIs/DRAApVpNQE3Nh8qZVu4plip+5TZJRZyqufZ4SN4BwkTZmtr5HK0baVXSRbaL lsgb/AFhrsuuO21zvGuEfLMb6PbmXNQa1REsA7z2Wqe0T/m4xhe5E5kcYjzcao7z dIOCgD52+CITSBoYdCsW4LUnyCX+3VBcJFkb4OIaMUUzXZxKXxPAgC7bDYU5qBrD t3bVyfdjFJN6G7lejotmyKqAkXKWC9tdgTJonZH3KfcdPOCz5VJMTC0gUuzsnmxs UFsZyajxmhtCjqlp6xIOgO7BBkMTJLpFR15NNHQBR8TL4AukxALBonzW6BEs3XQ2 wt1QiReOvAoVGgZDYl3MRpvF3FZ6RZ7MwYit1Z8t8MX/9WHhGh5AoOGSJNGnWcD8 shYjuaEIVWavWuy9v6HD9INAnO00KkyWlq6CpXpHtEilc8lLTcrC7ltKoNs4bKfA SC6G3lqQzV1lbprx/mJeBNurjwxGSsDnHw/RnrCJ7f9NKV8jeVD3hTu7TSGRImAv zsZ7Au0tBQCTYrD3mR834lYqrs5vVkuLNcLOPjXZ4ZXubkvdyBLA8ln2Lm8Qfnxz 3W+wNeFhIuzfAj5iKW7wMqSni6+ePl98EPVtfc2MPUsNbwE4wTRDc9OlU0jZ6Ir8 op6mqvXfgQBoagD24pMfHaRJ0ZxRGUAOa1AFEassrSjFRUAEYek= =JgUC -----END PGP SIGNATURE----- gpgv: Signature made Tue Jun 27 09:19:02 2023 UTC gpgv: using RSA key E3DE869822F99B6CBC35F279BF7DB622B303AC8B gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./python-biopython_1.80+dfsg-4ubuntu1.dsc: no acceptable signature found dpkg-source: info: extracting python-biopython in /<> dpkg-source: info: unpacking python-biopython_1.80+dfsg.orig.tar.xz dpkg-source: info: unpacking python-biopython_1.80+dfsg-4ubuntu1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying remove_mathml-qname.patch dpkg-source: info: applying privacy_breach.patch dpkg-source: info: applying privacy_breach_ie9.patch dpkg-source: info: applying fix-use-of-unversioned-python.patch dpkg-source: info: applying reproduciblebuild.patch dpkg-source: info: applying croak-on-muscle5.patch dpkg-source: info: applying muscle3.patch dpkg-source: info: applying port_tutorial_to_muscle3.patch dpkg-source: info: applying numpy-1.24.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=8 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-26341718 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-26341718 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-26341718 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -B -rfakeroot dpkg-buildpackage: info: source package python-biopython dpkg-buildpackage: info: source version 1.80+dfsg-4ubuntu1 dpkg-buildpackage: info: source distribution mantic dpkg-source --before-build . dpkg-buildpackage: info: host architecture riscv64 debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean pybuild --clean -i python{version} -p 3.11 I: pybuild base:275: python3.11 setup.py clean running clean removing '/<>/.pybuild/cpython3_3.11/build' (and everything under it) 'build/bdist.linux-riscv64' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it rm -rf .pybuild/ find . -name \*.pyc -exec rm {} \; cd Doc && make distclean make[2]: Entering directory '/<>/Doc' ( for f in ; do make clean -C $f ; done ) rm -f Tutorial.aux rm -f Tutorial.toc rm -f Tutorial.log rm -f Tutorial.out rm -f Tutorial.haux rm -f Tutorial.htoc rm -f biopdb_faq.aux rm -f biopdb_faq.log rm -f biopdb_faq.out rm -f Tutorial/*.aux ( for f in ; do make distclean -C $f ; done ) rm -f version.sh rm -f biopdb_faq.pdf rm -f Tutorial.pdf rm -f Tutorial.html rm -f Tutorial.txt rm -f *_motif.gif #output from hacha make[2]: Leaving directory '/<>/Doc' rm -f Doc/install/Installation.pdf rm -f Doc/install/Installation.txt rm -f Doc/install/Installation.html rm -f Doc/Tutorial.pdf Doc/biopdb_faq.pdf rm -f Doc/Tutorial/*.aux find Doc -name "*.pygtex" -o -name "*.pygstyle" -delete rm -rf biopython.egg-info rm -rf .pybuild if [ -d Tests_avoid ] ; then \ mv Tests_avoid/* Tests ; \ rmdir Tests_avoid ; \ fi rm -rf debian/tmp_tests make[1]: Leaving directory '/<>' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/python3-biopython.substvars debian/python-biopython-doc.substvars debian/python3-biopython-sql.substvars debian/files rm -fr -- debian/python3-biopython/ debian/tmp/ debian/python-biopython-doc/ debian/python3-biopython-sql/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules binary-arch dh binary-arch --with python3 --buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_autoreconf -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild pybuild --configure -i python{version} -p 3.11 I: pybuild base:275: python3.11 setup.py config running config debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build pybuild --build -i python{version} -p 3.11 I: pybuild base:275: /usr/bin/python3 setup.py build running build running build_py creating /<>/.pybuild/cpython3_3.11/build/Bio copying Bio/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio copying Bio/File.py -> /<>/.pybuild/cpython3_3.11/build/Bio copying Bio/kNN.py -> /<>/.pybuild/cpython3_3.11/build/Bio copying Bio/MaxEntropy.py -> /<>/.pybuild/cpython3_3.11/build/Bio copying Bio/SeqFeature.py -> /<>/.pybuild/cpython3_3.11/build/Bio copying Bio/pairwise2.py -> /<>/.pybuild/cpython3_3.11/build/Bio copying Bio/bgzf.py -> /<>/.pybuild/cpython3_3.11/build/Bio copying Bio/Seq.py -> /<>/.pybuild/cpython3_3.11/build/Bio copying Bio/_utils.py -> /<>/.pybuild/cpython3_3.11/build/Bio copying Bio/MarkovModel.py -> /<>/.pybuild/cpython3_3.11/build/Bio copying Bio/NaiveBayes.py -> /<>/.pybuild/cpython3_3.11/build/Bio copying Bio/LogisticRegression.py -> /<>/.pybuild/cpython3_3.11/build/Bio copying Bio/SeqRecord.py -> /<>/.pybuild/cpython3_3.11/build/Bio creating /<>/.pybuild/cpython3_3.11/build/Bio/Affy copying Bio/Affy/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Affy copying Bio/Affy/CelFile.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Affy creating /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/msf.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/hhr.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/mauve.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/stockholm.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/phylip.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/tabular.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/emboss.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/AlignInfo.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/interfaces.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/nexus.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/exonerate.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/bigpsl.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/maf.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/bed.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/a2m.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/bigbed.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/clustal.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/bigmaf.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/sam.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/fasta.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/psl.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align creating /<>/.pybuild/cpython3_3.11/build/Bio/Align/Applications copying Bio/Align/Applications/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/Applications copying Bio/Align/Applications/_Dialign.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/Applications copying Bio/Align/Applications/_ClustalOmega.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/Applications copying Bio/Align/Applications/_Prank.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/Applications copying Bio/Align/Applications/_Mafft.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/Applications copying Bio/Align/Applications/_TCoffee.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/Applications copying Bio/Align/Applications/_MSAProbs.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/Applications copying Bio/Align/Applications/_Probcons.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/Applications copying Bio/Align/Applications/_Muscle.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/Applications copying Bio/Align/Applications/_Clustalw.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/Applications creating /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices copying Bio/Align/substitution_matrices/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices creating /<>/.pybuild/cpython3_3.11/build/Bio/AlignIO copying Bio/AlignIO/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/AlignIO copying Bio/AlignIO/Interfaces.py -> /<>/.pybuild/cpython3_3.11/build/Bio/AlignIO copying Bio/AlignIO/EmbossIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/AlignIO copying Bio/AlignIO/NexusIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/AlignIO copying Bio/AlignIO/PhylipIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/AlignIO copying Bio/AlignIO/FastaIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/AlignIO copying Bio/AlignIO/ClustalIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/AlignIO copying Bio/AlignIO/StockholmIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/AlignIO copying Bio/AlignIO/MafIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/AlignIO copying Bio/AlignIO/MsfIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/AlignIO copying Bio/AlignIO/MauveIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/AlignIO creating /<>/.pybuild/cpython3_3.11/build/Bio/Alphabet copying Bio/Alphabet/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Alphabet creating /<>/.pybuild/cpython3_3.11/build/Bio/Application copying Bio/Application/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Application creating /<>/.pybuild/cpython3_3.11/build/Bio/Blast copying Bio/Blast/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Blast copying Bio/Blast/NCBIXML.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Blast copying Bio/Blast/ParseBlastTable.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Blast copying Bio/Blast/Applications.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Blast copying Bio/Blast/Record.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Blast copying Bio/Blast/NCBIWWW.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Blast creating /<>/.pybuild/cpython3_3.11/build/Bio/CAPS copying Bio/CAPS/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/CAPS creating /<>/.pybuild/cpython3_3.11/build/Bio/Cluster copying Bio/Cluster/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Cluster creating /<>/.pybuild/cpython3_3.11/build/Bio/codonalign copying Bio/codonalign/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/codonalign copying Bio/codonalign/codonseq.py -> /<>/.pybuild/cpython3_3.11/build/Bio/codonalign copying Bio/codonalign/codonalignment.py -> /<>/.pybuild/cpython3_3.11/build/Bio/codonalign creating /<>/.pybuild/cpython3_3.11/build/Bio/Compass copying Bio/Compass/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Compass creating /<>/.pybuild/cpython3_3.11/build/Bio/Data copying Bio/Data/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Data copying Bio/Data/SCOPData.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Data copying Bio/Data/IUPACData.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Data copying Bio/Data/PDBData.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Data copying Bio/Data/CodonTable.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Data creating /<>/.pybuild/cpython3_3.11/build/Bio/Emboss copying Bio/Emboss/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Emboss copying Bio/Emboss/PrimerSearch.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Emboss copying Bio/Emboss/Primer3.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Emboss copying Bio/Emboss/Applications.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Emboss creating /<>/.pybuild/cpython3_3.11/build/Bio/Entrez copying Bio/Entrez/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez copying Bio/Entrez/Parser.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez creating /<>/.pybuild/cpython3_3.11/build/Bio/ExPASy copying Bio/ExPASy/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/ExPASy copying Bio/ExPASy/Prosite.py -> /<>/.pybuild/cpython3_3.11/build/Bio/ExPASy copying Bio/ExPASy/ScanProsite.py -> /<>/.pybuild/cpython3_3.11/build/Bio/ExPASy copying Bio/ExPASy/Enzyme.py -> /<>/.pybuild/cpython3_3.11/build/Bio/ExPASy copying Bio/ExPASy/cellosaurus.py -> /<>/.pybuild/cpython3_3.11/build/Bio/ExPASy copying Bio/ExPASy/Prodoc.py -> /<>/.pybuild/cpython3_3.11/build/Bio/ExPASy creating /<>/.pybuild/cpython3_3.11/build/Bio/GenBank copying Bio/GenBank/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/GenBank copying Bio/GenBank/Scanner.py -> /<>/.pybuild/cpython3_3.11/build/Bio/GenBank copying Bio/GenBank/utils.py -> /<>/.pybuild/cpython3_3.11/build/Bio/GenBank copying Bio/GenBank/Record.py -> /<>/.pybuild/cpython3_3.11/build/Bio/GenBank creating /<>/.pybuild/cpython3_3.11/build/Bio/Geo copying Bio/Geo/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Geo copying Bio/Geo/Record.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Geo creating /<>/.pybuild/cpython3_3.11/build/Bio/Graphics copying Bio/Graphics/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics copying Bio/Graphics/DisplayRepresentation.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics copying Bio/Graphics/KGML_vis.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics copying Bio/Graphics/Comparative.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics copying Bio/Graphics/ColorSpiral.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics copying Bio/Graphics/BasicChromosome.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics copying Bio/Graphics/Distribution.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics creating /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Track.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Feature.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Diagram.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CrossLink.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_GraphSet.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Colors.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Graph.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram creating /<>/.pybuild/cpython3_3.11/build/Bio/HMM copying Bio/HMM/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/HMM copying Bio/HMM/MarkovModel.py -> /<>/.pybuild/cpython3_3.11/build/Bio/HMM copying Bio/HMM/Trainer.py -> /<>/.pybuild/cpython3_3.11/build/Bio/HMM copying Bio/HMM/Utilities.py -> /<>/.pybuild/cpython3_3.11/build/Bio/HMM copying Bio/HMM/DynamicProgramming.py -> /<>/.pybuild/cpython3_3.11/build/Bio/HMM creating /<>/.pybuild/cpython3_3.11/build/Bio/KEGG copying Bio/KEGG/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/KEGG copying Bio/KEGG/REST.py -> /<>/.pybuild/cpython3_3.11/build/Bio/KEGG creating /<>/.pybuild/cpython3_3.11/build/Bio/KEGG/Compound copying Bio/KEGG/Compound/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/KEGG/Compound creating /<>/.pybuild/cpython3_3.11/build/Bio/KEGG/Enzyme copying Bio/KEGG/Enzyme/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/KEGG/Enzyme creating /<>/.pybuild/cpython3_3.11/build/Bio/KEGG/Gene copying Bio/KEGG/Gene/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/KEGG/Gene creating /<>/.pybuild/cpython3_3.11/build/Bio/KEGG/Map copying Bio/KEGG/Map/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/KEGG/Map creating /<>/.pybuild/cpython3_3.11/build/Bio/PDB creating /<>/.pybuild/cpython3_3.11/build/Bio/PDB/mmtf copying Bio/PDB/mmtf/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB/mmtf copying Bio/PDB/mmtf/mmtfio.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB/mmtf copying Bio/PDB/mmtf/DefaultParser.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB/mmtf creating /<>/.pybuild/cpython3_3.11/build/Bio/KEGG/KGML copying Bio/KEGG/KGML/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_pathway.py -> /<>/.pybuild/cpython3_3.11/build/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_parser.py -> /<>/.pybuild/cpython3_3.11/build/Bio/KEGG/KGML creating /<>/.pybuild/cpython3_3.11/build/Bio/Medline copying Bio/Medline/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Medline creating /<>/.pybuild/cpython3_3.11/build/Bio/motifs copying Bio/motifs/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/motifs copying Bio/motifs/transfac.py -> /<>/.pybuild/cpython3_3.11/build/Bio/motifs copying Bio/motifs/xms.py -> /<>/.pybuild/cpython3_3.11/build/Bio/motifs copying Bio/motifs/thresholds.py -> /<>/.pybuild/cpython3_3.11/build/Bio/motifs copying Bio/motifs/matrix.py -> /<>/.pybuild/cpython3_3.11/build/Bio/motifs copying Bio/motifs/mast.py -> /<>/.pybuild/cpython3_3.11/build/Bio/motifs copying Bio/motifs/clusterbuster.py -> /<>/.pybuild/cpython3_3.11/build/Bio/motifs copying Bio/motifs/meme.py -> /<>/.pybuild/cpython3_3.11/build/Bio/motifs copying Bio/motifs/pfm.py -> /<>/.pybuild/cpython3_3.11/build/Bio/motifs copying Bio/motifs/alignace.py -> /<>/.pybuild/cpython3_3.11/build/Bio/motifs copying Bio/motifs/minimal.py -> /<>/.pybuild/cpython3_3.11/build/Bio/motifs creating /<>/.pybuild/cpython3_3.11/build/Bio/motifs/applications copying Bio/motifs/applications/_xxmotif.py -> /<>/.pybuild/cpython3_3.11/build/Bio/motifs/applications copying Bio/motifs/applications/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/motifs/applications creating /<>/.pybuild/cpython3_3.11/build/Bio/motifs/jaspar copying Bio/motifs/jaspar/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/motifs/jaspar copying Bio/motifs/jaspar/db.py -> /<>/.pybuild/cpython3_3.11/build/Bio/motifs/jaspar creating /<>/.pybuild/cpython3_3.11/build/Bio/Nexus copying Bio/Nexus/StandardData.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Nexus copying Bio/Nexus/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Nexus copying Bio/Nexus/Nodes.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Nexus copying Bio/Nexus/Trees.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Nexus copying Bio/Nexus/Nexus.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Nexus creating /<>/.pybuild/cpython3_3.11/build/Bio/NMR copying Bio/NMR/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/NMR copying Bio/NMR/xpktools.py -> /<>/.pybuild/cpython3_3.11/build/Bio/NMR copying Bio/NMR/NOEtools.py -> /<>/.pybuild/cpython3_3.11/build/Bio/NMR creating /<>/.pybuild/cpython3_3.11/build/Bio/Pathway copying Bio/Pathway/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Pathway creating /<>/.pybuild/cpython3_3.11/build/Bio/Pathway/Rep copying Bio/Pathway/Rep/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Pathway/Rep copying Bio/Pathway/Rep/MultiGraph.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Pathway/Rep copying Bio/Pathway/Rep/Graph.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Pathway/Rep copying Bio/PDB/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/Polypeptide.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/PDBExceptions.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/Model.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/Selection.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/Atom.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/MMCIF2Dict.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/mmcifio.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/SASA.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/FragmentMapper.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/Dice.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/Superimposer.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/SCADIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/PDBParser.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/NACCESS.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/MMCIFParser.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/StructureAlignment.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/Entity.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/Residue.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/ic_rebuild.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/Chain.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/AbstractPropertyMap.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/qcprot.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/internal_coords.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/HSExposure.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/Structure.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/PICIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/parse_pdb_header.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/StructureBuilder.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/cealign.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/NeighborSearch.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/PDBList.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/PDBIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/DSSP.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/PSEA.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/ResidueDepth.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/ic_data.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/vectors.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB creating /<>/.pybuild/cpython3_3.11/build/Bio/phenotype copying Bio/phenotype/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/phenotype copying Bio/phenotype/phen_micro.py -> /<>/.pybuild/cpython3_3.11/build/Bio/phenotype copying Bio/phenotype/pm_fitting.py -> /<>/.pybuild/cpython3_3.11/build/Bio/phenotype creating /<>/.pybuild/cpython3_3.11/build/Bio/PopGen copying Bio/PopGen/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PopGen creating /<>/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/EasyController.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/FileParser.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/Controller.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/LargeFileParser.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop creating /<>/.pybuild/cpython3_3.11/build/Bio/Restriction copying Bio/Restriction/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Restriction copying Bio/Restriction/Restriction_Dictionary.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Restriction copying Bio/Restriction/PrintFormat.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Restriction copying Bio/Restriction/Restriction.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Restriction creating /<>/.pybuild/cpython3_3.11/build/Bio/SCOP copying Bio/SCOP/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SCOP copying Bio/SCOP/Cla.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SCOP copying Bio/SCOP/Des.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SCOP copying Bio/SCOP/Residues.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SCOP copying Bio/SCOP/Raf.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SCOP copying Bio/SCOP/Hie.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SCOP copying Bio/SCOP/Dom.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SCOP creating /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO copying Bio/SearchIO/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO copying Bio/SearchIO/_index.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO copying Bio/SearchIO/BlatIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO copying Bio/SearchIO/FastaIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO copying Bio/SearchIO/_utils.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO creating /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_legacy copying Bio/SearchIO/_legacy/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_legacy copying Bio/SearchIO/_legacy/ParserSupport.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_legacy copying Bio/SearchIO/_legacy/NCBIStandalone.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_legacy creating /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/query.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/_base.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/hit.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/hsp.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model creating /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_xml.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_tab.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_text.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/BlastIO creating /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HHsuiteIO copying Bio/SearchIO/HHsuiteIO/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HHsuiteIO copying Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HHsuiteIO creating /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/_base.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_tab.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_text.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO creating /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/_base.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_text.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO creating /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/interproscan_xml.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/InterproscanIO creating /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/GckIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/PdbIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/Interfaces.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/PhdIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/SnapGeneIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/NibIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/_index.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/XdnaIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/QualityIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/PirIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/TabIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/SeqXmlIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/FastaIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/UniprotIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/InsdcIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/IgIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/SwissIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/SffIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/AceIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/TwoBitIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/AbiIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO creating /<>/.pybuild/cpython3_3.11/build/Bio/SeqUtils copying Bio/SeqUtils/CheckSum.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqUtils copying Bio/SeqUtils/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqUtils copying Bio/SeqUtils/MeltingTemp.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqUtils copying Bio/SeqUtils/IsoelectricPoint.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqUtils copying Bio/SeqUtils/ProtParam.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqUtils copying Bio/SeqUtils/CodonUsage.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqUtils copying Bio/SeqUtils/lcc.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqUtils copying Bio/SeqUtils/CodonUsageIndices.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqUtils copying Bio/SeqUtils/ProtParamData.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqUtils creating /<>/.pybuild/cpython3_3.11/build/Bio/Sequencing copying Bio/Sequencing/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Sequencing copying Bio/Sequencing/Ace.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Sequencing copying Bio/Sequencing/Phd.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Sequencing creating /<>/.pybuild/cpython3_3.11/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_Novoalign.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_bwa.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_samtools.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Sequencing/Applications creating /<>/.pybuild/cpython3_3.11/build/Bio/SVDSuperimposer copying Bio/SVDSuperimposer/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SVDSuperimposer creating /<>/.pybuild/cpython3_3.11/build/Bio/PDB/QCPSuperimposer copying Bio/PDB/QCPSuperimposer/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB/QCPSuperimposer creating /<>/.pybuild/cpython3_3.11/build/Bio/SwissProt copying Bio/SwissProt/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SwissProt copying Bio/SwissProt/KeyWList.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SwissProt creating /<>/.pybuild/cpython3_3.11/build/Bio/TogoWS copying Bio/TogoWS/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/TogoWS creating /<>/.pybuild/cpython3_3.11/build/Bio/Phylo copying Bio/Phylo/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo copying Bio/Phylo/NeXML.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo copying Bio/Phylo/BaseTree.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo copying Bio/Phylo/_cdao_owl.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo copying Bio/Phylo/Consensus.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo copying Bio/Phylo/NexusIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo copying Bio/Phylo/TreeConstruction.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo copying Bio/Phylo/PhyloXMLIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo copying Bio/Phylo/_utils.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo copying Bio/Phylo/_io.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo copying Bio/Phylo/Newick.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo copying Bio/Phylo/CDAOIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo copying Bio/Phylo/NewickIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo copying Bio/Phylo/PhyloXML.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo copying Bio/Phylo/CDAO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo copying Bio/Phylo/NeXMLIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo creating /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Phyml.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Fasttree.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Raxml.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/Applications creating /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_yn00.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/codeml.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_paml.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_baseml.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/chi2.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_codeml.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/yn00.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/baseml.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML creating /<>/.pybuild/cpython3_3.11/build/Bio/UniGene copying Bio/UniGene/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/UniGene creating /<>/.pybuild/cpython3_3.11/build/Bio/UniProt copying Bio/UniProt/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/UniProt copying Bio/UniProt/GOA.py -> /<>/.pybuild/cpython3_3.11/build/Bio/UniProt creating /<>/.pybuild/cpython3_3.11/build/Bio/Wise copying Bio/Wise/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Wise copying Bio/Wise/dnal.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Wise copying Bio/Wise/psw.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Wise creating /<>/.pybuild/cpython3_3.11/build/BioSQL copying BioSQL/__init__.py -> /<>/.pybuild/cpython3_3.11/build/BioSQL copying BioSQL/BioSeq.py -> /<>/.pybuild/cpython3_3.11/build/BioSQL copying BioSQL/DBUtils.py -> /<>/.pybuild/cpython3_3.11/build/BioSQL copying BioSQL/BioSeqDatabase.py -> /<>/.pybuild/cpython3_3.11/build/BioSQL copying BioSQL/Loader.py -> /<>/.pybuild/cpython3_3.11/build/BioSQL running egg_info creating biopython.egg-info writing biopython.egg-info/PKG-INFO writing dependency_links to biopython.egg-info/dependency_links.txt writing requirements to biopython.egg-info/requires.txt writing top-level names to biopython.egg-info/top_level.txt writing manifest file 'biopython.egg-info/SOURCES.txt' reading manifest file 'biopython.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.py{}' found anywhere in distribution warning: no previously-included files matching '*.py-e' found anywhere in distribution adding license file 'LICENSE' adding license file 'LICENSE.rst' writing manifest file 'biopython.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:201: _Warning: Package 'Bio.Align.substitution_matrices.data' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'Bio.Align.substitution_matrices.data' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'Bio.Align.substitution_matrices.data' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'Bio.Align.substitution_matrices.data' to be distributed and are already explicitly excluding 'Bio.Align.substitution_matrices.data' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:201: _Warning: Package 'Bio.Entrez.DTDs' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'Bio.Entrez.DTDs' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'Bio.Entrez.DTDs' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'Bio.Entrez.DTDs' to be distributed and are already explicitly excluding 'Bio.Entrez.DTDs' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:201: _Warning: Package 'Bio.Entrez.XSDs' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'Bio.Entrez.XSDs' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'Bio.Entrez.XSDs' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'Bio.Entrez.XSDs' to be distributed and are already explicitly excluding 'Bio.Entrez.XSDs' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying Bio/cpairwise2module.c -> /<>/.pybuild/cpython3_3.11/build/Bio copying Bio/Align/_aligners.c -> /<>/.pybuild/cpython3_3.11/build/Bio/Align creating /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER22 -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER6 -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER74 -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLASTN -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLASTP -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM45 -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM50 -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM62 -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM80 -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM90 -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/DAYHOFF -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/FENG -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/GENETIC -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/GONNET1992 -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/HOXD70 -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/JOHNSON -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/JONES -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/LEVIN -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MCLACHLAN -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MDM78 -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MEGABLAST -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/NUC.4.4 -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM250 -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM30 -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM70 -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/RAO -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/RISLER -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/SCHNEIDER -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/STR -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/TRANS -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Cluster/cluster.c -> /<>/.pybuild/cpython3_3.11/build/Bio/Cluster copying Bio/Cluster/cluster.h -> /<>/.pybuild/cpython3_3.11/build/Bio/Cluster copying Bio/Cluster/clustermodule.c -> /<>/.pybuild/cpython3_3.11/build/Bio/Cluster creating /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/BITS-embedded-index2.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/BITS-question-answer2.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-articlemeta1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-backmatter1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-chars1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-common-atts1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-common1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-default-classes1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-default-mixes1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-display1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-format1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-funding1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-journalmeta1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-link1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-list1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-math1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-modules1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-notat1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-para1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-phrase1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-references1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-related-object1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-section1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-xmlspecchars1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Gene.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_General.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_General.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medlars.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medline.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mim.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mime.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Organism.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Project.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Protein.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Pub.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PubMed.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_RNA.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Remap.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Rsite.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqres.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqset.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Sequence.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Submit.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Systems.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TSeq.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TxInit.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Variation.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_all.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NSE.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NSE.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/OMSSA.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/OMSSA.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PDB_General.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PDB_General.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PIR_General.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PIR_General.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PRF_General.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PRF_General.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/SP_General.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/SP_General.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/XHTMLtablesetup.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivearticle.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-classes.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-mixes.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-models.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-modules.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/articlemeta.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/backmatter.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_100301.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_110101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_120101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_130101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_140101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_150101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/chars.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/common.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/default-classes.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/default-mixes.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/display.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eInfo_020511.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eLink_090910.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eLink_101123.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/ePost_020511.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSearch_020511.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSpell.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSummary_041029.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/egquery.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/einfo.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/elink_020122.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esearch.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esummary-v1.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/format.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/htmltable.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsa.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsb.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsc.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsn.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamso.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsr.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isobox.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isocyr1.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isocyr2.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isodia.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk1.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk2.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk4.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isolat1.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isolat2.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomfrk.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomopf.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomscr.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isonum.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isopub.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isotech.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/journalmeta.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/link.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/list.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/math.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml-in-pubmed.mod -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml2.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml3-qname1.mod -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml3.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathmlsetup.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mmlalias.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mmlextra.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/modules.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_011101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_080101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_090101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_011101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_080101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_090101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_080101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_100101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/notat.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/para.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/phrase.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pmc-1.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_020114.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_080101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_090101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100301.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_110101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_120101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130501.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_140101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_150101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180601.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_190101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/references.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/section.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/taxon.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xhtml-table-1.mod -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xmlspecchars.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs creating /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/XSDs copying Bio/Entrez/XSDs/IPGReportSet.xsd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/XSDs copying Bio/motifs/_pwm.c -> /<>/.pybuild/cpython3_3.11/build/Bio/motifs copying Bio/Nexus/cnexus.c -> /<>/.pybuild/cpython3_3.11/build/Bio/Nexus copying Bio/PDB/ccealignmodule.c -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/kdtrees.c -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/SeqIO/_twoBitIO.c -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/PDB/QCPSuperimposer/qcprotmodule.c -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB/QCPSuperimposer running build_ext building 'Bio.Align._aligners' extension creating build creating build/temp.linux-riscv64-cpython-311 creating build/temp.linux-riscv64-cpython-311/Bio creating build/temp.linux-riscv64-cpython-311/Bio/Align riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.80+dfsg-4ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/Align/_aligners.c -o build/temp.linux-riscv64-cpython-311/Bio/Align/_aligners.o riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.80+dfsg-4ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-cpython-311/Bio/Align/_aligners.o -L/usr/lib/riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.11/build/Bio/Align/_aligners.cpython-311-riscv64-linux-gnu.so building 'Bio.cpairwise2' extension riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.80+dfsg-4ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/cpairwise2module.c -o build/temp.linux-riscv64-cpython-311/Bio/cpairwise2module.o Bio/cpairwise2module.c: In function ‘_get_match_score’: Bio/cpairwise2module.c:60:5: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations] 60 | if(!(py_result = PyEval_CallObject(py_match_fn, py_arglist))) | ^~ In file included from /usr/include/python3.11/Python.h:95, from Bio/cpairwise2module.c:16: /usr/include/python3.11/ceval.h:27:43: note: declared here 27 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.80+dfsg-4ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-cpython-311/Bio/cpairwise2module.o -L/usr/lib/riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.11/build/Bio/cpairwise2.cpython-311-riscv64-linux-gnu.so building 'Bio.Nexus.cnexus' extension creating build/temp.linux-riscv64-cpython-311/Bio/Nexus riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.80+dfsg-4ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/Nexus/cnexus.c -o build/temp.linux-riscv64-cpython-311/Bio/Nexus/cnexus.o riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.80+dfsg-4ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-cpython-311/Bio/Nexus/cnexus.o -L/usr/lib/riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.11/build/Bio/Nexus/cnexus.cpython-311-riscv64-linux-gnu.so building 'Bio.PDB.QCPSuperimposer.qcprotmodule' extension creating build/temp.linux-riscv64-cpython-311/Bio/PDB creating build/temp.linux-riscv64-cpython-311/Bio/PDB/QCPSuperimposer riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.80+dfsg-4ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/PDB/QCPSuperimposer/qcprotmodule.c -o build/temp.linux-riscv64-cpython-311/Bio/PDB/QCPSuperimposer/qcprotmodule.o riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.80+dfsg-4ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-cpython-311/Bio/PDB/QCPSuperimposer/qcprotmodule.o -L/usr/lib/riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.11/build/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-riscv64-linux-gnu.so building 'Bio.motifs._pwm' extension creating build/temp.linux-riscv64-cpython-311/Bio/motifs riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.80+dfsg-4ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/motifs/_pwm.c -o build/temp.linux-riscv64-cpython-311/Bio/motifs/_pwm.o riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.80+dfsg-4ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-cpython-311/Bio/motifs/_pwm.o -L/usr/lib/riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.11/build/Bio/motifs/_pwm.cpython-311-riscv64-linux-gnu.so building 'Bio.Cluster._cluster' extension creating build/temp.linux-riscv64-cpython-311/Bio/Cluster riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.80+dfsg-4ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/Cluster/cluster.c -o build/temp.linux-riscv64-cpython-311/Bio/Cluster/cluster.o riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.80+dfsg-4ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/Cluster/clustermodule.c -o build/temp.linux-riscv64-cpython-311/Bio/Cluster/clustermodule.o riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.80+dfsg-4ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-cpython-311/Bio/Cluster/cluster.o build/temp.linux-riscv64-cpython-311/Bio/Cluster/clustermodule.o -L/usr/lib/riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.11/build/Bio/Cluster/_cluster.cpython-311-riscv64-linux-gnu.so building 'Bio.PDB.kdtrees' extension riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.80+dfsg-4ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/PDB/kdtrees.c -o build/temp.linux-riscv64-cpython-311/Bio/PDB/kdtrees.o riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.80+dfsg-4ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-cpython-311/Bio/PDB/kdtrees.o -L/usr/lib/riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.11/build/Bio/PDB/kdtrees.cpython-311-riscv64-linux-gnu.so building 'Bio.PDB.ccealign' extension riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.80+dfsg-4ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/PDB/ccealignmodule.c -o build/temp.linux-riscv64-cpython-311/Bio/PDB/ccealignmodule.o riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.80+dfsg-4ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-cpython-311/Bio/PDB/ccealignmodule.o -L/usr/lib/riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.11/build/Bio/PDB/ccealign.cpython-311-riscv64-linux-gnu.so building 'Bio.SeqIO._twoBitIO' extension creating build/temp.linux-riscv64-cpython-311/Bio/SeqIO riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.80+dfsg-4ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/SeqIO/_twoBitIO.c -o build/temp.linux-riscv64-cpython-311/Bio/SeqIO/_twoBitIO.o riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.80+dfsg-4ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-cpython-311/Bio/SeqIO/_twoBitIO.o -L/usr/lib/riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/_twoBitIO.cpython-311-riscv64-linux-gnu.so cd Doc && make make[2]: Entering directory '/<>/Doc' sed "s/\@VERSION\@/1.80/g" version.in > version.sh chmod +x version.sh hevea -exec ./version.sh -exec xxdate.exe -fix Tutorial.tex Exclude comment 'comment' ./Tutorial/chapter_introduction.tex:91: Warning: Undefined citation: 'cock2009' ./Tutorial/chapter_introduction.tex:95: Warning: Undefined citation: 'chapman2000' ./Tutorial/chapter_introduction.tex:96: Warning: Undefined citation: 'hamelryck2003a' ./Tutorial/chapter_introduction.tex:97: Warning: Undefined citation: 'dehoon2004' ./Tutorial/chapter_introduction.tex:98: Warning: Undefined citation: 'pritchard2006' ./Tutorial/chapter_introduction.tex:99: Warning: Undefined citation: 'talevich2012' ./Tutorial/chapter_introduction.tex:100: Warning: Undefined citation: 'cock2010' ./Tutorial/chapter_introduction.tex:185: Warning: Undefined label: 'sec:seq-comparison' ./Tutorial/chapter_introduction.tex:191: Warning: Undefined label: 'sec:appendix-handles' ./Tutorial/chapter_quick_start.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:14: Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_quick_start.tex:14: Warning: Undefined label: 'chapter:advanced' ./Tutorial/chapter_quick_start.tex:19: Warning: Undefined label: 'chapter:seq_objects' ./Tutorial/chapter_quick_start.tex:45: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_quick_start.tex:65: Warning: Undefined label: 'sec:sequence-parsing' ./Tutorial/chapter_quick_start.tex:65: Warning: Undefined label: 'chapter:entrez' ./Tutorial/chapter_quick_start.tex:65: Warning: Undefined label: 'chapter:uniprot' ./Tutorial/chapter_quick_start.tex:65: Warning: Undefined label: 'sec:align_clustal' ./Tutorial/chapter_quick_start.tex:72: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_quick_start.tex:79: Warning: Undefined label: 'sec:connecting-with-biological-databases' ./Tutorial/chapter_quick_start.tex:145: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_quick_start.tex:145: Warning: Undefined label: 'chapter:align' ./Tutorial/chapter_quick_start.tex:150: Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_quick_start.tex:158: Warning: Undefined label: 'chapter:entrez' ./Tutorial/chapter_quick_start.tex:159: Warning: Undefined label: 'chapter:uniprot' ./Tutorial/chapter_quick_start.tex:169: Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_seq_objects.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined label: 'chapter:seq_annot' ./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_objects.tex:86: Warning: Undefined label: 'sec:mutable-seq' ./Tutorial/chapter_seq_objects.tex:155: Warning: Undefined label: 'sec:SeqRecord-format' ./Tutorial/chapter_seq_objects.tex:157: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_objects.tex:278: Warning: Undefined label: 'sec:SeqIO-reverse-complement' ./Tutorial/chapter_seq_objects.tex:353: Warning: Undefined label: 'sec:seq-module-functions' ./Tutorial/chapter_seq_objects.tex:469: Warning: Undefined label: 'sec:SeqIO-translate' ./Tutorial/chapter_seq_objects.tex:475: Warning: Undefined label: 'sec:seq-module-functions' ./Tutorial/chapter_seq_objects.tex:598: Warning: Undefined label: 'sec:seq-to-string' ./Tutorial/chapter_seq_objects.tex:741: Warning: Undefined label: 'sec:seq-to-string' ./Tutorial/chapter_seq_annot.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined label: 'chapter:seq_objects' ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined label: 'chapter:seq_objects' ./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_annot.tex:33: Warning: Undefined label: 'sec:FASTQ-filtering-example' ./Tutorial/chapter_seq_annot.tex:37: Warning: Undefined label: 'sec:seq_features' ./Tutorial/chapter_seq_annot.tex:47: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_annot.tex:130: Warning: Undefined label: 'chapter:quick_start' ./Tutorial/chapter_seq_annot.tex:132: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_annot.tex:211: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_annot.tex:275: Warning: Undefined label: 'sec:seq_features' ./Tutorial/chapter_seq_annot.tex:278: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_annot.tex:284: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:292: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:502: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:600: Warning: Undefined label: 'sec:seq-comparison' ./Tutorial/chapter_seq_annot.tex:608: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:648: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_annot.tex:651: Warning: Undefined label: 'sec:Bio.SeqIO-and-StringIO' ./Tutorial/chapter_seq_annot.tex:793: Warning: Undefined label: 'sec:SeqRecord-format' ./Tutorial/chapter_seq_annot.tex:805: Warning: Undefined label: 'sec:FASTQ-slicing-off-primer' ./Tutorial/chapter_seq_annot.tex:806: Warning: Undefined label: 'sec:FASTQ-slicing-off-adaptor' ./Tutorial/chapter_seq_annot.tex:819: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seqio.tex:4: Warning: Undefined label: 'chapter:quick_start' ./Tutorial/chapter_seqio.tex:4: Warning: Undefined label: 'chapter:seq_annot' ./Tutorial/chapter_seqio.tex:12: Warning: Undefined label: 'chapter:seq_annot' ./Tutorial/chapter_seqio.tex:12: Warning: Undefined label: 'chapter:seq_objects' ./Tutorial/chapter_seqio.tex:14: Warning: Undefined label: 'sec:low-level-fasta-fastq' ./Tutorial/chapter_seqio.tex:22: Warning: Undefined label: 'sec:SeqIO_Online' ./Tutorial/chapter_seqio.tex:22: Warning: Undefined label: 'sec:appendix-handles' ./Tutorial/chapter_seqio.tex:43: Warning: Undefined label: 'sec:sequence-parsing' ./Tutorial/chapter_seqio.tex:68: Warning: Undefined label: 'sec:sequence-parsing-plus-pylab' ./Tutorial/chapter_seqio.tex:150: Warning: Undefined label: 'chapter:seq_annot' ./Tutorial/chapter_seqio.tex:306: Warning: Undefined label: 'sec:writing-sequence-files' ./Tutorial/chapter_seqio.tex:326: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:329: Warning: Undefined label: 'sec:appendix-handles' ./Tutorial/chapter_seqio.tex:398: Warning: Undefined label: 'sec:SeqIO-index-bgzf' ./Tutorial/chapter_seqio.tex:401: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:413: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:413: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:414: Warning: Undefined label: 'sec:efetch' ./Tutorial/chapter_seqio.tex:504: Warning: Undefined label: 'chapter:entrez' ./Tutorial/chapter_seqio.tex:504: Warning: Undefined label: 'sec:entrez-guidelines' ./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:509: Warning: Undefined label: 'chapter:uniprot' ./Tutorial/chapter_seqio.tex:565: Warning: Undefined label: 'sec:seqio_todict' ./Tutorial/chapter_seqio.tex:571: Warning: Undefined label: 'sec:SeqIO-index' ./Tutorial/chapter_seqio.tex:575: Warning: Undefined label: 'sec:SeqIO-index-db' ./Tutorial/chapter_seqio.tex:578: Warning: Undefined label: 'sec:SeqIO-indexing-discussion' ./Tutorial/chapter_seqio.tex:581: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:588: Warning: Undefined label: 'sec:SeqIO-index' ./Tutorial/chapter_seqio.tex:661: Warning: Undefined label: 'sec:fasta-parsing' ./Tutorial/chapter_seqio.tex:783: Warning: Undefined label: 'sec:fastq-indexing' ./Tutorial/chapter_seqio.tex:804: Warning: Undefined label: 'sec:seqio-todict-functionkey' ./Tutorial/chapter_seqio.tex:866: Warning: Undefined label: 'sec:SeqIO-sort' ./Tutorial/chapter_seqio.tex:948: Warning: Undefined label: 'sec:seqio-index-getraw' ./Tutorial/chapter_seqio.tex:1189: Warning: Undefined label: 'sec:seqio-index-getraw' ./Tutorial/chapter_seqio.tex:1232: Warning: Undefined label: 'sec:SeqIO-fastq-conversion' ./Tutorial/chapter_seqio.tex:1232: Warning: Undefined label: 'sec:SeqIO-fasta-qual-conversion' ./Tutorial/chapter_seqio.tex:1247: Warning: Undefined label: 'sec:seq-reverse-complement' ./Tutorial/chapter_seqio.tex:1258: Warning: Undefined label: 'sec:SeqRecord-reverse-complement' ./Tutorial/chapter_seqio.tex:1311: Warning: Undefined label: 'sec:SeqIO-translate' ./Tutorial/chapter_seqio.tex:1331: Warning: Undefined label: 'sec:SeqRecord-format' ./Tutorial/chapter_seqio.tex:1412: Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_align.tex:31: Warning: Undefined label: 'sec:appendix-handles' ./Tutorial/chapter_align.tex:35: Warning: Undefined label: 'sec:AlignIO-count-argument' ./Tutorial/chapter_align.tex:113: Warning: Undefined label: 'sec:alignment-format' ./Tutorial/chapter_align.tex:444: Warning: Undefined label: 'sec:SeqIO-conversion' ./Tutorial/chapter_align.tex:633: Warning: Undefined label: 'sec:SeqRecord-format' ./Tutorial/chapter_align.tex:813: Warning: Undefined label: 'sec:SeqRecord-addition' ./Tutorial/chapter_align.tex:892: Warning: Undefined label: 'sec:subs_mat_ex' ./Tutorial/chapter_align.tex:913: Warning: Undefined label: 'sec:pairwise' ./Tutorial/chapter_align.tex:917: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_align.tex:947: Warning: Undefined label: 'sec:emboss-needle-water' ./Tutorial/chapter_align.tex:955: Warning: '_' occurring outside math mode ./Tutorial/chapter_align.tex:1093: Warning: Undefined label: 'chapter:phylo' ./Tutorial/chapter_align.tex:1317: Warning: Undefined label: 'sec:appendix-handles' ./Tutorial/chapter_align.tex:1492: Warning: Undefined citation: 'durbin1998' ./Tutorial/chapter_align.tex:1505: Warning: Undefined label: 'sec:pairwise-aligner' ./Tutorial/chapter_align.tex:1578: Warning: Undefined citation: 'waterman1987' ./Tutorial/chapter_align.tex:1608: Warning: Undefined label: 'sec:pairwise-substitution-scores' ./Tutorial/chapter_align.tex:1608: Warning: Undefined label: 'sec:pairwise-affine-gapscores' ./Tutorial/chapter_align.tex:1608: Warning: Undefined label: 'sec:pairwise-general-gapscores' ./Tutorial/chapter_align.tex:1609: Warning: Undefined label: 'sec:pairwise-basic' ./Tutorial/chapter_align.tex:1612: Warning: Undefined label: 'sec:pairwise-affine-gapscores' ./Tutorial/chapter_align.tex:1613: Warning: Undefined label: 'sec:pairwise-general-gapscores' ./Tutorial/chapter_align.tex:1639: Warning: Undefined citation: 'altschul1990' ./Tutorial/chapter_align.tex:1639: Warning: Undefined label: 'sec:pairwise-affine-gapscores' ./Tutorial/chapter_align.tex:1668: Warning: Undefined citation: 'altschul1990' ./Tutorial/chapter_align.tex:1772: Warning: Undefined label: 'table:align-meta-attributes' ./Tutorial/chapter_align.tex:1908: Warning: Undefined label: 'sec:pairwise-examples' ./Tutorial/chapter_align.tex:2424: Warning: Undefined citation: 'kent2002' ./Tutorial/chapter_align.tex:2496: Warning: Multiple definitions for label: sec:pairwise-general-gapscores ./Tutorial/chapter_align.tex:2725: Warning: Undefined citation: 'schneider2005' ./Tutorial/chapter_align.tex:2725: Warning: Undefined label: 'sec:substitution_matrices' ./Tutorial/chapter_align.tex:2932: Warning: '_' occurring outside math mode ./Tutorial/chapter_align.tex:3282: Warning: Undefined citation: 'altschul1990' ./Tutorial/chapter_align.tex:3354: Warning: Undefined citation: 'henikoff1992' ./Tutorial/chapter_align.tex:3354: Warning: Undefined citation: 'dayhoff1978' ./Tutorial/chapter_align.tex:3379: Warning: Undefined citation: 'schneider2005' ./Tutorial/chapter_align.tex:3379: Warning: Suppressing nested a element ./Tutorial/chapter_align.tex:3391: Warning: Undefined label: 'sec:pairwise' ./Tutorial/chapter_blast.tex:18: Warning: Undefined label: 'chapter:searchio' ./Tutorial/chapter_blast.tex:73: Warning: Undefined label: 'sec:parsing-blast' ./Tutorial/chapter_blast.tex:133: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_blast.tex:138: Warning: Undefined label: 'sec:parsing-blast' ./Tutorial/chapter_blast.tex:160: Warning: Undefined label: 'sec:parsing-blast' ./Tutorial/chapter_blast.tex:169: Warning: Undefined label: 'sec:parsing-blast' ./Tutorial/chapter_blast.tex:178: Warning: Undefined label: 'sec:running-www-blast' ./Tutorial/chapter_blast.tex:206: Warning: Undefined label: 'sec:alignment-tools' ./Tutorial/chapter_blast.tex:241: Warning: Undefined label: 'sec:parsing-blast' ./Tutorial/chapter_blast.tex:287: Warning: Undefined label: 'sec:running-www-blast' ./Tutorial/chapter_blast.tex:289: Warning: Undefined label: 'sec:running-local-blast' ./Tutorial/chapter_blast.tex:304: Warning: Undefined label: 'sec:appendix-handles' ./Tutorial/chapter_blast.tex:340: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_blast.tex:340: Warning: Undefined label: 'chapter:align' ./Tutorial/chapter_blast.tex:452: Warning: Undefined label: 'fig:blastrecord' ./Tutorial/chapter_blast.tex:468: Warning: Undefined label: 'fig:psiblastrecord' ./Tutorial/chapter_searchio.tex:739: Warning: Undefined label: 'chapter:seq_annot' ./Tutorial/chapter_searchio.tex:1089: Warning: Undefined label: 'sec:SeqIO-index' ./Tutorial/chapter_entrez.tex:21: Warning: Undefined label: 'sec:entrez-specialized-parsers' ./Tutorial/chapter_entrez.tex:60: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:63: Warning: Undefined label: 'sec:BioSQL' ./Tutorial/chapter_entrez.tex:216: Warning: Undefined label: 'sec:efetch' ./Tutorial/chapter_entrez.tex:220: Warning: Undefined label: 'sec:entrez-einfo' ./Tutorial/chapter_entrez.tex:236: Warning: Undefined label: 'sec:efetch' ./Tutorial/chapter_entrez.tex:299: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:325: Warning: Undefined label: 'sec:SeqIO_GenBank_Online' ./Tutorial/chapter_entrez.tex:325: Warning: Undefined label: 'sec:efetch' ./Tutorial/chapter_entrez.tex:419: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_entrez.tex:481: Warning: Undefined label: 'sec:entrez-specialized-parsers' ./Tutorial/chapter_entrez.tex:483: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:565: Warning: Undefined label: 'sec:elink-citations' ./Tutorial/chapter_entrez.tex:571: Warning: Undefined label: 'sec:entrez_example_genbank' ./Tutorial/chapter_entrez.tex:780: Warning: Undefined label: 'sec:SeqIO_GenBank_Online' ./Tutorial/chapter_entrez.tex:780: Warning: Undefined label: 'sec:efetch' ./Tutorial/chapter_entrez.tex:902: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1065: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1068: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1072: Warning: Undefined label: 'sec:orchids' ./Tutorial/chapter_entrez.tex:1115: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1159: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1159: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1161: Warning: Undefined label: 'sec:orchids' ./Tutorial/chapter_entrez.tex:1216: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1251: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1258: Warning: Undefined label: 'sec:SeqIO_GenBank_Online' ./Tutorial/chapter_entrez.tex:1259: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1311: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_entrez.tex:1335: Warning: Undefined label: 'sec:entrez-guidelines' ./Tutorial/chapter_entrez.tex:1336: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1396: Warning: Undefined label: 'sec:entrez-search-fetch-genbank' ./Tutorial/chapter_entrez.tex:1418: Warning: Undefined label: 'sec:entrez_example_genbank' ./Tutorial/chapter_entrez.tex:1507: Warning: Undefined label: 'sec:entrez-and-medline' ./Tutorial/chapter_entrez.tex:1512: Warning: Undefined label: 'sec:elink' ./Tutorial/chapter_entrez.tex:1537: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_uniprot.tex:12: Warning: Undefined label: 'sec:SeqIO_ExPASy_and_SwissProt' ./Tutorial/chapter_uniprot.tex:37: Warning: Undefined label: 'sec:expasy_swissprot' ./Tutorial/chapter_uniprot.tex:45: Warning: Undefined label: 'sec:SeqIO_ExPASy_and_SwissProt' ./Tutorial/chapter_uniprot.tex:343: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:345: Warning: Undefined label: 'sec:orchids' ./Tutorial/chapter_pdb.tex:84: Warning: Undefined label: 'sec:problem_structures' ./Tutorial/chapter_pdb.tex:275: Warning: Undefined label: 'fig:smcra' ./Tutorial/chapter_pdb.tex:284: Warning: Undefined label: 'sec:problem_structures' ./Tutorial/chapter_pdb.tex:421: Warning: Undefined label: 'sec:hetero_problems' ./Tutorial/chapter_pdb.tex:466: Warning: Undefined label: 'sec:point_mutations' ./Tutorial/chapter_pdb.tex:483: Warning: Undefined label: 'sec:disordered_atoms' ./Tutorial/chapter_pdb.tex:592: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:606: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:610: Warning: Undefined label: 'fig:smcra' ./Tutorial/chapter_pdb.tex:646: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:657: Warning: Undefined label: 'fig:smcra' ./Tutorial/chapter_pdb.tex:683: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:973: Warning: Undefined label: 'table:ic-attribs' ./Tutorial/chapter_pdb.tex:1018: Warning: Undefined citation: 'golub1989' ./Tutorial/chapter_pdb.tex:1046: Warning: Undefined citation: 'hamelryck2005' ./Tutorial/chapter_pdb.tex:1081: Warning: Undefined label: 'table:DSSP-codes' ./Tutorial/chapter_pdb.tex:1121: Warning: Undefined label: 'sec:residue_depth' ./Tutorial/chapter_pdb.tex:1124: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:1172: Warning: Undefined citation: 'hamelryck2003a' ./Tutorial/chapter_pdb.tex:1186: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:1383: Warning: Undefined citation: 'hamelryck2003b' ./Tutorial/chapter_pdb.tex:1384: Warning: Undefined citation: 'majumdar2005' ./Tutorial/chapter_phylo.tex:9: Warning: Undefined citation: 'talevich2012' ./Tutorial/chapter_phylo.tex:96: Warning: Undefined label: 'fig:phylo-simple-draw' ./Tutorial/chapter_phylo.tex:201: Warning: Undefined label: 'fig:phylo-color-draw' ./Tutorial/chapter_phylo.tex:823: Warning: Undefined label: 'sec:PhyloXML' ./Tutorial/chapter_motifs.tex:8: Warning: Undefined label: 'sec:links' ./Tutorial/chapter_motifs.tex:165: Warning: Undefined citation: 'cornish1985' ./Tutorial/chapter_motifs.tex:166: Warning: Undefined citation: 'cavener1987' ./Tutorial/chapter_motifs.tex:542: Warning: Undefined citation: 'bailey1994' ./Tutorial/chapter_motifs.tex:688: Warning: Undefined citation: 'matys2003' ./Tutorial/chapter_motifs.tex:772: Warning: Undefined label: 'table:transfaccodes' ./Tutorial/chapter_cluster.tex:6: Warning: Undefined citation: 'dehoon2004' ./Tutorial/chapter_cluster.tex:30: Warning: Undefined citation: 'lecuyer1988' ./Tutorial/chapter_cluster.tex:30: Warning: Undefined citation: 'kachitvichyanukul1988' ./Tutorial/chapter_cluster.tex:154: Warning: Undefined citation: 'snedecor1989' ./Tutorial/chapter_cluster.tex:183: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:278: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:346: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:556: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:600: Warning: Undefined citation: 'kohonen1997' ./Tutorial/chapter_cluster.tex:600: Warning: Undefined citation: 'tamayo1999' ./Tutorial/chapter_cluster.tex:647: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:660: Warning: Undefined citation: 'yeung2001' ./Tutorial/chapter_cluster.tex:668: Warning: Undefined citation: 'golub1971' ./Tutorial/chapter_cluster.tex:802: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:805: Warning: Undefined label: 'sec:distancematrix' ./Tutorial/chapter_cluster.tex:823: Warning: Undefined label: 'sec:clustercentroids' ./Tutorial/chapter_cluster.tex:846: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:871: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:900: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:922: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:954: Warning: Undefined citation: 'hihara2001' ./Tutorial/chapter_learning.tex:40: Warning: Undefined label: 'eq:OP' ./Tutorial/chapter_learning.tex:40: Warning: Undefined label: 'eq:NOP' ./Tutorial/chapter_learning.tex:75: Warning: Undefined label: 'table:training' ./Tutorial/chapter_learning.tex:197: Warning: Undefined label: 'eq:OP' ./Tutorial/chapter_learning.tex:197: Warning: Undefined label: 'eq:NOP' ./Tutorial/chapter_learning.tex:261: Warning: Undefined label: 'eq:OP' ./Tutorial/chapter_learning.tex:261: Warning: Undefined label: 'eq:NOP' ./Tutorial/chapter_learning.tex:263: Warning: Undefined label: 'eq:OP' ./Tutorial/chapter_learning.tex:263: Warning: Undefined label: 'eq:NOP' ./Tutorial/chapter_learning.tex:273: Warning: Undefined label: 'sec:LogisticRegression' ./Tutorial/chapter_learning.tex:277: Warning: Undefined label: 'table:training' ./Tutorial/chapter_learning.tex:285: Warning: Undefined label: 'sec:LogisticRegressionTraining' ./Tutorial/chapter_graphics.tex:18: Warning: Undefined citation: 'pritchard2006' ./Tutorial/chapter_graphics.tex:28: Warning: Undefined citation: 'toth2006' ./Tutorial/chapter_graphics.tex:31: Warning: Undefined citation: 'vanderauwera2009' ./Tutorial/chapter_graphics.tex:36: Warning: Undefined label: 'chapter:seq_annot' ./Tutorial/chapter_graphics.tex:36: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:64: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:220: Warning: Undefined label: 'sec:seq_features' ./Tutorial/chapter_graphics.tex:268: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:268: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:326: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:326: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:345: Warning: Undefined label: 'sec:gd_nice_example' ./Tutorial/chapter_graphics.tex:352: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:409: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:409: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:485: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:485: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:488: Warning: Undefined label: 'sec:gd_top_down' ./Tutorial/chapter_graphics.tex:591: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:591: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:596: Warning: Undefined citation: 'proux2002' ./Tutorial/chapter_graphics.tex:605: Warning: Undefined label: 'sec:efetch' ./Tutorial/chapter_graphics.tex:608: Warning: Undefined label: 'sec:SeqRecord-slicing' ./Tutorial/chapter_graphics.tex:610: Warning: Undefined label: 'sec:SeqRecord-reverse-complement' ./Tutorial/chapter_graphics.tex:752: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:752: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:759: Warning: Undefined citation: 'proux2002' ./Tutorial/chapter_graphics.tex:1012: Warning: Undefined citation: 'jupe2012' ./Tutorial/chapter_phenotype.tex:231: Warning: Optional argument to \item in itemize environment ./Tutorial/chapter_phenotype.tex:233: Warning: Optional argument to \item in itemize environment ./Tutorial/chapter_phenotype.tex:235: Warning: Optional argument to \item in itemize environment ./Tutorial/chapter_cookbook.tex:22: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_cookbook.tex:58: Warning: Undefined label: 'sec:low-level-fasta-fastq' ./Tutorial/chapter_cookbook.tex:146: Warning: Undefined label: 'sec:Bio.SeqIO-and-StringIO' ./Tutorial/chapter_cookbook.tex:201: Warning: Undefined label: 'sec:translation' ./Tutorial/chapter_cookbook.tex:206: Warning: Undefined label: 'sec:SeqIO-reverse-complement' ./Tutorial/chapter_cookbook.tex:338: Warning: Undefined label: 'sec:seqio-index-getraw' ./Tutorial/chapter_cookbook.tex:443: Warning: Undefined label: 'sec:low-level-fasta-fastq' ./Tutorial/chapter_cookbook.tex:457: Warning: Undefined label: 'sec:low-level-fasta-fastq' ./Tutorial/chapter_cookbook.tex:480: Warning: Undefined label: 'sec:SeqRecord-slicing' ./Tutorial/chapter_cookbook.tex:643: Warning: Undefined label: 'sec:SeqIO-conversion' ./Tutorial/chapter_cookbook.tex:646: Warning: Undefined citation: 'cock2010' ./Tutorial/chapter_cookbook.tex:801: Warning: Undefined label: 'sec:SeqIO-index' ./Tutorial/chapter_cookbook.tex:823: Warning: Undefined label: 'sec:SeqIO-index' ./Tutorial/chapter_cookbook.tex:825: Warning: Undefined label: 'sec:SeqIO-sort' ./Tutorial/chapter_cookbook.tex:839: Warning: Undefined label: 'sec:SeqIO-conversion' ./Tutorial/chapter_cookbook.tex:905: Warning: Undefined label: 'sec:translation' ./Tutorial/chapter_cookbook.tex:1024: Warning: Undefined label: 'sec:gd_nice_example' ./Tutorial/chapter_cookbook.tex:1041: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_cookbook.tex:1418: Warning: Undefined label: 'chapter:align' ./Tutorial/chapter_cookbook.tex:1421: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1425: Warning: Undefined label: 'chapter:align' ./Tutorial/chapter_cookbook.tex:1436: Warning: Undefined label: 'sec:consensus' ./Tutorial/chapter_cookbook.tex:1437: Warning: Undefined label: 'sec:pssm' ./Tutorial/chapter_cookbook.tex:1438: Warning: Undefined label: 'sec:getting_info_content' ./Tutorial/chapter_cookbook.tex:1439: Warning: Undefined label: 'sec:sub_matrix' ./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined label: 'sec:summary_info' ./Tutorial/chapter_cookbook.tex:1538: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1538: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1565: Warning: Undefined label: 'sec:summary_info' ./Tutorial/chapter_cookbook.tex:1617: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1626: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1626: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1640: Warning: Undefined label: 'sec:align_clustal' ./Tutorial/chapter_cookbook.tex:1748: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_testing.tex:55: Warning: Undefined label: 'sec:doctest' ./Tutorial/chapter_testing.tex:282: Warning: Undefined label: 'sec:doctest' ./Tutorial/chapter_contributing.tex:32: Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_contributing.tex:38: Warning: '_' occurring outside math mode ./Tutorial/chapter_contributing.tex:85: Warning: Undefined label: 'chapter:testing' ./Tutorial/chapter_contributing.tex:101: Warning: Undefined label: 'chapter:testing' ./Tutorial/chapter_appendix.tex:91: Warning: Undefined label: 'sec:SeqIO_compressed' HeVeA Warning: Label(s) may have changed. Rerun me to get cross-references right. Run, run, again... Exclude comment 'comment' ./Tutorial/chapter_quick_start.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:14: Warning: Undefined label: 'chapter:advanced' ./Tutorial/chapter_seq_objects.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_annot.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_annot.tex:278: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:326: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:401: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:413: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:413: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:581: Warning: '_' occurring outside math mode ./Tutorial/chapter_align.tex:955: Warning: '_' occurring outside math mode ./Tutorial/chapter_align.tex:2496: Warning: Multiple definitions for label: sec:pairwise-general-gapscores ./Tutorial/chapter_align.tex:2932: Warning: '_' occurring outside math mode ./Tutorial/chapter_align.tex:3379: Warning: Suppressing nested a element ./Tutorial/chapter_entrez.tex:1065: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1068: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1159: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1159: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:343: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:592: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:606: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:646: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:683: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:1124: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:1186: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:268: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:268: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:326: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:326: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:352: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:409: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:409: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:485: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:485: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:591: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:591: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:752: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:752: Warning: '_' occurring outside math mode ./Tutorial/chapter_phenotype.tex:231: Warning: Optional argument to \item in itemize environment ./Tutorial/chapter_phenotype.tex:233: Warning: Optional argument to \item in itemize environment ./Tutorial/chapter_phenotype.tex:235: Warning: Optional argument to \item in itemize environment ./Tutorial/chapter_cookbook.tex:1421: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1538: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1538: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1617: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1626: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1626: Warning: '_' occurring outside math mode ./Tutorial/chapter_contributing.tex:38: Warning: '_' occurring outside math mode Fixpoint reached in 2 step(s) hevea -exec ./version.sh -exec xxdate.exe -fix -text Tutorial.tex Exclude comment 'comment' ./Tutorial.tex:73: Warning: tt_mode is an empty style ./Tutorial.tex:100: Warning: Application of '\'' on 'n' failed ./Tutorial.htoc:378: Warning: Application of '\"' on 'i' failed ./Tutorial/chapter_introduction.tex:82: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:82: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:96: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:96: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:97: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:97: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:98: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:98: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:99: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:99: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:99: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:99: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:138: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:138: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:139: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:139: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:152: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:152: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:156: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:156: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:161: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:161: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:162: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:162: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:176: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:176: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:177: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:177: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:178: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:178: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:182: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:182: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:187: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:187: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:187: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:187: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:194: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:194: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:194: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:194: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:195: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:195: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:197: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:197: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:197: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:197: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:200: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:200: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:205: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:205: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:207: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:207: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:212: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:212: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:216: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:216: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:219: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:219: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:222: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:222: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:222: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:222: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:223: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:223: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:226: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:226: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:229: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:229: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:229: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:229: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:229: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:229: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:231: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:231: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:14: Warning: Undefined label: 'chapter:advanced' ./Tutorial/chapter_quick_start.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:21: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:21: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:21: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:21: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:21: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:21: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:33: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:33: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:72: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:72: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:74: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:74: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:79: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:79: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:84: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:93: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:93: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:118: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:141: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:141: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:145: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:145: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:145: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:145: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:147: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:147: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:147: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:147: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:160: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:160: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:1: Warning: line too long ./Tutorial/chapter_seq_objects.tex:1: Warning: line too long ./Tutorial/chapter_seq_objects.tex:1: Warning: line too long ./Tutorial/chapter_seq_objects.tex:1: Warning: line too long ./Tutorial/chapter_seq_objects.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_objects.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:7: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:7: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:9: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:9: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:44: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:44: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:44: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:44: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:73: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:73: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:84: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:84: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:86: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:86: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:86: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:86: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:133: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:133: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:133: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:133: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:156: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:156: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:161: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:161: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:197: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:197: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:197: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:197: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:210: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:210: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:210: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:210: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:239: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:239: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:253: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:253: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:278: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:278: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:279: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:279: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:296: Warning: Command not found: \downarrow ./Tutorial/chapter_seq_objects.tex:305: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:305: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:319: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:319: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:319: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:319: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:339: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:339: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:351: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:351: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:351: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:351: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:351: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:351: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:352: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:352: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:359: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:359: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:416: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:416: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:433: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:433: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:469: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:469: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:470: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:470: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:474: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:474: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:474: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:474: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:577: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:577: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:602: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:602: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:602: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:602: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:610: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:610: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:610: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:610: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:641: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:641: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:641: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:641: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:675: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:675: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:675: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:675: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:692: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:692: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:702: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:702: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:727: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:727: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:727: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:727: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:727: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:727: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:729: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:729: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:729: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:729: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:731: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:731: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:731: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:731: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:741: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:741: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:741: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:741: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:747: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:747: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:748: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:748: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:748: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:748: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:764: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:764: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:25: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:25: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:37: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:37: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:44: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:44: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:46: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:46: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:46: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:46: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:48: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:48: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:52: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:52: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:52: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:52: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:76: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:76: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:86: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:86: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:86: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:86: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:99: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:99: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:112: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:112: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:112: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:112: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:113: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:113: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:120: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_annot.tex:130: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:130: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:131: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:131: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:131: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:131: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:139: Warning: line too long ./Tutorial/chapter_seq_annot.tex:142: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:142: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:143: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:143: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:144: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:144: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:165: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:165: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:197: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_annot.tex:211: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:211: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:218: Warning: line too long ./Tutorial/chapter_seq_annot.tex:227: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:227: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:227: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:227: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:248: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:248: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:258: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:258: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:266: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:266: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:266: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:266: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:274: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:274: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:278: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_annot.tex:282: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:282: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:284: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:284: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:284: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:284: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:286: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:286: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:291: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:291: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:293: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:293: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:298: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:298: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:301: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:301: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:302: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:302: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:304: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:304: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:313: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:313: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:320: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:320: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:327: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:327: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:328: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:328: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:338: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:338: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:340: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:340: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:350: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:350: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:371: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:371: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:375: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:375: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:377: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:377: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:380: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:380: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:382: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:382: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:383: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:383: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:384: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:384: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:420: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:420: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:453: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:453: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:453: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:453: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:472: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:472: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:472: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:472: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:502: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:502: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:508: Warning: line too long ./Tutorial/chapter_seq_annot.tex:522: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:522: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:522: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:522: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:531: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:531: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:544: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:544: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:544: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:544: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:548: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:548: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:566: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:566: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:566: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:566: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:567: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:567: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:568: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:568: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:568: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:568: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:577: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:577: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:577: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:577: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:604: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:604: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:608: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:608: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:608: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:608: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:610: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:610: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:610: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:610: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:616: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:616: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:616: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:616: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:618: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:618: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:647: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:647: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:648: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:648: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:649: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:649: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:651: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:651: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:656: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:656: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:656: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:656: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:668: Warning: line too long ./Tutorial/chapter_seq_annot.tex:675: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:675: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:675: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:675: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:683: Warning: line too long ./Tutorial/chapter_seq_annot.tex:704: Warning: line too long ./Tutorial/chapter_seq_annot.tex:704: Warning: line too long ./Tutorial/chapter_seq_annot.tex:708: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:708: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:715: Warning: line too long ./Tutorial/chapter_seq_annot.tex:722: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:722: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:725: Warning: line too long ./Tutorial/chapter_seq_annot.tex:746: Warning: line too long ./Tutorial/chapter_seq_annot.tex:746: Warning: line too long ./Tutorial/chapter_seq_annot.tex:812: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:812: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:812: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:812: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:819: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:819: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:835: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:835: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:880: Warning: line too long ./Tutorial/chapter_seq_annot.tex:897: Warning: line too long ./Tutorial/chapter_seq_annot.tex:916: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:916: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:938: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:938: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:939: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:939: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:951: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:951: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:954: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:954: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:954: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:954: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:956: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:956: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:956: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:956: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1: Warning: line too long ./Tutorial/chapter_seqio.tex:1: Warning: line too long ./Tutorial/chapter_seqio.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:5: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:5: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:12: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:12: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:12: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:12: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:14: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:14: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:14: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:14: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:28: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:28: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:28: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:28: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:32: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:32: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:32: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:32: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:43: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:43: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:54: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:54: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:67: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:67: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:75: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:75: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:75: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:75: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:77: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:77: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:93: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:93: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:93: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:93: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:103: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:103: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:104: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:104: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:145: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:145: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:149: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:149: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:150: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:180: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:180: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:198: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:248: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:257: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:257: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:290: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:290: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:291: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:291: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:307: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:307: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:307: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:307: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:308: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:308: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:309: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:309: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:326: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:328: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:328: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:332: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:332: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:333: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:333: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:345: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:345: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:370: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:370: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:401: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:404: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:404: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:413: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:413: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:421: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:421: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:448: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:448: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:471: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:471: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:504: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:504: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:511: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:511: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:540: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:540: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:540: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:540: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:550: Warning: line too long ./Tutorial/chapter_seqio.tex:560: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:560: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:564: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:564: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:566: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:566: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:567: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:567: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:569: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:569: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:570: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:570: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:572: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:572: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:581: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:584: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:584: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:590: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:590: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:591: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:591: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:600: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:600: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:601: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:601: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:602: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:602: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:605: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:605: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:627: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:627: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:640: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:640: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:661: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:661: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:661: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:661: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:663: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:663: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:676: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:676: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:698: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:698: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:742: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:742: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:747: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:747: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:778: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:778: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:781: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:781: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:804: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:804: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:819: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:819: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:834: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:834: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:835: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:835: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:837: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:837: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:842: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:842: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:850: Warning: line too long ./Tutorial/chapter_seqio.tex:851: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:851: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:864: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:864: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:867: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:867: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:873: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:873: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:879: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:879: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:885: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:885: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:934: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:934: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:947: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:947: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:976: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:976: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:978: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:978: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:979: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:979: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:979: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:979: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:982: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:982: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:982: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:982: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1026: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1026: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1034: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1034: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1036: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1036: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1038: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1038: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1039: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1039: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1039: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1039: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1041: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1041: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1045: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1045: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1045: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1045: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1050: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1050: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1050: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1050: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1062: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1062: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1062: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1062: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1067: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1067: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1073: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1073: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1082: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1082: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1125: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1125: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1154: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1154: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1155: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1155: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1155: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1155: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1155: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1155: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1157: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1157: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1164: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1164: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1167: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1167: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1189: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1189: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1190: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1190: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1198: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:1218: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1218: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1235: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1235: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1243: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1243: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1247: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1247: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1247: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1247: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1257: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1257: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1258: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1258: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1258: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1258: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1318: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1318: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1331: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1331: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1331: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1331: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1333: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1333: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1342: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1342: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1350: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1350: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1355: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1355: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1356: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1356: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1357: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1357: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1360: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1360: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1363: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1363: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1364: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1364: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1367: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1367: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1393: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1393: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1394: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1394: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1: Warning: line too long ./Tutorial/chapter_align.tex:1: Warning: line too long ./Tutorial/chapter_align.tex:1: Warning: line too long ./Tutorial/chapter_align.tex:1: Warning: line too long ./Tutorial/chapter_align.tex:1: Warning: line too long ./Tutorial/chapter_align.tex:1: Warning: line too long ./Tutorial/chapter_align.tex:8: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:8: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:11: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:11: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:12: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:12: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:13: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:13: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:13: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:13: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:32: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:32: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:35: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:35: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:93: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:93: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:113: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:113: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:165: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:165: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:167: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:167: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:178: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:178: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:191: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:191: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:221: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:221: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:266: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:266: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:266: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:266: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:335: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:335: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:336: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:336: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:336: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:336: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:336: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:336: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:338: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:338: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:338: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:338: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:368: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:368: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:368: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:368: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:370: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:370: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:370: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:370: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:370: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:370: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:376: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:376: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:377: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:377: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:434: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:434: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:434: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:434: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:434: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:434: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:436: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:436: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:442: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:442: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:443: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:443: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:445: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:445: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:445: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:445: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:446: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:446: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:457: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:457: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:457: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:457: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:467: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:467: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:467: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:467: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:469: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:469: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:469: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:469: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:614: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:614: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:615: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:615: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:616: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:616: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:631: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:631: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:631: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:631: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:633: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:633: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:633: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:633: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:664: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:664: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:665: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:665: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:666: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:666: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:666: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:666: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:687: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:687: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:687: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:687: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:688: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:688: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:748: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:748: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:814: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:814: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:894: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:894: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:894: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:894: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:913: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:913: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:917: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:917: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:921: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:921: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:933: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:933: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:944: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:944: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:955: Warning: '_' occurring outside math mode ./Tutorial/chapter_align.tex:958: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:958: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1016: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1016: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1016: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1016: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1022: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1022: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1023: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1023: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1024: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1024: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1048: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1048: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1050: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1050: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1069: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1069: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1098: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1098: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1127: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1127: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1150: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1150: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1161: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1161: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1204: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1204: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1238: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1238: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1377: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1377: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1457: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1457: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1487: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1487: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1488: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1488: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1497: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1497: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1504: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1504: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1504: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1504: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1523: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1523: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1535: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1535: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1535: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1535: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1554: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1554: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1554: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1554: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1556: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1556: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1556: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1556: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1557: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1557: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1558: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1558: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1583: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1583: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1613: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1613: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1623: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1623: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1623: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1623: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1636: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1636: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1695: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1695: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1707: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1707: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1707: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1707: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1708: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1708: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1708: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1708: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1709: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1709: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1709: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1709: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1722: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1722: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1729: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1729: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1729: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1729: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1730: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1730: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1730: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1730: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1731: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1731: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1731: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1731: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1732: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1732: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1732: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1732: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1733: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1733: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1733: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1733: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1734: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1734: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1734: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1734: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1772: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1772: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1780: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1780: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1780: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1780: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1780: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1780: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1781: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1781: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1781: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1781: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1781: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1781: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1782: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1782: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1782: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1782: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1782: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1782: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1783: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1783: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1783: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1783: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1783: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1783: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1784: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1784: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1784: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1784: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1784: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1784: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1785: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1785: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1785: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1785: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1785: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1785: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1786: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1786: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1786: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1786: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1786: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1786: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1787: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1787: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1787: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1787: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1787: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1787: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1788: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1788: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1788: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1788: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1788: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1788: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1789: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1789: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1789: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1789: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1789: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1789: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1790: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1790: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1790: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1790: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1790: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1790: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1791: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1791: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1791: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1791: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1791: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1791: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1792: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1792: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1792: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1792: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1792: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1792: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1793: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1793: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1793: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1793: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1793: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1793: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1794: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1794: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1794: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1794: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1794: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1794: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1795: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1795: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1795: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1795: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1795: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1795: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1796: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1796: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1797: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1797: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1797: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1797: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1797: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1797: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1798: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1798: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1799: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1799: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1799: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1799: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1799: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1799: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1801: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1801: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1802: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1802: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1802: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1802: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1802: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1802: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1803: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1803: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1805: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1805: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1805: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1805: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1805: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1805: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1806: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1806: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1806: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1806: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1806: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1806: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1807: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1807: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1807: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1807: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1807: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1807: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1808: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1808: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1808: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1808: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1808: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1808: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1812: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1812: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1812: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1812: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1812: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1812: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1813: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1813: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1813: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1813: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1813: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1813: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1815: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1815: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1815: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1815: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1815: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1815: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1816: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1816: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1816: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1816: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1816: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1816: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1818: Warning: overfull line in array : array too wide ./Tutorial/chapter_align.tex:1818: Warning: line too long ./Tutorial/chapter_align.tex:1818: Warning: line too long ./Tutorial/chapter_align.tex:1818: Warning: line too long ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1910: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1910: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1946: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1946: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1984: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1984: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1984: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1984: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1984: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1984: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1988: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1988: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1988: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1988: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1989: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1989: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1999: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1999: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1999: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1999: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2030: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2030: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2053: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2053: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2053: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2053: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2054: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2054: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2054: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2054: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2055: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2055: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2055: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2055: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2067: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2067: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2091: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2091: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2102: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2102: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2164: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2164: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2192: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2192: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2203: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2203: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2295: Warning: line too long ./Tutorial/chapter_align.tex:2311: Warning: line too long ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2392: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2392: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2392: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2392: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2411: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2411: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2411: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2411: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2412: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2412: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2424: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2424: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2428: Warning: line too long ./Tutorial/chapter_align.tex:2431: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2431: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2433: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2433: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2434: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2434: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2435: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2435: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2479: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2479: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2479: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2479: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2485: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2485: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2493: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2493: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2496: Warning: Multiple definitions for label: sec:pairwise-general-gapscores ./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2519: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2519: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2519: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2519: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2612: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2612: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2612: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2612: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2698: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2698: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2698: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2698: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2758: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2758: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2758: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2758: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2864: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2864: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2932: Warning: '_' occurring outside math mode ./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2938: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2938: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2951: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2951: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2958: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2958: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2975: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2975: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2993: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2993: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2993: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2993: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3007: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3007: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3030: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3030: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3049: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3049: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3070: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3070: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3119: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3119: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3119: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3119: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3217: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3217: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3217: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3217: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3263: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3263: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3282: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3282: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3302: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3302: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3315: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3315: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3315: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3315: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3350: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3350: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3369: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3369: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3391: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3391: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3393: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3393: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3396: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3396: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3400: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3400: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3416: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3416: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3425: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3425: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3429: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3429: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3442: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3442: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3443: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3443: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3448: Warning: line too long ./Tutorial/chapter_align.tex:3450: Warning: line too long ./Tutorial/chapter_align.tex:3468: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3468: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3491: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3491: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3508: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3508: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3511: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3511: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3528: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3528: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3529: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3529: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3552: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3552: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3565: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3565: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3572: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3572: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:1: Warning: line too long ./Tutorial/chapter_blast.tex:1: Warning: line too long ./Tutorial/chapter_blast.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:20: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:20: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:29: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:29: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:29: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:29: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:35: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:35: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:45: Warning: line too long ./Tutorial/chapter_blast.tex:53: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:53: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:60: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:60: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:65: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:65: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:68: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:68: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:69: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:69: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:70: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:70: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:72: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:72: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:74: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:74: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:121: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:121: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:132: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:132: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:135: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:135: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:146: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:146: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:147: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:147: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:157: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:157: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:159: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:159: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:202: Warning: '_' occurring outside math mode ./Tutorial/chapter_blast.tex:202: Warning: '_' occurring outside math mode ./Tutorial/chapter_blast.tex:225: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:225: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:236: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:236: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:238: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:238: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:240: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:240: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:248: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:248: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:259: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:259: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:259: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:259: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:273: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:273: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:303: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:303: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:303: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:303: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:307: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:307: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:339: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:339: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:339: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:339: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:341: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:341: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:341: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:341: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:342: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:342: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:342: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:342: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:344: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:344: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:344: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:344: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:348: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:348: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:369: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:369: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:388: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:388: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:440: Warning: line too long ./Tutorial/chapter_blast.tex:442: Warning: line too long ./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:452: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:452: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:452: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:452: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:456: Warning: Image in text ./Tutorial/chapter_blast.tex:472: Warning: Image in text ./Tutorial/chapter_blast.tex:488: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:488: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:488: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:488: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:489: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:489: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:494: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:494: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:501: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:501: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:502: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:502: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:507: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:507: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1: Warning: line too long ./Tutorial/chapter_searchio.tex:17: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:17: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:18: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:18: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:21: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:21: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:27: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:27: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:29: Warning: '_' occurring outside math mode ./Tutorial/chapter_searchio.tex:31: Warning: '_' occurring outside math mode ./Tutorial/chapter_searchio.tex:32: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:32: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:40: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:40: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:41: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:41: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:42: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:42: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:44: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:44: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:46: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:46: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:47: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:47: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:72: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:72: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:77: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:77: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:78: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:78: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:78: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:78: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:79: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:79: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:79: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:79: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:80: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:80: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:81: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:81: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:82: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:82: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:83: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:83: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:83: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:83: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:84: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:84: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:85: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:85: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:86: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:86: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:87: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:87: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:88: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:88: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:88: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:88: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:88: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:88: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:89: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:89: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:90: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:90: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:90: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:90: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:96: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:96: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:96: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:96: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:100: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:100: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:100: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:100: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:103: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:103: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:104: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:104: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:105: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:105: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:106: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:106: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:110: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:110: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:167: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:167: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:168: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:168: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:178: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:178: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:204: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:204: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:221: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:221: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:242: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:242: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:242: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:242: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:243: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:243: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:244: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:244: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:248: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:248: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:249: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:249: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:263: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:263: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:264: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:264: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:274: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:274: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:287: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:287: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:315: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:315: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:315: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:315: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:326: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:326: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:337: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:337: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:352: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:352: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:353: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:353: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:354: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:354: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:355: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:355: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:357: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:357: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:359: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:359: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:359: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:359: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:360: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:360: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:361: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:361: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:361: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:361: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:386: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:386: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:388: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:388: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:389: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:389: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:389: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:389: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:391: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:391: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:392: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:392: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:394: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:394: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:394: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:394: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:394: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:394: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:398: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:398: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:398: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:398: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:401: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:401: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:404: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:404: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:405: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:405: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:405: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:405: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:405: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:405: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:406: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:406: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:406: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:406: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:407: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:407: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:407: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:407: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:409: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:409: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:409: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:409: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:410: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:410: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:413: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:413: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:414: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:414: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:416: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:416: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:416: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:416: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:416: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:416: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:439: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:439: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:439: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:439: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:440: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:440: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:440: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:440: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:443: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:443: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:444: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:444: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:444: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:444: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:445: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:445: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:445: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:445: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:446: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:446: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:446: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:446: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:448: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:448: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:468: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:468: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:468: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:468: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:468: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:468: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:469: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:469: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:474: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:474: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:475: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:475: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:476: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:476: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:477: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:477: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:503: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:503: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:504: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:504: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:506: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:506: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:506: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:506: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:507: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:507: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:557: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:557: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:561: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:561: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:562: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:562: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:563: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:563: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:565: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:565: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:566: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:566: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:577: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:577: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:577: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:577: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:577: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:577: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:588: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:588: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:589: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:589: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:589: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:589: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:589: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:589: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:590: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:590: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:590: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:590: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:591: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:591: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:615: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:615: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:615: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:615: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:616: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:616: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:618: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:618: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:618: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:618: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:619: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:619: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:619: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:619: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:619: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:619: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:620: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:620: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:620: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:620: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:621: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:621: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:621: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:621: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:621: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:621: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:622: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:622: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:622: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:622: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:622: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:622: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:627: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:627: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:630: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:630: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:632: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:632: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:633: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:633: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:634: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:634: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:656: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:656: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:656: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:656: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:656: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:656: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:657: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:657: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:660: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:660: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:673: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:673: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:673: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:673: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:686: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:686: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:700: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:700: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:705: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:705: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:719: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:719: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:720: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:720: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:727: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:727: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:727: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:727: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:733: Warning: line too long ./Tutorial/chapter_searchio.tex:735: Warning: line too long ./Tutorial/chapter_searchio.tex:738: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:738: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:740: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:740: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:740: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:740: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:741: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:741: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:743: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:743: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:744: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:744: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:744: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:744: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:756: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:756: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:776: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:776: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:777: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:777: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:777: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:777: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:777: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:777: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:778: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:778: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:792: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:792: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:820: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:820: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:843: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:843: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:849: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:849: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:850: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:850: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:852: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:852: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:853: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:853: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:878: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:878: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:881: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:881: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:881: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:881: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:881: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:881: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:883: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:883: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:883: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:883: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:884: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:884: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:884: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:884: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:885: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:885: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:885: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:885: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:886: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:886: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:886: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:886: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:888: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:888: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:892: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:892: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:903: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:903: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:903: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:903: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:903: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:903: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:904: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:904: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:910: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:910: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:915: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:915: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:917: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:917: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:922: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:922: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:923: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:923: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:966: Warning: line too long ./Tutorial/chapter_searchio.tex:973: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:973: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:983: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:983: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:983: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:983: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:993: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:993: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:996: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:996: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1000: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1000: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1003: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1003: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1008: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1008: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1008: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1008: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1009: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1009: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1009: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1009: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1010: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1010: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1010: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1010: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1011: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1011: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1014: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1014: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1015: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1015: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1015: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1015: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1023: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1023: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1023: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1023: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1023: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1023: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1024: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1024: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1024: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1024: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1025: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1025: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1025: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1025: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1027: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1027: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1030: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1030: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1031: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1031: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1031: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1031: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1032: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1032: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1035: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1035: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1055: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1055: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1057: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1057: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1058: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1058: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1083: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1083: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1084: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1084: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1088: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1088: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1088: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1088: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1090: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1090: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1093: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1093: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1119: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1119: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1119: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1119: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1132: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1132: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1132: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1132: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1139: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1139: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1140: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1140: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1141: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1141: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1165: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1165: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1167: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1167: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1167: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1167: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1168: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1168: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1168: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1168: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1177: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1177: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1177: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1177: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1: Warning: line too long ./Tutorial/chapter_entrez.tex:1: Warning: line too long ./Tutorial/chapter_entrez.tex:1: Warning: line too long ./Tutorial/chapter_entrez.tex:1: Warning: line too long ./Tutorial/chapter_entrez.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:6: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:6: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:7: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:7: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:11: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:11: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:17: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:17: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:27: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:27: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:38: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:38: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:78: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:78: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:127: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:127: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:135: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:135: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:171: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:171: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:200: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:200: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:259: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:259: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:287: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:287: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:287: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:287: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:302: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:302: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:323: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:323: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:323: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:323: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:323: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:323: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:325: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:325: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:325: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:325: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:409: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:409: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:409: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:409: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:417: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:417: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:419: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:419: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:419: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:419: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:441: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:441: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:466: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:466: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:466: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:466: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:481: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:481: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:483: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:483: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:483: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:483: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:488: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:488: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:501: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:501: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:501: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:501: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:511: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:511: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:533: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:533: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:573: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:573: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:591: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:591: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:609: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:609: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:609: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:609: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:609: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:609: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:611: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:611: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:611: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:611: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:611: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:611: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:617: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:617: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:617: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:617: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:619: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:619: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:619: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:619: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:652: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:652: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:690: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:690: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:750: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:750: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:750: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:750: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:761: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:761: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:761: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:761: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:761: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:761: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:770: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:770: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:776: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:776: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:778: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:778: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:778: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:778: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:778: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:778: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:780: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:780: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:780: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:780: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:784: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:784: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:784: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:784: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:784: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:784: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:813: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:813: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:837: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:837: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:852: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:852: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:861: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:861: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:866: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:866: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:866: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:866: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:909: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:909: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:913: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:913: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:949: Warning: line too long ./Tutorial/chapter_entrez.tex:991: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:991: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:991: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:991: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:991: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:991: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:993: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:993: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1000: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1000: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1000: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1000: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1008: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1008: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1008: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1008: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1022: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1022: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1022: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1022: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1022: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1022: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1029: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1029: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1029: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1029: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1031: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1031: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1031: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1031: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1045: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1045: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1046: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1046: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1047: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1047: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1051: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1051: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1065: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1068: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1086: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1086: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1106: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1106: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1117: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1117: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1159: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1159: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1177: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1177: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1190: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1190: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1201: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1201: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1202: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1202: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1214: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1214: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1258: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1258: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1311: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1311: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1311: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1311: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1311: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1311: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1355: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1355: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1397: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1397: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1398: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1398: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1404: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1404: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1405: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1405: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1440: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1440: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1507: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1507: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:1: Warning: line too long ./Tutorial/chapter_uniprot.tex:8: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:8: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:31: Warning: line too long ./Tutorial/chapter_uniprot.tex:34: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:34: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:47: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:47: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:53: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:53: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:77: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:77: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:80: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:80: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:80: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:80: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:80: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:80: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:82: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:82: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:89: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:89: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:123: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:123: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:138: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:138: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:189: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:189: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:191: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:191: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:239: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:239: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:251: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:251: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:286: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:286: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:286: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:286: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:286: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:286: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:318: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:318: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:318: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:318: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:318: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:318: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:340: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:340: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:343: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:381: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:381: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:391: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:391: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:400: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:400: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:409: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:409: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:420: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:420: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:420: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:420: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:446: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:446: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:448: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:448: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:466: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:466: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:466: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:466: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:474: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:474: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:497: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:497: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:497: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:1: Warning: line too long ./Tutorial/chapter_pdb.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:25: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:25: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:86: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:86: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:86: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:86: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:113: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:113: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:113: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:113: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:113: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:113: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:115: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:115: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:116: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:116: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:116: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:116: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:116: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:116: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:118: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:118: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:118: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:118: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:118: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:118: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:121: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:121: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:122: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:122: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:125: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:125: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:201: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:201: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:202: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:202: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:203: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:203: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:204: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:204: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:288: Warning: Image in text ./Tutorial/chapter_pdb.tex:350: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:350: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:351: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:351: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:352: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:352: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:353: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:353: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:357: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:357: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:359: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:359: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:363: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:363: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:391: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:391: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:391: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:391: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:417: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:417: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:592: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:606: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:646: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:683: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:760: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:760: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:768: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:768: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:770: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:770: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:770: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:770: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:771: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:771: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:995: Warning: overfull line in array : array too wide ./Tutorial/chapter_pdb.tex:995: Warning: line too long ./Tutorial/chapter_pdb.tex:995: Warning: line too long ./Tutorial/chapter_pdb.tex:995: Warning: line too long ./Tutorial/chapter_pdb.tex:995: Warning: line too long ./Tutorial/chapter_pdb.tex:995: Warning: line too long ./Tutorial/chapter_pdb.tex:995: Warning: line too long ./Tutorial/chapter_pdb.tex:995: Warning: line too long ./Tutorial/chapter_pdb.tex:995: Warning: line too long ./Tutorial/chapter_pdb.tex:1124: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:1186: Warning: '_' occurring outside math mode ./Tutorial/chapter_popgen.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_popgen.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_popgen.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_popgen.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:34: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:34: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:70: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:70: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:96: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:96: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:107: Warning: Image in text ./Tutorial/chapter_phylo.tex:123: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:123: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:125: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:125: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:125: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:125: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:183: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:183: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:194: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:194: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:208: Warning: Image in text ./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:281: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:281: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:302: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:302: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:318: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:318: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:333: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:333: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:343: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:343: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:357: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:357: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:357: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:357: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:375: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:375: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:388: Warning: line too long ./Tutorial/chapter_phylo.tex:392: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:392: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:401: Warning: Image in text ./Tutorial/chapter_phylo.tex:417: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:417: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:423: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:423: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:423: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:423: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:423: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:423: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:424: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:424: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:424: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:424: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:425: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:425: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:426: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:426: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:427: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:427: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:428: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:428: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:428: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:428: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:430: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:430: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:430: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:430: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:431: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:431: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:432: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:432: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:432: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:432: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:434: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:434: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:435: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:435: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:435: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:435: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:435: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:435: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:451: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:451: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:452: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:452: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:452: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:452: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:462: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:462: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:483: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:483: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:484: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:484: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:484: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:484: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:510: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:510: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:523: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:523: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:524: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:524: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:526: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:526: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:535: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:535: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:545: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:545: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:549: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:549: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:586: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:586: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:612: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:612: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:613: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:613: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:617: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:617: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:648: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:648: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:669: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:669: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:673: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:673: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:701: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:701: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:719: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:719: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:720: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:720: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:748: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:748: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1: Warning: line too long ./Tutorial/chapter_motifs.tex:5: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:5: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:11: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:11: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:12: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:12: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:14: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:14: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:14: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:14: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:27: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:27: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:36: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:36: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:37: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:37: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:63: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:63: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:85: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:85: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:138: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:138: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:146: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:146: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:208: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:208: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:208: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:208: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:210: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:210: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:211: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:211: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:212: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:212: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:213: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:213: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:214: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:214: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:215: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:215: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:216: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:216: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:217: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:217: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:218: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:218: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:219: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:219: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:220: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:220: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:221: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:221: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:224: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:224: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:224: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:224: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:230: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:230: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:248: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:248: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:257: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:257: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:304: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:304: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:306: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:306: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:409: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:409: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:409: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:409: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:426: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:426: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:426: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:426: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:455: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:455: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:497: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:497: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:501: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:501: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:501: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:501: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:503: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:503: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:503: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:503: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:503: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:503: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:509: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:509: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:509: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:509: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:509: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:509: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:511: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:511: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:550: Warning: line too long ./Tutorial/chapter_motifs.tex:552: Warning: line too long ./Tutorial/chapter_motifs.tex:558: Warning: line too long ./Tutorial/chapter_motifs.tex:560: Warning: line too long ./Tutorial/chapter_motifs.tex:569: Warning: line too long ./Tutorial/chapter_motifs.tex:573: Warning: line too long ./Tutorial/chapter_motifs.tex:575: Warning: line too long ./Tutorial/chapter_motifs.tex:584: Warning: line too long ./Tutorial/chapter_motifs.tex:586: Warning: line too long ./Tutorial/chapter_motifs.tex:587: Warning: line too long ./Tutorial/chapter_motifs.tex:589: Warning: line too long ./Tutorial/chapter_motifs.tex:595: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:595: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:603: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:603: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:604: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:604: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:620: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:620: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:621: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:621: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:657: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:657: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:710: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:710: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:712: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:712: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:743: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:743: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:743: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:743: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:743: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:743: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:747: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:747: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:749: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:749: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:757: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:757: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:757: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:757: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:758: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:758: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:779: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:779: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:780: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:780: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:781: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:781: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:782: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:782: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:783: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:783: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:784: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:784: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:785: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:785: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:786: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:786: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:787: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:787: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:788: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:788: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:789: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:789: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:790: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:790: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:791: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:791: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:792: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:792: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:793: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:793: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:794: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:794: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:795: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:795: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:796: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:796: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:797: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:797: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:798: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:798: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:803: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:803: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:810: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:810: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:811: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:811: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:812: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:812: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:813: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:813: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:814: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:814: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:873: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:873: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:873: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:873: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:882: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:882: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:882: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:882: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:942: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:942: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:960: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:960: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:974: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:974: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:987: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:987: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1025: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1025: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1044: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1044: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1065: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1065: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1082: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1082: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1082: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1082: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1093: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1093: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1093: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1093: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1102: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1102: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1110: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1110: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1167: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1167: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1168: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1168: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1169: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1169: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1189: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1189: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1214: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1214: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1313: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1313: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1344: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1344: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1344: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1344: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1344: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1344: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1371: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1371: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1371: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1371: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1384: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1384: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1421: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1421: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1421: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1421: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1446: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1446: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1465: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1465: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1492: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1492: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1492: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1492: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1497: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1497: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1504: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1504: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1513: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1513: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1530: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1530: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1531: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1531: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1532: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1532: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1533: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1533: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1534: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1534: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1565: Warning: '_' occurring outside math mode ./Tutorial/chapter_motifs.tex:1566: Warning: '_' occurring outside math mode ./Tutorial/chapter_motifs.tex:1566: Warning: '_' occurring outside math mode ./Tutorial/chapter_motifs.tex:1567: Warning: '_' occurring outside math mode ./Tutorial/chapter_cluster.tex:6: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:6: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:6: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:6: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:8: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:8: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:35: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:35: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:37: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:37: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:39: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:39: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:41: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:41: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:43: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:43: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:47: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:47: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:49: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:49: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:51: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:51: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:68: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:68: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:76: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:76: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:84: Warning: Application of '\=' on 'x' failed ./Tutorial/chapter_cluster.tex:84: Warning: Application of '\=' on 'y' failed ./Tutorial/chapter_cluster.tex:86: Warning: Application of '\=' on 'x' failed ./Tutorial/chapter_cluster.tex:86: Warning: Application of '\=' on 'y' failed ./Tutorial/chapter_cluster.tex:112: Warning: Undefined block in text mode: 'DIV' [class="equationcontainer"] ./Tutorial/chapter_cluster.tex:115: Warning: Undefined block in text mode: 'DIV' [] ./Tutorial/chapter_cluster.tex:117: Warning: Application of '\=' on 'x' failed ./Tutorial/chapter_cluster.tex:117: Warning: Application of '\=' on 'y' failed ./Tutorial/chapter_cluster.tex:162: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:162: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:167: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:167: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:167: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:167: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:167: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:167: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:174: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:174: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:176: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:176: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:176: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:176: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:178: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:178: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:178: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:178: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:179: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:179: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:179: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:179: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:180: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:180: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:180: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:180: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:182: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:182: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:182: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:182: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:225: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:225: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:225: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:225: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:233: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:233: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:235: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:235: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:235: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:235: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:237: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:237: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:237: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:237: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:238: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:238: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:238: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:238: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:239: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:239: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:239: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:239: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:240: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:240: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:240: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:240: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:241: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:241: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:241: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:241: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:258: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:258: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:262: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:262: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:262: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:262: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:263: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:263: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:263: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:263: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:264: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:264: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:264: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:264: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:265: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:265: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:265: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:265: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:266: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:266: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:266: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:266: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:267: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:267: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:267: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:267: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:268: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:268: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:268: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:268: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:271: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:271: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:272: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:272: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:273: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:273: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:274: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:274: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:275: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:275: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:277: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:277: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:277: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:277: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:279: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:279: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:279: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:279: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:280: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:280: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:280: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:280: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:280: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:280: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:281: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:281: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:281: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:281: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:281: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:281: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:288: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:288: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:318: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:318: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:318: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:318: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:326: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:326: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:328: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:328: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:328: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:328: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:330: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:330: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:330: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:330: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:332: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:332: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:332: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:332: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:333: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:333: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:333: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:333: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:334: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:334: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:334: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:334: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:336: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:336: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:336: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:336: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:337: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:337: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:337: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:337: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:338: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:338: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:338: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:338: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:341: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:341: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:342: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:342: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:344: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:344: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:345: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:345: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:345: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:345: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:347: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:347: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:348: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:348: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:348: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:348: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:356: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:356: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:365: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:365: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:382: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:382: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:382: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:382: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:384: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:384: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:384: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:384: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:385: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:385: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:385: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:385: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:386: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:386: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:386: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:386: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:398: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:398: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:417: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:417: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:417: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:417: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:417: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:417: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:419: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:419: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:420: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:420: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:421: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:421: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:423: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:423: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:423: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:423: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:423: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:423: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:447: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:447: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:447: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:447: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:447: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:447: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:449: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:449: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:449: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:449: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:449: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:449: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:463: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:463: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:474: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:474: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:488: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:488: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:488: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:488: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:507: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:507: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:509: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:509: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:509: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:509: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:513: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:513: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:515: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:515: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:519: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:519: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:521: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:521: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:525: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:525: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:525: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:525: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:527: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:527: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:531: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:531: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:531: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:531: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:539: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:539: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:541: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:541: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:541: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:541: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:543: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:543: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:543: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:543: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:544: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:544: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:544: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:544: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:545: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:545: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:545: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:545: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:547: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:547: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:547: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:547: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:550: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:550: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:551: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:551: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:552: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:552: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:553: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:553: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:555: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:555: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:555: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:555: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:566: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:566: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:583: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:583: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:583: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:583: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:584: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:584: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:587: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:587: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:588: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:588: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:589: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:589: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:607: Warning: Cannot output that numerical entity: U+00B7 ./Tutorial/chapter_cluster.tex:611: Warning: Cannot output that numerical entity: U+00B7 ./Tutorial/chapter_cluster.tex:616: Warning: Cannot output that numerical entity: U+00B7 ./Tutorial/chapter_cluster.tex:623: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:623: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:625: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:625: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:632: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:632: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:634: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:634: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:634: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:634: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:636: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:636: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:636: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:636: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:637: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:637: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:637: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:637: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:638: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:638: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:638: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:638: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:640: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:640: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:640: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:640: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:642: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:642: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:642: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:642: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:643: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:643: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:644: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:644: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:644: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:644: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:646: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:646: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:646: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:646: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:650: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:650: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:652: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:652: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:654: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:654: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:670: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:670: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:675: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:675: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:677: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:677: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:678: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:678: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:679: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:679: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:680: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:680: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:681: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:681: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:683: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:683: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:686: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:686: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:686: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:686: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:690: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:690: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:692: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:692: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:692: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:692: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:711: Warning: line too long ./Tutorial/chapter_cluster.tex:714: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:714: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:716: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:716: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:716: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:716: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:749: Warning: overfull line in array : array too wide ./Tutorial/chapter_cluster.tex:749: Warning: line too long ./Tutorial/chapter_cluster.tex:749: Warning: line too long ./Tutorial/chapter_cluster.tex:755: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:755: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:758: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:758: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:761: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:761: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:764: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:764: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:767: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:767: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:768: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:768: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:768: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:768: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:770: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:770: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:771: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:771: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:771: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:771: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:774: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:774: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:774: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:774: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:776: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:776: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:779: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:779: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:780: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:780: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:780: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:780: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:782: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:782: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:783: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:783: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:783: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:783: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:785: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:785: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:789: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:789: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:789: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:789: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:799: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:799: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:799: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:799: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:801: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:801: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:801: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:801: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:815: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:815: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:815: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:815: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:816: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:816: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:817: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:817: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:817: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:817: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:818: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:818: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:818: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:818: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:819: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:819: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:819: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:819: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:823: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:823: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:832: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:832: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:832: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:832: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:833: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:833: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:833: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:833: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:834: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:834: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:834: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:834: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:835: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:835: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:835: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:835: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:836: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:836: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:836: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:836: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:839: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:839: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:840: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:840: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:841: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:841: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:842: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:842: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:843: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:843: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:845: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:845: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:845: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:845: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:847: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:847: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:847: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:847: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:848: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:848: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:848: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:848: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:848: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:848: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:849: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:849: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:849: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:849: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:849: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:849: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:860: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:860: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:860: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:860: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:862: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:862: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:862: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:862: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:865: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:865: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:866: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:866: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:867: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:867: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:868: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:868: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:870: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:870: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:870: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:870: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:872: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:872: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:886: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:886: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:886: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:886: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:888: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:888: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:888: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:888: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:890: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:890: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:890: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:890: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:891: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:891: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:891: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:891: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:892: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:892: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:892: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:892: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:895: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:895: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:896: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:896: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:898: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:898: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:899: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:899: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:899: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:899: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:913: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:913: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:913: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:913: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:915: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:915: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:915: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:915: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:917: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:917: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:917: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:917: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:918: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:918: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:919: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:919: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:919: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:919: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:921: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:921: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:921: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:921: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:925: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:925: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:927: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:927: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:929: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:929: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:941: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:941: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:942: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:942: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:943: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:943: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:944: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:944: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:944: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:944: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:944: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:944: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:945: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:945: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:946: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:946: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:946: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:946: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:946: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:946: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:952: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:952: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:952: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:952: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:954: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:954: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:954: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:954: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:971: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:971: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:971: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:971: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:971: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:971: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:986: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:986: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:986: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:986: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:986: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:986: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:26: Warning: Undefined block in text mode: 'DIV' [class="equationcontainer"] ./Tutorial/chapter_learning.tex:28: Warning: Undefined block in text mode: 'SPAN' [class="equationnumber"] ./Tutorial/chapter_learning.tex:28: Warning: Undefined block in text mode: 'SPAN' [] ./Tutorial/chapter_learning.tex:28: Warning: Undefined block in text mode: 'DIV' [] ./Tutorial/chapter_learning.tex:36: Warning: Undefined block in text mode: 'DIV' [class="equationcontainer"] ./Tutorial/chapter_learning.tex:37: Warning: Undefined block in text mode: 'SPAN' [class="equationnumber-valign"] ./Tutorial/chapter_learning.tex:37: Warning: Undefined block in text mode: 'SPAN' [] ./Tutorial/chapter_learning.tex:39: Warning: Undefined block in text mode: 'SPAN' [class="equationnumber-valign"] ./Tutorial/chapter_learning.tex:39: Warning: Undefined block in text mode: 'SPAN' [] ./Tutorial/chapter_learning.tex:39: Warning: overfull line in array : array too wide ./Tutorial/chapter_learning.tex:39: Warning: overfull line in array : array too wide ./Tutorial/chapter_learning.tex:39: Warning: Undefined block in text mode: 'DIV' [] ./Tutorial/chapter_learning.tex:70: Warning: overfull line in array : array too wide ./Tutorial/chapter_learning.tex:70: Warning: line too long ./Tutorial/chapter_learning.tex:70: Warning: line too long ./Tutorial/chapter_learning.tex:70: Warning: line too long ./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:168: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:168: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:197: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:197: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:273: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:273: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:289: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:289: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:289: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:289: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:289: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:289: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:302: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:302: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:330: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:330: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:337: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:337: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:337: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:337: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:397: Warning: Application of '\"' on 'i' failed ./Tutorial/chapter_learning.tex:399: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:399: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:403: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:403: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:407: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:407: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:407: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:407: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:16: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:16: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:34: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:34: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:35: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:35: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:63: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:63: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:68: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:89: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:89: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:90: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:90: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:105: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:105: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:106: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:106: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:132: Warning: Image in text ./Tutorial/chapter_graphics.tex:132: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:144: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:144: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:163: Warning: Image in text ./Tutorial/chapter_graphics.tex:163: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:212: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:212: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:212: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:212: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:219: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:219: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:219: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:219: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:221: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:221: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:223: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:223: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:268: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:268: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:271: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:271: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:277: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:277: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:279: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:279: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:325: Warning: Image in text ./Tutorial/chapter_graphics.tex:325: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:325: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:326: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:326: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:352: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:396: Warning: Image in text ./Tutorial/chapter_graphics.tex:396: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:409: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:409: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:430: Warning: Image in text ./Tutorial/chapter_graphics.tex:430: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:430: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:430: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:459: Warning: Image in text ./Tutorial/chapter_graphics.tex:459: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:459: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:459: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:473: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:473: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:482: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:482: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:482: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:482: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:485: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:485: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:564: Warning: Image in text ./Tutorial/chapter_graphics.tex:564: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:564: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:566: Warning: Image in text ./Tutorial/chapter_graphics.tex:566: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:566: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:591: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:591: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:599: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:599: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:600: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:600: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:601: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:601: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:728: Warning: Image in text ./Tutorial/chapter_graphics.tex:728: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:728: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:752: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:752: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:841: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:841: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:843: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:843: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:843: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:843: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:843: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:873: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:873: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:874: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:874: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:874: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:874: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:875: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:875: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:876: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:876: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:890: Warning: Image in text ./Tutorial/chapter_graphics.tex:890: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:890: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:914: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:914: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:923: Warning: Image in text ./Tutorial/chapter_graphics.tex:923: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:923: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:953: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:953: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:954: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:954: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:1004: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:1004: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:1006: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:1006: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:1011: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:1011: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:1035: Warning: line too long ./Tutorial/chapter_graphics.tex:1036: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:1036: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:1057: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:1057: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:1110: Warning: Image in text ./Tutorial/chapter_graphics.tex:1110: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:1125: Warning: line too long ./Tutorial/chapter_graphics.tex:1190: Warning: Image in text ./Tutorial/chapter_graphics.tex:1190: Warning: '_' occurring outside math mode ./Tutorial/chapter_kegg.tex:1: Warning: line too long ./Tutorial/chapter_kegg.tex:1: Warning: line too long ./Tutorial/chapter_kegg.tex:1: Warning: line too long ./Tutorial/chapter_kegg.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_kegg.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_kegg.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_kegg.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phenotype.tex:5: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phenotype.tex:5: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phenotype.tex:10: Warning: '_' occurring outside math mode ./Tutorial/chapter_phenotype.tex:16: Warning: '_' occurring outside math mode ./Tutorial/chapter_phenotype.tex:30: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phenotype.tex:30: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phenotype.tex:32: Warning: '_' occurring outside math mode ./Tutorial/chapter_phenotype.tex:231: Warning: Optional argument to \item in itemize environment ./Tutorial/chapter_phenotype.tex:233: Warning: Optional argument to \item in itemize environment ./Tutorial/chapter_phenotype.tex:235: Warning: Optional argument to \item in itemize environment ./Tutorial/chapter_cookbook.tex:1: Warning: line too long ./Tutorial/chapter_cookbook.tex:1: Warning: line too long ./Tutorial/chapter_cookbook.tex:1: Warning: line too long ./Tutorial/chapter_cookbook.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:55: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:55: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:55: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:55: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:60: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:60: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:103: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:105: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:105: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:105: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:105: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:115: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:115: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:116: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:116: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:125: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:125: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:126: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:126: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:126: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:126: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:145: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:145: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:201: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:201: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:202: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:202: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:202: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:202: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:205: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:205: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:207: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:207: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:208: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:208: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:243: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:243: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:252: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:252: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:253: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:253: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:263: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:263: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:267: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:267: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:280: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:280: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:283: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:283: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:310: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:310: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:326: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:326: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:329: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:329: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:330: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:330: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:333: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:333: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:334: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:334: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:334: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:334: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:335: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:335: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:337: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:337: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:337: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:337: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:357: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:357: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:357: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:357: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:359: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:359: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:391: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:391: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:391: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:391: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:397: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:397: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:439: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:439: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:442: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:442: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:452: Warning: line too long ./Tutorial/chapter_cookbook.tex:454: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:454: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:456: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:456: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:459: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:459: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:460: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:460: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:461: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:461: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:480: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:480: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:561: Warning: line too long ./Tutorial/chapter_cookbook.tex:593: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:593: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:595: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:595: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:644: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:644: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:655: Warning: Undefined block in text mode: 'DIV' [class="equationcontainer"] ./Tutorial/chapter_cookbook.tex:657: Warning: Undefined block in text mode: 'SPAN' [class="equationnumber"] ./Tutorial/chapter_cookbook.tex:657: Warning: Undefined block in text mode: 'SPAN' [] ./Tutorial/chapter_cookbook.tex:657: Warning: Undefined block in text mode: 'DIV' [] ./Tutorial/chapter_cookbook.tex:675: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:675: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:686: Warning: Undefined block in text mode: 'DIV' [class="equationcontainer"] ./Tutorial/chapter_cookbook.tex:688: Warning: Undefined block in text mode: 'SPAN' [class="equationnumber"] ./Tutorial/chapter_cookbook.tex:688: Warning: Undefined block in text mode: 'SPAN' [] ./Tutorial/chapter_cookbook.tex:688: Warning: Undefined block in text mode: 'DIV' [] ./Tutorial/chapter_cookbook.tex:694: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:694: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:695: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:695: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:714: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:714: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:715: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:715: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:715: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:715: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:759: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:759: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:764: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:764: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:764: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:764: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:766: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:766: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:777: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:777: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:796: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:796: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:799: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:799: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:804: Warning: line too long ./Tutorial/chapter_cookbook.tex:821: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:821: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:826: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:826: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:839: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:839: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:904: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:915: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:915: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:915: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:915: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1031: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1031: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1041: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1041: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1042: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1042: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1053: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1056: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1056: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1094: Warning: Image in text ./Tutorial/chapter_cookbook.tex:1094: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1117: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1117: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1118: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1118: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1127: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1129: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1129: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1163: Warning: Image in text ./Tutorial/chapter_cookbook.tex:1163: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1211: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1242: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1242: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1265: Warning: Image in text ./Tutorial/chapter_cookbook.tex:1265: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1287: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1287: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1308: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1308: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1341: Warning: Image in text ./Tutorial/chapter_cookbook.tex:1341: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1341: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1363: Warning: line too long ./Tutorial/chapter_cookbook.tex:1364: Warning: line too long ./Tutorial/chapter_cookbook.tex:1369: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1369: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1391: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1391: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1397: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1397: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1398: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1398: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1412: Warning: Image in text ./Tutorial/chapter_cookbook.tex:1421: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1425: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1425: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1425: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1425: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1433: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1433: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1451: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1451: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1453: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1453: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1484: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1484: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1491: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1491: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1511: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1511: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1513: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1513: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1528: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1528: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1538: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1538: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1565: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1565: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1571: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1571: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1582: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1582: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1584: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1584: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1592: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1592: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1617: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1626: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1626: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1642: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1642: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1743: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1748: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1748: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:1: Warning: line too long ./Tutorial/chapter_testing.tex:1: Warning: line too long ./Tutorial/chapter_testing.tex:1: Warning: line too long ./Tutorial/chapter_testing.tex:1: Warning: line too long ./Tutorial/chapter_testing.tex:1: Warning: line too long ./Tutorial/chapter_testing.tex:1: Warning: line too long ./Tutorial/chapter_testing.tex:5: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:5: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:34: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:34: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:48: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:48: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:62: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:62: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:68: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:68: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:73: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:73: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:74: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:74: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:74: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:74: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:75: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:75: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:111: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:111: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:120: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:120: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:121: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:121: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:145: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:145: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:150: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:150: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:154: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:154: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:154: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:154: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:189: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:189: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:193: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:193: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:195: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:195: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:195: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:195: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:197: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:197: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:198: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:198: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:201: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:201: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:212: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:212: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:222: Warning: line too long ./Tutorial/chapter_testing.tex:275: Warning: line too long ./Tutorial/chapter_testing.tex:284: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:284: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:297: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:297: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:301: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:301: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:311: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:311: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:313: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:313: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:318: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:318: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:319: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:319: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:354: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:354: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:355: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:355: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:371: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:371: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:373: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:373: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:389: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:389: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:400: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:400: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:401: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:401: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:402: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:402: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:403: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:403: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:403: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:403: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:404: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:404: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:407: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:407: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:409: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:409: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_contributing.tex:11: Warning: '_' occurring outside math mode ./Tutorial/chapter_contributing.tex:38: Warning: '_' occurring outside math mode ./Tutorial/chapter_contributing.tex:68: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_contributing.tex:68: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_contributing.tex:80: Warning: '_' occurring outside math mode ./Tutorial/chapter_appendix.tex:35: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_appendix.tex:35: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_appendix.tex:37: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_appendix.tex:37: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_appendix.tex:38: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_appendix.tex:38: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_appendix.tex:41: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_appendix.tex:41: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_appendix.tex:53: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_appendix.tex:53: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_appendix.tex:54: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_appendix.tex:54: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_appendix.tex:98: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_appendix.tex:98: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial.tex:126: Warning: line too long ./Tutorial.tex:137: Warning: Application of '\'' on 'e' failed ./Tutorial.tex:137: Warning: Application of '\'' on 'o' failed ./Tutorial.tex:141: Warning: Application of '\"' on 'u' failed ./Tutorial.tex:215: Warning: Application of '\"' on 'o' failed ./Tutorial.tex:215: Warning: Application of '\"' on 'u' failed HeVeA Warning: Label(s) may have changed. Rerun me to get cross-references right. Run, run, again... Exclude comment 'comment' ./Tutorial.tex:73: Warning: tt_mode is an empty style ./Tutorial.haux:561: Giving up command: \@hevea@cbrace ./Tutorial.tex:73: Giving up command: \input ./Tutorial.tex:73: Warning: Failure while reading .haux ./Tutorial.tex:100: Warning: Application of '\'' on 'n' failed ./Tutorial/chapter_introduction.tex:82: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:82: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:91: Warning: Undefined citation: 'cock2009' ./Tutorial/chapter_introduction.tex:95: Warning: Undefined citation: 'chapman2000' ./Tutorial/chapter_introduction.tex:96: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:96: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:96: Warning: Undefined citation: 'hamelryck2003a' ./Tutorial/chapter_introduction.tex:97: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:97: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:97: Warning: Undefined citation: 'dehoon2004' ./Tutorial/chapter_introduction.tex:98: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:98: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:98: Warning: Undefined citation: 'pritchard2006' ./Tutorial/chapter_introduction.tex:99: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:99: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:99: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:99: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:99: Warning: Undefined citation: 'talevich2012' ./Tutorial/chapter_introduction.tex:100: Warning: Undefined citation: 'cock2010' ./Tutorial/chapter_introduction.tex:138: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:138: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:139: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:139: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:152: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:152: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:156: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:156: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:161: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:161: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:162: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:162: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:176: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:176: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:177: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:177: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:178: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:178: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:182: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:182: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:185: Warning: Undefined label: 'sec:seq-comparison' ./Tutorial/chapter_introduction.tex:187: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:187: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:187: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:187: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:191: Warning: Undefined label: 'sec:appendix-handles' ./Tutorial/chapter_introduction.tex:194: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:194: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:194: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:194: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:195: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:195: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:197: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:197: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:197: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:197: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:200: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:200: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:205: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:205: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:207: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:207: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:212: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:212: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:216: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:216: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:219: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:219: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:222: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:222: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:222: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:222: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:223: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:223: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:226: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:226: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:229: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:229: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:229: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:229: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:229: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:229: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:231: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:231: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:14: Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_quick_start.tex:14: Warning: Undefined label: 'chapter:advanced' ./Tutorial/chapter_quick_start.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:19: Warning: Undefined label: 'chapter:seq_objects' ./Tutorial/chapter_quick_start.tex:21: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:21: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:21: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:21: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:21: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:21: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:33: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:33: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:45: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_quick_start.tex:65: Warning: Undefined label: 'sec:sequence-parsing' ./Tutorial/chapter_quick_start.tex:65: Warning: Undefined label: 'chapter:entrez' ./Tutorial/chapter_quick_start.tex:65: Warning: Undefined label: 'chapter:uniprot' ./Tutorial/chapter_quick_start.tex:65: Warning: Undefined label: 'sec:align_clustal' ./Tutorial/chapter_quick_start.tex:72: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:72: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:72: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_quick_start.tex:74: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:74: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:79: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:79: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:79: Warning: Undefined label: 'sec:connecting-with-biological-databases' ./Tutorial/chapter_quick_start.tex:84: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:93: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:93: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:118: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:141: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:141: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:145: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_quick_start.tex:145: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:145: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:145: Warning: Undefined label: 'chapter:align' ./Tutorial/chapter_quick_start.tex:145: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:145: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:147: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:147: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:147: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:147: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:150: Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_quick_start.tex:158: Warning: Undefined label: 'chapter:entrez' ./Tutorial/chapter_quick_start.tex:159: Warning: Undefined label: 'chapter:uniprot' ./Tutorial/chapter_quick_start.tex:160: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:160: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:169: Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_seq_objects.tex:1: Warning: line too long ./Tutorial/chapter_seq_objects.tex:1: Warning: line too long ./Tutorial/chapter_seq_objects.tex:1: Warning: line too long ./Tutorial/chapter_seq_objects.tex:1: Warning: line too long ./Tutorial/chapter_seq_objects.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_objects.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined label: 'chapter:seq_annot' ./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_objects.tex:7: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:7: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:9: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:9: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:44: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:44: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:44: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:44: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:73: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:73: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:84: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:84: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:86: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:86: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:86: Warning: Undefined label: 'sec:mutable-seq' ./Tutorial/chapter_seq_objects.tex:86: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:86: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:133: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:133: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:133: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:133: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:155: Warning: Undefined label: 'sec:SeqRecord-format' ./Tutorial/chapter_seq_objects.tex:156: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:156: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:157: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_objects.tex:161: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:161: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:197: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:197: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:197: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:197: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:210: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:210: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:210: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:210: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:239: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:239: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:253: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:253: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:278: Warning: Undefined label: 'sec:SeqIO-reverse-complement' ./Tutorial/chapter_seq_objects.tex:278: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:278: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:279: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:279: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:296: Warning: Command not found: \downarrow ./Tutorial/chapter_seq_objects.tex:305: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:305: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:319: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:319: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:319: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:319: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:339: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:339: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:351: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:351: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:351: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:351: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:351: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:351: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:352: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:352: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:353: Warning: Undefined label: 'sec:seq-module-functions' ./Tutorial/chapter_seq_objects.tex:359: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:359: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:416: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:416: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:433: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:433: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:469: Warning: Undefined label: 'sec:SeqIO-translate' ./Tutorial/chapter_seq_objects.tex:469: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:469: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:470: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:470: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:474: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:474: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:474: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:474: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:475: Warning: Undefined label: 'sec:seq-module-functions' ./Tutorial/chapter_seq_objects.tex:577: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:577: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:598: Warning: Undefined label: 'sec:seq-to-string' ./Tutorial/chapter_seq_objects.tex:602: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:602: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:602: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:602: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:610: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:610: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:610: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:610: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:641: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:641: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:641: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:641: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:675: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:675: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:675: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:675: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:692: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:692: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:702: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:702: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:727: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:727: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:727: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:727: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:727: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:727: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:729: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:729: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:729: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:729: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:731: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:731: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:731: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:731: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:741: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:741: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:741: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:741: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:741: Warning: Undefined label: 'sec:seq-to-string' ./Tutorial/chapter_seq_objects.tex:747: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:747: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:748: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:748: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:748: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:748: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:764: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:764: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined label: 'chapter:seq_objects' ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined label: 'chapter:seq_objects' ./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_annot.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:25: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:25: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:33: Warning: Undefined label: 'sec:FASTQ-filtering-example' ./Tutorial/chapter_seq_annot.tex:37: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:37: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:37: Warning: Undefined label: 'sec:seq_features' ./Tutorial/chapter_seq_annot.tex:44: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:44: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:46: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:46: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:46: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:46: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:47: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_annot.tex:48: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:48: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:52: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:52: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:52: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:52: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:76: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:76: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:86: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:86: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:86: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:86: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:99: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:99: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:112: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:112: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:112: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:112: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:113: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:113: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:120: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_annot.tex:130: Warning: Undefined label: 'chapter:quick_start' ./Tutorial/chapter_seq_annot.tex:130: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:130: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:131: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:131: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:131: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:131: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:132: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_annot.tex:139: Warning: line too long ./Tutorial/chapter_seq_annot.tex:142: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:142: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:143: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:143: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:144: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:144: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:165: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:165: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:197: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_annot.tex:211: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:211: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:211: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_annot.tex:218: Warning: line too long ./Tutorial/chapter_seq_annot.tex:227: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:227: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:227: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:227: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:248: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:248: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:258: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:258: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:266: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:266: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:266: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:266: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:274: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:274: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:275: Warning: Undefined label: 'sec:seq_features' ./Tutorial/chapter_seq_annot.tex:278: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_annot.tex:282: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:282: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:284: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:284: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:284: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:284: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:284: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:286: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:286: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:291: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:291: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:292: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:293: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:293: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:298: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:298: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:301: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:301: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:302: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:302: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:304: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:304: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:313: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:313: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:320: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:320: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:327: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:327: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:328: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:328: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:338: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:338: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:340: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:340: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:350: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:350: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:371: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:371: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:375: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:375: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:377: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:377: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:380: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:380: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:382: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:382: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:383: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:383: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:384: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:384: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:420: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:420: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:453: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:453: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:453: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:453: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:472: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:472: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:472: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:472: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:502: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:502: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:502: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:508: Warning: line too long ./Tutorial/chapter_seq_annot.tex:522: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:522: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:522: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:522: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:531: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:531: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:544: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:544: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:544: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:544: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:548: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:548: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:566: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:566: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:566: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:566: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:567: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:567: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:568: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:568: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:568: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:568: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:577: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:577: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:577: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:577: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:600: Warning: Undefined label: 'sec:seq-comparison' ./Tutorial/chapter_seq_annot.tex:604: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:604: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:608: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:608: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:608: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:608: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:608: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:610: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:610: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:610: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:610: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:616: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:616: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:616: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:616: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:618: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:618: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:647: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:647: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:648: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:648: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:648: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_annot.tex:649: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:649: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:651: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:651: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:651: Warning: Undefined label: 'sec:Bio.SeqIO-and-StringIO' ./Tutorial/chapter_seq_annot.tex:656: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:656: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:656: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:656: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:668: Warning: line too long ./Tutorial/chapter_seq_annot.tex:675: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:675: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:675: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:675: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:683: Warning: line too long ./Tutorial/chapter_seq_annot.tex:704: Warning: line too long ./Tutorial/chapter_seq_annot.tex:704: Warning: line too long ./Tutorial/chapter_seq_annot.tex:708: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:708: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:715: Warning: line too long ./Tutorial/chapter_seq_annot.tex:722: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:722: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:725: Warning: line too long ./Tutorial/chapter_seq_annot.tex:746: Warning: line too long ./Tutorial/chapter_seq_annot.tex:746: Warning: line too long ./Tutorial/chapter_seq_annot.tex:793: Warning: Undefined label: 'sec:SeqRecord-format' ./Tutorial/chapter_seq_annot.tex:805: Warning: Undefined label: 'sec:FASTQ-slicing-off-primer' ./Tutorial/chapter_seq_annot.tex:806: Warning: Undefined label: 'sec:FASTQ-slicing-off-adaptor' ./Tutorial/chapter_seq_annot.tex:812: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:812: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:812: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:812: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:819: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_annot.tex:819: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:819: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:835: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:835: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:880: Warning: line too long ./Tutorial/chapter_seq_annot.tex:897: Warning: line too long ./Tutorial/chapter_seq_annot.tex:916: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:916: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:938: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:938: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:939: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:939: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:951: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:951: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:954: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:954: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:954: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:954: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:956: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:956: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:956: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:956: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1: Warning: line too long ./Tutorial/chapter_seqio.tex:1: Warning: line too long ./Tutorial/chapter_seqio.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:4: Warning: Undefined label: 'chapter:quick_start' ./Tutorial/chapter_seqio.tex:4: Warning: Undefined label: 'chapter:seq_annot' ./Tutorial/chapter_seqio.tex:5: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:5: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:12: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:12: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:12: Warning: Undefined label: 'chapter:seq_annot' ./Tutorial/chapter_seqio.tex:12: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:12: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:12: Warning: Undefined label: 'chapter:seq_objects' ./Tutorial/chapter_seqio.tex:14: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:14: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:14: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:14: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:14: Warning: Undefined label: 'sec:low-level-fasta-fastq' ./Tutorial/chapter_seqio.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:22: Warning: Undefined label: 'sec:SeqIO_Online' ./Tutorial/chapter_seqio.tex:22: Warning: Undefined label: 'sec:appendix-handles' ./Tutorial/chapter_seqio.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:28: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:28: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:28: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:28: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:32: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:32: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:32: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:32: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:43: Warning: Undefined label: 'sec:sequence-parsing' ./Tutorial/chapter_seqio.tex:43: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:43: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:54: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:54: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:67: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:67: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:68: Warning: Undefined label: 'sec:sequence-parsing-plus-pylab' ./Tutorial/chapter_seqio.tex:75: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:75: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:75: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:75: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:77: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:77: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:93: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:93: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:93: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:93: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:103: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:103: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:104: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:104: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:145: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:145: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:149: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:149: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:150: Warning: Undefined label: 'chapter:seq_annot' ./Tutorial/chapter_seqio.tex:150: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:180: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:180: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:198: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:248: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:257: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:257: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:290: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:290: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:291: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:291: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:306: Warning: Undefined label: 'sec:writing-sequence-files' ./Tutorial/chapter_seqio.tex:307: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:307: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:307: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:307: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:308: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:308: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:309: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:309: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:326: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:328: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:328: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:329: Warning: Undefined label: 'sec:appendix-handles' ./Tutorial/chapter_seqio.tex:332: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:332: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:333: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:333: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:345: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:345: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:370: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:370: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:398: Warning: Undefined label: 'sec:SeqIO-index-bgzf' ./Tutorial/chapter_seqio.tex:401: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:404: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:404: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:413: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:413: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:414: Warning: Undefined label: 'sec:efetch' ./Tutorial/chapter_seqio.tex:421: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:421: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:448: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:448: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:471: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:471: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:504: Warning: Undefined label: 'chapter:entrez' ./Tutorial/chapter_seqio.tex:504: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:504: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:504: Warning: Undefined label: 'sec:entrez-guidelines' ./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:509: Warning: Undefined label: 'chapter:uniprot' ./Tutorial/chapter_seqio.tex:511: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:511: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:540: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:540: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:540: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:540: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:550: Warning: line too long ./Tutorial/chapter_seqio.tex:560: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:560: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:564: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:564: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:565: Warning: Undefined label: 'sec:seqio_todict' ./Tutorial/chapter_seqio.tex:566: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:566: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:567: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:567: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:569: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:569: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:570: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:570: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:571: Warning: Undefined label: 'sec:SeqIO-index' ./Tutorial/chapter_seqio.tex:572: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:572: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:575: Warning: Undefined label: 'sec:SeqIO-index-db' ./Tutorial/chapter_seqio.tex:578: Warning: Undefined label: 'sec:SeqIO-indexing-discussion' ./Tutorial/chapter_seqio.tex:581: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:584: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:584: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:588: Warning: Undefined label: 'sec:SeqIO-index' ./Tutorial/chapter_seqio.tex:590: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:590: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:591: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:591: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:600: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:600: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:601: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:601: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:602: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:602: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:605: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:605: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:627: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:627: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:640: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:640: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:661: Warning: Undefined label: 'sec:fasta-parsing' ./Tutorial/chapter_seqio.tex:661: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:661: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:661: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:661: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:663: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:663: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:676: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:676: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:698: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:698: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:742: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:742: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:747: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:747: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:778: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:778: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:781: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:781: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:783: Warning: Undefined label: 'sec:fastq-indexing' ./Tutorial/chapter_seqio.tex:804: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:804: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:804: Warning: Undefined label: 'sec:seqio-todict-functionkey' ./Tutorial/chapter_seqio.tex:819: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:819: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:834: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:834: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:835: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:835: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:837: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:837: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:842: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:842: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:850: Warning: line too long ./Tutorial/chapter_seqio.tex:851: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:851: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:864: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:864: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:866: Warning: Undefined label: 'sec:SeqIO-sort' ./Tutorial/chapter_seqio.tex:867: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:867: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:873: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:873: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:879: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:879: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:885: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:885: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:934: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:934: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:947: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:947: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:948: Warning: Undefined label: 'sec:seqio-index-getraw' ./Tutorial/chapter_seqio.tex:976: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:976: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:978: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:978: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:979: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:979: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:979: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:979: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:982: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:982: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:982: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:982: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1026: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1026: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1034: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1034: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1036: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1036: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1038: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1038: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1039: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1039: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1039: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1039: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1041: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1041: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1045: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1045: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1045: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1045: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1050: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1050: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1050: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1050: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1062: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1062: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1062: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1062: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1067: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1067: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1073: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1073: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1082: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1082: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1125: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1125: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1154: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1154: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1155: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1155: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1155: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1155: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1155: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1155: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1157: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1157: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1164: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1164: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1167: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1167: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1189: Warning: Undefined label: 'sec:seqio-index-getraw' ./Tutorial/chapter_seqio.tex:1189: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1189: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1190: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1190: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1198: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:1218: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1218: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1232: Warning: Undefined label: 'sec:SeqIO-fastq-conversion' ./Tutorial/chapter_seqio.tex:1232: Warning: Undefined label: 'sec:SeqIO-fasta-qual-conversion' ./Tutorial/chapter_seqio.tex:1235: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1235: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1243: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1243: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1247: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1247: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1247: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1247: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1247: Warning: Undefined label: 'sec:seq-reverse-complement' ./Tutorial/chapter_seqio.tex:1257: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1257: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1258: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1258: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1258: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1258: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1258: Warning: Undefined label: 'sec:SeqRecord-reverse-complement' ./Tutorial/chapter_seqio.tex:1311: Warning: Undefined label: 'sec:SeqIO-translate' ./Tutorial/chapter_seqio.tex:1316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1318: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1318: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1331: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1331: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1331: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1331: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1331: Warning: Undefined label: 'sec:SeqRecord-format' ./Tutorial/chapter_seqio.tex:1333: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1333: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1342: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1342: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1350: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1350: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1355: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1355: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1356: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1356: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1357: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1357: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1360: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1360: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1363: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1363: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1364: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1364: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1367: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1367: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1393: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1393: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1394: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1394: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1412: Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_align.tex:1: Warning: line too long ./Tutorial/chapter_align.tex:1: Warning: line too long ./Tutorial/chapter_align.tex:1: Warning: line too long ./Tutorial/chapter_align.tex:1: Warning: line too long ./Tutorial/chapter_align.tex:1: Warning: line too long ./Tutorial/chapter_align.tex:1: Warning: line too long ./Tutorial/chapter_align.tex:8: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:8: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:11: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:11: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:12: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:12: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:13: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:13: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:13: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:13: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:31: Warning: Undefined label: 'sec:appendix-handles' ./Tutorial/chapter_align.tex:32: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:32: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:35: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:35: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:35: Warning: Undefined label: 'sec:AlignIO-count-argument' ./Tutorial/chapter_align.tex:93: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:93: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:113: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:113: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:113: Warning: Undefined label: 'sec:alignment-format' ./Tutorial/chapter_align.tex:165: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:165: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:167: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:167: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:178: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:178: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:191: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:191: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:221: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:221: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:266: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:266: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:266: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:266: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:335: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:335: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:336: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:336: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:336: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:336: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:336: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:336: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:338: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:338: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:338: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:338: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:368: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:368: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:368: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:368: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:370: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:370: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:370: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:370: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:370: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:370: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:376: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:376: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:377: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:377: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:434: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:434: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:434: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:434: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:434: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:434: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:436: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:436: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:442: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:442: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:443: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:443: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:444: Warning: Undefined label: 'sec:SeqIO-conversion' ./Tutorial/chapter_align.tex:445: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:445: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:445: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:445: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:446: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:446: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:457: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:457: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:457: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:457: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:467: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:467: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:467: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:467: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:469: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:469: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:469: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:469: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:614: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:614: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:615: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:615: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:616: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:616: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:631: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:631: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:631: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:631: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:633: Warning: Undefined label: 'sec:SeqRecord-format' ./Tutorial/chapter_align.tex:633: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:633: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:633: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:633: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:664: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:664: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:665: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:665: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:666: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:666: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:666: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:666: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:687: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:687: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:687: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:687: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:688: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:688: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:748: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:748: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:813: Warning: Undefined label: 'sec:SeqRecord-addition' ./Tutorial/chapter_align.tex:814: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:814: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:892: Warning: Undefined label: 'sec:subs_mat_ex' ./Tutorial/chapter_align.tex:894: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:894: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:894: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:894: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:913: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:913: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:913: Warning: Undefined label: 'sec:pairwise' ./Tutorial/chapter_align.tex:917: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:917: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:917: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_align.tex:921: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:921: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:933: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:933: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:944: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:944: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:947: Warning: Undefined label: 'sec:emboss-needle-water' ./Tutorial/chapter_align.tex:955: Warning: '_' occurring outside math mode ./Tutorial/chapter_align.tex:958: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:958: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1016: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1016: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1016: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1016: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1022: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1022: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1023: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1023: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1024: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1024: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1048: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1048: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1050: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1050: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1069: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1069: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1093: Warning: Undefined label: 'chapter:phylo' ./Tutorial/chapter_align.tex:1098: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1098: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1127: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1127: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1150: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1150: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1161: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1161: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1204: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1204: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1238: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1238: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1317: Warning: Undefined label: 'sec:appendix-handles' ./Tutorial/chapter_align.tex:1377: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1377: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1457: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1457: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1487: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1487: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1488: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1488: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1492: Warning: Undefined citation: 'durbin1998' ./Tutorial/chapter_align.tex:1497: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1497: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1504: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1504: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1504: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1504: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1505: Warning: Undefined label: 'sec:pairwise-aligner' ./Tutorial/chapter_align.tex:1523: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1523: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1535: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1535: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1535: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1535: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1554: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1554: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1554: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1554: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1556: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1556: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1556: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1556: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1557: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1557: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1558: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1558: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1578: Warning: Undefined citation: 'waterman1987' ./Tutorial/chapter_align.tex:1583: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1583: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1608: Warning: Undefined label: 'sec:pairwise-substitution-scores' ./Tutorial/chapter_align.tex:1608: Warning: Undefined label: 'sec:pairwise-affine-gapscores' ./Tutorial/chapter_align.tex:1608: Warning: Undefined label: 'sec:pairwise-general-gapscores' ./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1609: Warning: Undefined label: 'sec:pairwise-basic' ./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1612: Warning: Undefined label: 'sec:pairwise-affine-gapscores' ./Tutorial/chapter_align.tex:1613: Warning: Undefined label: 'sec:pairwise-general-gapscores' ./Tutorial/chapter_align.tex:1613: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1613: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1623: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1623: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1623: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1623: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1636: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1636: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1639: Warning: Undefined citation: 'altschul1990' ./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1639: Warning: Undefined label: 'sec:pairwise-affine-gapscores' ./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1668: Warning: Undefined citation: 'altschul1990' ./Tutorial/chapter_align.tex:1668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1695: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1695: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1707: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1707: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1707: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1707: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1708: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1708: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1708: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1708: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1709: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1709: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1709: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1709: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1722: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1722: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1729: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1729: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1729: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1729: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1730: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1730: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1730: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1730: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1731: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1731: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1731: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1731: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1732: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1732: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1732: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1732: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1733: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1733: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1733: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1733: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1734: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1734: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1734: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1734: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1772: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1772: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1772: Warning: Undefined label: 'table:align-meta-attributes' ./Tutorial/chapter_align.tex:1780: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1780: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1780: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1780: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1780: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1780: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1781: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1781: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1781: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1781: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1781: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1781: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1782: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1782: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1782: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1782: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1782: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1782: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1783: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1783: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1783: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1783: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1783: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1783: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1784: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1784: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1784: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1784: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1784: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1784: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1785: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1785: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1785: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1785: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1785: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1785: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1786: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1786: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1786: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1786: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1786: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1786: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1787: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1787: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1787: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1787: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1787: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1787: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1788: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1788: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1788: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1788: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1788: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1788: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1789: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1789: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1789: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1789: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1789: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1789: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1790: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1790: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1790: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1790: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1790: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1790: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1791: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1791: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1791: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1791: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1791: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1791: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1792: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1792: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1792: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1792: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1792: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1792: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1793: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1793: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1793: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1793: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1793: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1793: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1794: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1794: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1794: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1794: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1794: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1794: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1795: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1795: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1795: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1795: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1795: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1795: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1796: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1796: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1797: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1797: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1797: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1797: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1797: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1797: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1798: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1798: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1799: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1799: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1799: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1799: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1799: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1799: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1801: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1801: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1802: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1802: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1802: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1802: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1802: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1802: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1803: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1803: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1805: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1805: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1805: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1805: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1805: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1805: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1806: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1806: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1806: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1806: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1806: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1806: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1807: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1807: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1807: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1807: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1807: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1807: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1808: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1808: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1808: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1808: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1808: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1808: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1812: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1812: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1812: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1812: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1812: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1812: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1813: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1813: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1813: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1813: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1813: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1813: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1815: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1815: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1815: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1815: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1815: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1815: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1816: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1816: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1816: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1816: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1816: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1816: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1818: Warning: overfull line in array : array too wide ./Tutorial/chapter_align.tex:1818: Warning: line too long ./Tutorial/chapter_align.tex:1818: Warning: line too long ./Tutorial/chapter_align.tex:1818: Warning: line too long ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined label: 'sec:pairwise-examples' ./Tutorial/chapter_align.tex:1910: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1910: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1946: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1946: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1984: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1984: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1984: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1984: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1984: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1984: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1988: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1988: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1988: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1988: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1989: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1989: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1999: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1999: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1999: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1999: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2030: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2030: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2053: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2053: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2053: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2053: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2054: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2054: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2054: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2054: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2055: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2055: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2055: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2055: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2067: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2067: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2091: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2091: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2102: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2102: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2164: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2164: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2192: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2192: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2203: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2203: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2295: Warning: line too long ./Tutorial/chapter_align.tex:2311: Warning: line too long ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2392: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2392: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2392: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2392: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2411: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2411: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2411: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2411: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2412: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2412: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2424: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2424: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2424: Warning: Undefined citation: 'kent2002' ./Tutorial/chapter_align.tex:2428: Warning: line too long ./Tutorial/chapter_align.tex:2431: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2431: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2433: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2433: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2434: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2434: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2435: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2435: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2479: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2479: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2479: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2479: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2485: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2485: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2493: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2493: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2496: Warning: Multiple definitions for label: sec:pairwise-general-gapscores ./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2519: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2519: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2519: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2519: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2612: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2612: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2612: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2612: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2698: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2698: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2698: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2698: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2725: Warning: Undefined citation: 'schneider2005' ./Tutorial/chapter_align.tex:2725: Warning: Undefined label: 'sec:substitution_matrices' ./Tutorial/chapter_align.tex:2758: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2758: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2758: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2758: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2864: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2864: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2932: Warning: '_' occurring outside math mode ./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2938: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2938: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2951: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2951: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2958: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2958: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2975: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2975: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2993: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2993: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2993: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2993: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3007: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3007: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3030: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3030: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3049: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3049: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3070: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3070: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3119: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3119: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3119: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3119: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3217: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3217: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3217: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3217: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3263: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3263: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3282: Warning: Undefined citation: 'altschul1990' ./Tutorial/chapter_align.tex:3282: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3282: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3302: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3302: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3315: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3315: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3315: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3315: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3350: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3350: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3354: Warning: Undefined citation: 'henikoff1992' ./Tutorial/chapter_align.tex:3354: Warning: Undefined citation: 'dayhoff1978' ./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3369: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3369: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3379: Warning: Undefined citation: 'schneider2005' ./Tutorial/chapter_align.tex:3391: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3391: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3391: Warning: Undefined label: 'sec:pairwise' ./Tutorial/chapter_align.tex:3393: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3393: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3396: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3396: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3400: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3400: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3416: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3416: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3425: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3425: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3429: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3429: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3442: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3442: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3443: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3443: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3448: Warning: line too long ./Tutorial/chapter_align.tex:3450: Warning: line too long ./Tutorial/chapter_align.tex:3468: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3468: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3491: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3491: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3508: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3508: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3511: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3511: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3528: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3528: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3529: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3529: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3552: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3552: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3565: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3565: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3572: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3572: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:1: Warning: line too long ./Tutorial/chapter_blast.tex:1: Warning: line too long ./Tutorial/chapter_blast.tex:18: Warning: Undefined label: 'chapter:searchio' ./Tutorial/chapter_blast.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:20: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:20: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:29: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:29: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:29: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:29: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:35: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:35: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:45: Warning: line too long ./Tutorial/chapter_blast.tex:53: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:53: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:60: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:60: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:65: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:65: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:68: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:68: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:69: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:69: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:70: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:70: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:72: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:72: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:73: Warning: Undefined label: 'sec:parsing-blast' ./Tutorial/chapter_blast.tex:74: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:74: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:121: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:121: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:132: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:132: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:133: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_blast.tex:135: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:135: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:138: Warning: Undefined label: 'sec:parsing-blast' ./Tutorial/chapter_blast.tex:146: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:146: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:147: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:147: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:157: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:157: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:159: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:159: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:160: Warning: Undefined label: 'sec:parsing-blast' ./Tutorial/chapter_blast.tex:169: Warning: Undefined label: 'sec:parsing-blast' ./Tutorial/chapter_blast.tex:178: Warning: Undefined label: 'sec:running-www-blast' ./Tutorial/chapter_blast.tex:202: Warning: '_' occurring outside math mode ./Tutorial/chapter_blast.tex:202: Warning: '_' occurring outside math mode ./Tutorial/chapter_blast.tex:206: Warning: Undefined label: 'sec:alignment-tools' ./Tutorial/chapter_blast.tex:225: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:225: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:236: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:236: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:238: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:238: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:240: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:240: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:241: Warning: Undefined label: 'sec:parsing-blast' ./Tutorial/chapter_blast.tex:248: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:248: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:259: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:259: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:259: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:259: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:273: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:273: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:287: Warning: Undefined label: 'sec:running-www-blast' ./Tutorial/chapter_blast.tex:289: Warning: Undefined label: 'sec:running-local-blast' ./Tutorial/chapter_blast.tex:303: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:303: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:303: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:303: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:304: Warning: Undefined label: 'sec:appendix-handles' ./Tutorial/chapter_blast.tex:307: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:307: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:339: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:339: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:339: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:339: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:340: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_blast.tex:340: Warning: Undefined label: 'chapter:align' ./Tutorial/chapter_blast.tex:341: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:341: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:341: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:341: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:342: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:342: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:342: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:342: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:344: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:344: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:344: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:344: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:348: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:348: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:369: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:369: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:388: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:388: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:440: Warning: line too long ./Tutorial/chapter_blast.tex:442: Warning: line too long ./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:452: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:452: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:452: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:452: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:452: Warning: Undefined label: 'fig:blastrecord' ./Tutorial/chapter_blast.tex:456: Warning: Image in text ./Tutorial/chapter_blast.tex:468: Warning: Undefined label: 'fig:psiblastrecord' ./Tutorial/chapter_blast.tex:472: Warning: Image in text ./Tutorial/chapter_blast.tex:488: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:488: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:488: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:488: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:489: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:489: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:494: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:494: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:501: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:501: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:502: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:502: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:507: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:507: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1: Warning: line too long ./Tutorial/chapter_searchio.tex:17: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:17: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:18: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:18: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:21: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:21: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:27: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:27: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:29: Warning: '_' occurring outside math mode ./Tutorial/chapter_searchio.tex:31: Warning: '_' occurring outside math mode ./Tutorial/chapter_searchio.tex:32: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:32: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:40: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:40: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:41: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:41: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:42: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:42: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:44: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:44: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:46: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:46: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:47: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:47: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:72: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:72: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:77: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:77: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:78: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:78: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:78: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:78: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:79: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:79: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:79: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:79: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:80: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:80: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:81: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:81: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:82: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:82: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:83: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:83: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:83: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:83: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:84: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:84: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:85: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:85: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:86: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:86: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:87: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:87: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:88: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:88: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:88: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:88: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:88: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:88: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:89: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:89: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:90: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:90: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:90: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:90: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:96: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:96: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:96: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:96: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:100: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:100: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:100: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:100: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:103: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:103: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:104: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:104: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:105: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:105: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:106: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:106: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:110: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:110: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:167: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:167: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:168: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:168: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:178: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:178: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:204: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:204: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:221: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:221: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:242: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:242: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:242: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:242: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:243: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:243: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:244: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:244: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:248: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:248: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:249: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:249: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:263: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:263: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:264: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:264: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:274: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:274: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:287: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:287: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:315: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:315: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:315: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:315: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:326: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:326: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:337: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:337: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:352: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:352: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:353: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:353: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:354: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:354: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:355: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:355: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:357: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:357: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:359: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:359: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:359: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:359: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:360: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:360: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:361: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:361: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:361: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:361: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:386: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:386: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:388: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:388: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:389: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:389: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:389: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:389: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:391: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:391: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:392: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:392: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:394: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:394: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:394: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:394: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:394: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:394: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:398: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:398: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:398: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:398: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:401: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:401: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:404: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:404: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:405: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:405: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:405: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:405: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:405: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:405: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:406: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:406: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:406: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:406: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:407: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:407: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:407: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:407: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:409: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:409: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:409: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:409: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:410: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:410: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:413: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:413: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:414: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:414: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:416: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:416: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:416: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:416: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:416: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:416: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:439: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:439: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:439: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:439: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:440: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:440: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:440: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:440: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:443: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:443: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:444: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:444: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:444: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:444: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:445: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:445: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:445: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:445: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:446: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:446: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:446: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:446: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:448: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:448: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:468: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:468: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:468: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:468: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:468: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:468: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:469: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:469: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:474: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:474: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:475: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:475: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:476: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:476: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:477: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:477: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:503: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:503: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:504: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:504: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:506: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:506: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:506: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:506: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:507: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:507: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:557: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:557: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:561: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:561: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:562: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:562: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:563: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:563: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:565: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:565: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:566: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:566: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:577: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:577: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:577: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:577: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:577: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:577: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:588: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:588: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:589: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:589: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:589: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:589: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:589: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:589: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:590: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:590: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:590: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:590: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:591: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:591: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:615: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:615: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:615: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:615: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:616: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:616: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:618: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:618: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:618: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:618: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:619: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:619: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:619: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:619: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:619: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:619: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:620: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:620: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:620: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:620: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:621: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:621: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:621: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:621: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:621: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:621: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:622: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:622: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:622: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:622: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:622: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:622: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:627: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:627: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:630: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:630: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:632: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:632: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:633: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:633: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:634: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:634: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:656: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:656: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:656: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:656: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:656: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:656: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:657: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:657: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:660: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:660: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:673: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:673: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:673: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:673: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:686: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:686: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:700: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:700: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:705: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:705: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:719: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:719: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:720: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:720: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:727: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:727: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:727: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:727: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:733: Warning: line too long ./Tutorial/chapter_searchio.tex:735: Warning: line too long ./Tutorial/chapter_searchio.tex:738: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:738: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:739: Warning: Undefined label: 'chapter:seq_annot' ./Tutorial/chapter_searchio.tex:740: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:740: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:740: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:740: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:741: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:741: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:743: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:743: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:744: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:744: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:744: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:744: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:756: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:756: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:776: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:776: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:777: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:777: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:777: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:777: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:777: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:777: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:778: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:778: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:792: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:792: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:820: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:820: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:843: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:843: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:849: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:849: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:850: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:850: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:852: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:852: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:853: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:853: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:878: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:878: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:881: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:881: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:881: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:881: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:881: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:881: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:883: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:883: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:883: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:883: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:884: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:884: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:884: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:884: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:885: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:885: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:885: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:885: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:886: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:886: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:886: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:886: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:888: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:888: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:892: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:892: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:903: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:903: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:903: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:903: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:903: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:903: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:904: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:904: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:910: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:910: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:915: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:915: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:917: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:917: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:922: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:922: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:923: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:923: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:966: Warning: line too long ./Tutorial/chapter_searchio.tex:973: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:973: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:983: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:983: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:983: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:983: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:993: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:993: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:996: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:996: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1000: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1000: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1003: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1003: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1008: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1008: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1008: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1008: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1009: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1009: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1009: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1009: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1010: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1010: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1010: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1010: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1011: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1011: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1014: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1014: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1015: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1015: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1015: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1015: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1023: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1023: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1023: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1023: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1023: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1023: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1024: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1024: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1024: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1024: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1025: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1025: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1025: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1025: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1027: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1027: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1030: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1030: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1031: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1031: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1031: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1031: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1032: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1032: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1035: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1035: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1055: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1055: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1057: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1057: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1058: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1058: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1083: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1083: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1084: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1084: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1088: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1088: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1088: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1088: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1089: Warning: Undefined label: 'sec:SeqIO-index' ./Tutorial/chapter_searchio.tex:1090: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1090: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1093: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1093: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1119: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1119: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1119: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1119: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1132: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1132: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1132: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1132: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1139: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1139: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1140: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1140: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1141: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1141: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1165: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1165: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1167: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1167: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1167: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1167: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1168: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1168: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1168: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1168: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1177: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1177: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1177: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1177: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1: Warning: line too long ./Tutorial/chapter_entrez.tex:1: Warning: line too long ./Tutorial/chapter_entrez.tex:1: Warning: line too long ./Tutorial/chapter_entrez.tex:1: Warning: line too long ./Tutorial/chapter_entrez.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:6: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:6: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:7: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:7: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:11: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:11: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:17: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:17: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:21: Warning: Undefined label: 'sec:entrez-specialized-parsers' ./Tutorial/chapter_entrez.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:27: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:27: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:38: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:38: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:60: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:63: Warning: Undefined label: 'sec:BioSQL' ./Tutorial/chapter_entrez.tex:78: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:78: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:127: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:127: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:135: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:135: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:171: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:171: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:200: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:200: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:216: Warning: Undefined label: 'sec:efetch' ./Tutorial/chapter_entrez.tex:220: Warning: Undefined label: 'sec:entrez-einfo' ./Tutorial/chapter_entrez.tex:236: Warning: Undefined label: 'sec:efetch' ./Tutorial/chapter_entrez.tex:259: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:259: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:287: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:287: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:287: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:287: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:299: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:302: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:302: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:323: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:323: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:323: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:323: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:323: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:323: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:325: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:325: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:325: Warning: Undefined label: 'sec:SeqIO_GenBank_Online' ./Tutorial/chapter_entrez.tex:325: Warning: Undefined label: 'sec:efetch' ./Tutorial/chapter_entrez.tex:325: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:325: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:409: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:409: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:409: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:409: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:417: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:417: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:419: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:419: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:419: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_entrez.tex:419: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:419: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:441: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:441: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:466: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:466: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:466: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:466: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:481: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:481: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:481: Warning: Undefined label: 'sec:entrez-specialized-parsers' ./Tutorial/chapter_entrez.tex:483: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:483: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:483: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:483: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:483: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:488: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:488: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:501: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:501: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:501: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:501: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:511: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:511: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:533: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:533: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:565: Warning: Undefined label: 'sec:elink-citations' ./Tutorial/chapter_entrez.tex:571: Warning: Undefined label: 'sec:entrez_example_genbank' ./Tutorial/chapter_entrez.tex:573: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:573: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:591: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:591: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:609: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:609: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:609: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:609: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:609: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:609: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:611: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:611: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:611: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:611: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:611: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:611: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:617: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:617: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:617: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:617: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:619: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:619: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:619: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:619: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:652: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:652: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:690: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:690: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:750: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:750: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:750: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:750: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:761: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:761: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:761: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:761: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:761: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:761: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:770: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:770: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:776: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:776: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:778: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:778: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:778: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:778: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:778: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:778: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:780: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:780: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:780: Warning: Undefined label: 'sec:SeqIO_GenBank_Online' ./Tutorial/chapter_entrez.tex:780: Warning: Undefined label: 'sec:efetch' ./Tutorial/chapter_entrez.tex:780: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:780: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:784: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:784: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:784: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:784: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:784: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:784: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:813: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:813: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:837: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:837: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:852: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:852: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:861: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:861: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:866: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:866: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:866: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:866: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:902: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:909: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:909: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:913: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:913: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:949: Warning: line too long ./Tutorial/chapter_entrez.tex:991: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:991: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:991: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:991: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:991: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:991: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:993: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:993: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1000: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1000: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1000: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1000: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1008: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1008: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1008: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1008: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1022: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1022: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1022: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1022: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1022: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1022: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1029: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1029: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1029: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1029: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1031: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1031: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1031: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1031: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1045: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1045: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1046: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1046: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1047: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1047: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1051: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1051: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1065: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1068: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1072: Warning: Undefined label: 'sec:orchids' ./Tutorial/chapter_entrez.tex:1086: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1086: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1106: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1106: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1115: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1117: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1117: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1159: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1159: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1161: Warning: Undefined label: 'sec:orchids' ./Tutorial/chapter_entrez.tex:1177: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1177: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1190: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1190: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1201: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1201: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1202: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1202: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1214: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1214: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1216: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1251: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1258: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1258: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1258: Warning: Undefined label: 'sec:SeqIO_GenBank_Online' ./Tutorial/chapter_entrez.tex:1259: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1311: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1311: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1311: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1311: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1311: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1311: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1311: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_entrez.tex:1335: Warning: Undefined label: 'sec:entrez-guidelines' ./Tutorial/chapter_entrez.tex:1336: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1355: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1355: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1396: Warning: Undefined label: 'sec:entrez-search-fetch-genbank' ./Tutorial/chapter_entrez.tex:1397: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1397: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1398: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1398: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1404: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1404: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1405: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1405: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1418: Warning: Undefined label: 'sec:entrez_example_genbank' ./Tutorial/chapter_entrez.tex:1418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1440: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1440: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1507: Warning: Undefined label: 'sec:entrez-and-medline' ./Tutorial/chapter_entrez.tex:1507: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1507: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1512: Warning: Undefined label: 'sec:elink' ./Tutorial/chapter_entrez.tex:1537: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_uniprot.tex:1: Warning: line too long ./Tutorial/chapter_uniprot.tex:8: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:8: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:12: Warning: Undefined label: 'sec:SeqIO_ExPASy_and_SwissProt' ./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:31: Warning: line too long ./Tutorial/chapter_uniprot.tex:34: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:34: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:37: Warning: Undefined label: 'sec:expasy_swissprot' ./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:45: Warning: Undefined label: 'sec:SeqIO_ExPASy_and_SwissProt' ./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:47: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:47: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:53: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:53: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:77: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:77: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:80: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:80: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:80: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:80: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:80: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:80: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:82: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:82: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:89: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:89: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:123: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:123: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:138: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:138: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:189: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:189: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:191: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:191: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:239: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:239: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:251: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:251: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:286: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:286: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:286: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:286: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:286: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:286: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:318: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:318: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:318: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:318: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:318: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:318: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:340: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:340: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:343: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:345: Warning: Undefined label: 'sec:orchids' ./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:381: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:381: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:391: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:391: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:400: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:400: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:409: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:409: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:420: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:420: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:420: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:420: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:446: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:446: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:448: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:448: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:466: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:466: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:466: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:466: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:474: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:474: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:497: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:497: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:497: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:1: Warning: line too long ./Tutorial/chapter_pdb.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:25: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:25: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:84: Warning: Undefined label: 'sec:problem_structures' ./Tutorial/chapter_pdb.tex:86: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:86: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:86: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:86: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:113: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:113: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:113: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:113: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:113: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:113: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:115: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:115: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:116: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:116: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:116: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:116: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:116: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:116: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:118: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:118: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:118: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:118: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:118: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:118: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:121: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:121: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:122: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:122: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:125: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:125: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:201: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:201: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:202: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:202: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:203: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:203: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:204: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:204: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:275: Warning: Undefined label: 'fig:smcra' ./Tutorial/chapter_pdb.tex:284: Warning: Undefined label: 'sec:problem_structures' ./Tutorial/chapter_pdb.tex:288: Warning: Image in text ./Tutorial/chapter_pdb.tex:350: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:350: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:351: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:351: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:352: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:352: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:353: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:353: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:357: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:357: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:359: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:359: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:363: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:363: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:391: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:391: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:391: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:391: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:417: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:417: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:421: Warning: Undefined label: 'sec:hetero_problems' ./Tutorial/chapter_pdb.tex:466: Warning: Undefined label: 'sec:point_mutations' ./Tutorial/chapter_pdb.tex:483: Warning: Undefined label: 'sec:disordered_atoms' ./Tutorial/chapter_pdb.tex:592: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:606: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:610: Warning: Undefined label: 'fig:smcra' ./Tutorial/chapter_pdb.tex:646: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:657: Warning: Undefined label: 'fig:smcra' ./Tutorial/chapter_pdb.tex:683: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:760: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:760: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:768: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:768: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:770: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:770: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:770: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:770: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:771: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:771: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:973: Warning: Undefined label: 'table:ic-attribs' ./Tutorial/chapter_pdb.tex:995: Warning: overfull line in array : array too wide ./Tutorial/chapter_pdb.tex:995: Warning: line too long ./Tutorial/chapter_pdb.tex:995: Warning: line too long ./Tutorial/chapter_pdb.tex:995: Warning: line too long ./Tutorial/chapter_pdb.tex:995: Warning: line too long ./Tutorial/chapter_pdb.tex:995: Warning: line too long ./Tutorial/chapter_pdb.tex:995: Warning: line too long ./Tutorial/chapter_pdb.tex:995: Warning: line too long ./Tutorial/chapter_pdb.tex:995: Warning: line too long ./Tutorial/chapter_pdb.tex:1018: Warning: Undefined citation: 'golub1989' ./Tutorial/chapter_pdb.tex:1046: Warning: Undefined citation: 'hamelryck2005' ./Tutorial/chapter_pdb.tex:1081: Warning: Undefined label: 'table:DSSP-codes' ./Tutorial/chapter_pdb.tex:1121: Warning: Undefined label: 'sec:residue_depth' ./Tutorial/chapter_pdb.tex:1124: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:1172: Warning: Undefined citation: 'hamelryck2003a' ./Tutorial/chapter_pdb.tex:1186: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:1383: Warning: Undefined citation: 'hamelryck2003b' ./Tutorial/chapter_pdb.tex:1384: Warning: Undefined citation: 'majumdar2005' ./Tutorial/chapter_popgen.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_popgen.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_popgen.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_popgen.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:9: Warning: Undefined citation: 'talevich2012' ./Tutorial/chapter_phylo.tex:34: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:34: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:70: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:70: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:96: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:96: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:96: Warning: Undefined label: 'fig:phylo-simple-draw' ./Tutorial/chapter_phylo.tex:107: Warning: Image in text ./Tutorial/chapter_phylo.tex:123: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:123: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:125: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:125: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:125: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:125: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:183: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:183: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:194: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:194: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:201: Warning: Undefined label: 'fig:phylo-color-draw' ./Tutorial/chapter_phylo.tex:208: Warning: Image in text ./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:281: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:281: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:302: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:302: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:318: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:318: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:333: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:333: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:343: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:343: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:357: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:357: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:357: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:357: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:375: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:375: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:388: Warning: line too long ./Tutorial/chapter_phylo.tex:392: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:392: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:401: Warning: Image in text ./Tutorial/chapter_phylo.tex:417: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:417: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:423: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:423: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:423: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:423: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:423: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:423: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:424: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:424: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:424: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:424: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:425: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:425: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:426: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:426: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:427: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:427: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:428: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:428: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:428: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:428: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:430: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:430: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:430: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:430: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:431: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:431: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:432: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:432: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:432: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:432: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:434: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:434: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:435: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:435: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:435: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:435: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:435: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:435: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:451: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:451: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:452: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:452: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:452: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:452: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:462: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:462: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:483: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:483: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:484: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:484: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:484: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:484: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:510: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:510: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:523: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:523: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:524: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:524: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:526: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:526: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:535: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:535: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:545: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:545: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:549: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:549: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:586: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:586: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:612: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:612: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:613: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:613: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:617: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:617: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:648: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:648: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:669: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:669: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:673: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:673: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:701: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:701: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:719: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:719: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:720: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:720: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:748: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:748: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:823: Warning: Undefined label: 'sec:PhyloXML' ./Tutorial/chapter_motifs.tex:1: Warning: line too long ./Tutorial/chapter_motifs.tex:5: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:5: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:8: Warning: Undefined label: 'sec:links' ./Tutorial/chapter_motifs.tex:11: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:11: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:12: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:12: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:14: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:14: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:14: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:14: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:27: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:27: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:36: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:36: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:37: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:37: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:63: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:63: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:85: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:85: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:138: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:138: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:146: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:146: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:165: Warning: Undefined citation: 'cornish1985' ./Tutorial/chapter_motifs.tex:166: Warning: Undefined citation: 'cavener1987' ./Tutorial/chapter_motifs.tex:208: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:208: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:208: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:208: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:210: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:210: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:211: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:211: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:212: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:212: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:213: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:213: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:214: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:214: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:215: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:215: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:216: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:216: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:217: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:217: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:218: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:218: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:219: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:219: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:220: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:220: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:221: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:221: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:224: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:224: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:224: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:224: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:230: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:230: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:248: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:248: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:257: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:257: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:304: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:304: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:306: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:306: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:409: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:409: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:409: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:409: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:426: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:426: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:426: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:426: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:455: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:455: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:497: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:497: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:501: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:501: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:501: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:501: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:503: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:503: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:503: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:503: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:503: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:503: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:509: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:509: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:509: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:509: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:509: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:509: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:511: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:511: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:542: Warning: Undefined citation: 'bailey1994' ./Tutorial/chapter_motifs.tex:550: Warning: line too long ./Tutorial/chapter_motifs.tex:552: Warning: line too long ./Tutorial/chapter_motifs.tex:558: Warning: line too long ./Tutorial/chapter_motifs.tex:560: Warning: line too long ./Tutorial/chapter_motifs.tex:569: Warning: line too long ./Tutorial/chapter_motifs.tex:573: Warning: line too long ./Tutorial/chapter_motifs.tex:575: Warning: line too long ./Tutorial/chapter_motifs.tex:584: Warning: line too long ./Tutorial/chapter_motifs.tex:586: Warning: line too long ./Tutorial/chapter_motifs.tex:587: Warning: line too long ./Tutorial/chapter_motifs.tex:589: Warning: line too long ./Tutorial/chapter_motifs.tex:595: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:595: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:603: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:603: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:604: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:604: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:620: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:620: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:621: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:621: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:657: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:657: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:688: Warning: Undefined citation: 'matys2003' ./Tutorial/chapter_motifs.tex:710: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:710: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:712: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:712: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:743: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:743: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:743: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:743: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:743: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:743: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:747: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:747: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:749: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:749: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:757: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:757: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:757: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:757: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:758: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:758: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:772: Warning: Undefined label: 'table:transfaccodes' ./Tutorial/chapter_motifs.tex:779: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:779: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:780: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:780: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:781: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:781: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:782: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:782: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:783: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:783: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:784: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:784: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:785: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:785: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:786: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:786: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:787: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:787: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:788: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:788: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:789: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:789: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:790: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:790: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:791: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:791: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:792: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:792: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:793: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:793: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:794: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:794: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:795: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:795: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:796: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:796: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:797: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:797: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:798: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:798: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:803: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:803: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:810: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:810: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:811: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:811: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:812: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:812: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:813: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:813: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:814: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:814: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:873: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:873: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:873: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:873: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:882: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:882: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:882: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:882: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:942: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:942: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:960: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:960: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:974: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:974: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:987: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:987: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1025: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1025: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1044: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1044: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1065: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1065: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1082: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1082: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1082: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1082: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1093: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1093: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1093: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1093: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1102: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1102: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1110: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1110: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1167: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1167: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1168: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1168: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1169: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1169: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1189: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1189: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1214: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1214: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1313: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1313: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1344: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1344: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1344: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1344: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1344: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1344: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1371: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1371: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1371: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1371: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1384: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1384: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1421: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1421: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1421: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1421: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1446: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1446: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1465: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1465: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1492: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1492: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1492: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1492: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1497: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1497: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1504: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1504: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1513: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1513: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1530: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1530: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1531: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1531: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1532: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1532: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1533: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1533: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1534: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1534: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1565: Warning: '_' occurring outside math mode ./Tutorial/chapter_motifs.tex:1566: Warning: '_' occurring outside math mode ./Tutorial/chapter_motifs.tex:1566: Warning: '_' occurring outside math mode ./Tutorial/chapter_motifs.tex:1567: Warning: '_' occurring outside math mode ./Tutorial/chapter_cluster.tex:6: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:6: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:6: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:6: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:6: Warning: Undefined citation: 'dehoon2004' ./Tutorial/chapter_cluster.tex:8: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:8: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:30: Warning: Undefined citation: 'lecuyer1988' ./Tutorial/chapter_cluster.tex:30: Warning: Undefined citation: 'kachitvichyanukul1988' ./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:35: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:35: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:37: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:37: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:39: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:39: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:41: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:41: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:43: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:43: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:47: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:47: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:49: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:49: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:51: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:51: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:68: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:68: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:76: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:76: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:84: Warning: Application of '\=' on 'x' failed ./Tutorial/chapter_cluster.tex:84: Warning: Application of '\=' on 'y' failed ./Tutorial/chapter_cluster.tex:86: Warning: Application of '\=' on 'x' failed ./Tutorial/chapter_cluster.tex:86: Warning: Application of '\=' on 'y' failed ./Tutorial/chapter_cluster.tex:112: Warning: Undefined block in text mode: 'DIV' [class="equationcontainer"] ./Tutorial/chapter_cluster.tex:115: Warning: Undefined block in text mode: 'DIV' [] ./Tutorial/chapter_cluster.tex:117: Warning: Application of '\=' on 'x' failed ./Tutorial/chapter_cluster.tex:117: Warning: Application of '\=' on 'y' failed ./Tutorial/chapter_cluster.tex:154: Warning: Undefined citation: 'snedecor1989' ./Tutorial/chapter_cluster.tex:162: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:162: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:167: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:167: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:167: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:167: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:167: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:167: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:174: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:174: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:176: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:176: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:176: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:176: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:178: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:178: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:178: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:178: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:179: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:179: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:179: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:179: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:180: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:180: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:180: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:180: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:182: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:182: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:182: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:182: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:183: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:225: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:225: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:225: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:225: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:233: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:233: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:235: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:235: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:235: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:235: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:237: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:237: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:237: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:237: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:238: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:238: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:238: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:238: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:239: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:239: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:239: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:239: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:240: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:240: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:240: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:240: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:241: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:241: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:241: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:241: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:258: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:258: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:262: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:262: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:262: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:262: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:263: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:263: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:263: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:263: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:264: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:264: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:264: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:264: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:265: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:265: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:265: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:265: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:266: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:266: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:266: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:266: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:267: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:267: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:267: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:267: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:268: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:268: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:268: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:268: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:271: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:271: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:272: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:272: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:273: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:273: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:274: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:274: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:275: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:275: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:277: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:277: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:277: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:277: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:278: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:279: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:279: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:279: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:279: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:280: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:280: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:280: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:280: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:280: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:280: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:281: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:281: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:281: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:281: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:281: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:281: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:288: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:288: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:318: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:318: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:318: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:318: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:326: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:326: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:328: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:328: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:328: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:328: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:330: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:330: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:330: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:330: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:332: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:332: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:332: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:332: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:333: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:333: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:333: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:333: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:334: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:334: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:334: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:334: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:336: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:336: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:336: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:336: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:337: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:337: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:337: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:337: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:338: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:338: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:338: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:338: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:341: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:341: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:342: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:342: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:344: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:344: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:345: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:345: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:345: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:345: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:346: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:347: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:347: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:348: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:348: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:348: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:348: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:356: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:356: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:365: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:365: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:382: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:382: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:382: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:382: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:384: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:384: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:384: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:384: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:385: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:385: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:385: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:385: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:386: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:386: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:386: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:386: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:398: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:398: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:417: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:417: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:417: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:417: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:417: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:417: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:419: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:419: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:420: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:420: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:421: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:421: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:423: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:423: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:423: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:423: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:423: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:423: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:447: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:447: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:447: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:447: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:447: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:447: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:449: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:449: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:449: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:449: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:449: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:449: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:463: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:463: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:474: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:474: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:488: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:488: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:488: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:488: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:507: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:507: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:509: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:509: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:509: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:509: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:513: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:513: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:515: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:515: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:519: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:519: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:521: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:521: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:525: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:525: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:525: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:525: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:527: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:527: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:531: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:531: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:531: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:531: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:539: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:539: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:541: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:541: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:541: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:541: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:543: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:543: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:543: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:543: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:544: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:544: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:544: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:544: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:545: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:545: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:545: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:545: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:547: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:547: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:547: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:547: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:550: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:550: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:551: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:551: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:552: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:552: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:553: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:553: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:555: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:555: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:555: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:555: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:556: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:566: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:566: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:583: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:583: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:583: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:583: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:584: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:584: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:587: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:587: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:588: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:588: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:589: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:589: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:600: Warning: Undefined citation: 'kohonen1997' ./Tutorial/chapter_cluster.tex:600: Warning: Undefined citation: 'tamayo1999' ./Tutorial/chapter_cluster.tex:607: Warning: Cannot output that numerical entity: U+00B7 ./Tutorial/chapter_cluster.tex:611: Warning: Cannot output that numerical entity: U+00B7 ./Tutorial/chapter_cluster.tex:616: Warning: Cannot output that numerical entity: U+00B7 ./Tutorial/chapter_cluster.tex:623: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:623: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:625: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:625: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:632: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:632: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:634: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:634: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:634: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:634: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:636: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:636: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:636: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:636: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:637: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:637: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:637: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:637: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:638: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:638: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:638: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:638: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:640: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:640: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:640: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:640: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:642: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:642: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:642: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:642: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:643: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:643: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:644: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:644: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:644: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:644: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:646: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:646: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:646: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:646: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:647: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:650: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:650: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:652: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:652: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:654: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:654: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:660: Warning: Undefined citation: 'yeung2001' ./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:668: Warning: Undefined citation: 'golub1971' ./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:670: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:670: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:675: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:675: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:677: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:677: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:678: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:678: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:679: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:679: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:680: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:680: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:681: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:681: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:683: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:683: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:686: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:686: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:686: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:686: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:690: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:690: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:692: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:692: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:692: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:692: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:711: Warning: line too long ./Tutorial/chapter_cluster.tex:714: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:714: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:716: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:716: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:716: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:716: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:749: Warning: overfull line in array : array too wide ./Tutorial/chapter_cluster.tex:749: Warning: line too long ./Tutorial/chapter_cluster.tex:749: Warning: line too long ./Tutorial/chapter_cluster.tex:755: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:755: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:758: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:758: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:761: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:761: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:764: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:764: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:767: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:767: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:768: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:768: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:768: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:768: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:770: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:770: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:771: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:771: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:771: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:771: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:774: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:774: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:774: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:774: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:776: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:776: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:779: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:779: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:780: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:780: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:780: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:780: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:782: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:782: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:783: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:783: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:783: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:783: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:785: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:785: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:789: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:789: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:789: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:789: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:799: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:799: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:799: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:799: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:801: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:801: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:801: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:801: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:802: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:805: Warning: Undefined label: 'sec:distancematrix' ./Tutorial/chapter_cluster.tex:815: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:815: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:815: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:815: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:816: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:816: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:817: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:817: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:817: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:817: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:818: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:818: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:818: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:818: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:819: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:819: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:819: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:819: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:823: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:823: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:823: Warning: Undefined label: 'sec:clustercentroids' ./Tutorial/chapter_cluster.tex:832: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:832: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:832: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:832: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:833: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:833: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:833: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:833: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:834: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:834: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:834: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:834: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:835: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:835: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:835: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:835: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:836: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:836: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:836: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:836: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:839: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:839: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:840: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:840: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:841: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:841: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:842: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:842: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:843: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:843: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:845: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:845: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:845: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:845: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:846: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:847: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:847: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:847: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:847: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:848: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:848: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:848: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:848: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:848: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:848: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:849: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:849: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:849: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:849: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:849: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:849: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:860: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:860: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:860: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:860: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:862: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:862: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:862: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:862: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:865: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:865: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:866: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:866: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:867: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:867: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:868: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:868: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:870: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:870: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:870: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:870: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:871: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:872: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:872: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:886: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:886: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:886: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:886: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:888: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:888: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:888: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:888: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:890: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:890: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:890: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:890: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:891: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:891: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:891: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:891: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:892: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:892: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:892: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:892: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:895: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:895: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:896: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:896: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:898: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:898: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:899: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:899: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:899: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:899: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:900: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:913: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:913: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:913: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:913: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:915: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:915: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:915: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:915: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:917: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:917: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:917: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:917: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:918: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:918: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:919: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:919: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:919: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:919: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:921: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:921: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:921: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:921: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:922: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:925: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:925: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:927: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:927: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:929: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:929: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:941: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:941: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:942: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:942: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:943: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:943: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:944: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:944: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:944: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:944: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:944: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:944: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:945: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:945: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:946: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:946: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:946: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:946: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:946: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:946: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:952: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:952: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:952: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:952: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:954: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:954: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:954: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:954: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:954: Warning: Undefined citation: 'hihara2001' ./Tutorial/chapter_cluster.tex:971: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:971: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:971: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:971: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:971: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:971: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:986: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:986: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:986: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:986: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:986: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:986: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:26: Warning: Undefined block in text mode: 'DIV' [class="equationcontainer"] ./Tutorial/chapter_learning.tex:28: Warning: Undefined block in text mode: 'SPAN' [class="equationnumber"] ./Tutorial/chapter_learning.tex:28: Warning: Undefined block in text mode: 'SPAN' [] ./Tutorial/chapter_learning.tex:28: Warning: Undefined block in text mode: 'DIV' [] ./Tutorial/chapter_learning.tex:36: Warning: Undefined block in text mode: 'DIV' [class="equationcontainer"] ./Tutorial/chapter_learning.tex:37: Warning: Undefined block in text mode: 'SPAN' [class="equationnumber-valign"] ./Tutorial/chapter_learning.tex:37: Warning: Undefined block in text mode: 'SPAN' [] ./Tutorial/chapter_learning.tex:39: Warning: Undefined block in text mode: 'SPAN' [class="equationnumber-valign"] ./Tutorial/chapter_learning.tex:39: Warning: Undefined block in text mode: 'SPAN' [] ./Tutorial/chapter_learning.tex:39: Warning: overfull line in array : array too wide ./Tutorial/chapter_learning.tex:39: Warning: overfull line in array : array too wide ./Tutorial/chapter_learning.tex:39: Warning: Undefined block in text mode: 'DIV' [] ./Tutorial/chapter_learning.tex:40: Warning: Undefined label: 'eq:OP' ./Tutorial/chapter_learning.tex:40: Warning: Undefined label: 'eq:NOP' ./Tutorial/chapter_learning.tex:70: Warning: overfull line in array : array too wide ./Tutorial/chapter_learning.tex:70: Warning: line too long ./Tutorial/chapter_learning.tex:70: Warning: line too long ./Tutorial/chapter_learning.tex:70: Warning: line too long ./Tutorial/chapter_learning.tex:75: Warning: Undefined label: 'table:training' ./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:168: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:168: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:197: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:197: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:197: Warning: Undefined label: 'eq:OP' ./Tutorial/chapter_learning.tex:197: Warning: Undefined label: 'eq:NOP' ./Tutorial/chapter_learning.tex:261: Warning: Undefined label: 'eq:OP' ./Tutorial/chapter_learning.tex:261: Warning: Undefined label: 'eq:NOP' ./Tutorial/chapter_learning.tex:263: Warning: Undefined label: 'eq:OP' ./Tutorial/chapter_learning.tex:263: Warning: Undefined label: 'eq:NOP' ./Tutorial/chapter_learning.tex:273: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:273: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:273: Warning: Undefined label: 'sec:LogisticRegression' ./Tutorial/chapter_learning.tex:277: Warning: Undefined label: 'table:training' ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined label: 'sec:LogisticRegressionTraining' ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:289: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:289: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:289: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:289: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:289: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:289: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:302: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:302: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:330: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:330: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:337: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:337: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:337: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:337: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:397: Warning: Application of '\"' on 'i' failed ./Tutorial/chapter_learning.tex:399: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:399: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:403: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:403: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:407: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:407: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:407: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:407: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:16: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:16: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:18: Warning: Undefined citation: 'pritchard2006' ./Tutorial/chapter_graphics.tex:28: Warning: Undefined citation: 'toth2006' ./Tutorial/chapter_graphics.tex:31: Warning: Undefined citation: 'vanderauwera2009' ./Tutorial/chapter_graphics.tex:34: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:34: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:35: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:35: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:36: Warning: Undefined label: 'chapter:seq_annot' ./Tutorial/chapter_graphics.tex:36: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:63: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:63: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:64: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_graphics.tex:68: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:89: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:89: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:90: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:90: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:105: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:105: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:106: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:106: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:132: Warning: Image in text ./Tutorial/chapter_graphics.tex:132: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:144: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:144: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:163: Warning: Image in text ./Tutorial/chapter_graphics.tex:163: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:212: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:212: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:212: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:212: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:219: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:219: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:219: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:219: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:220: Warning: Undefined label: 'sec:seq_features' ./Tutorial/chapter_graphics.tex:221: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:221: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:223: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:223: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:268: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:268: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:271: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:271: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:277: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:277: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:279: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:279: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:325: Warning: Image in text ./Tutorial/chapter_graphics.tex:325: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:325: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:326: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:326: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:345: Warning: Undefined label: 'sec:gd_nice_example' ./Tutorial/chapter_graphics.tex:352: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:396: Warning: Image in text ./Tutorial/chapter_graphics.tex:396: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:409: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:409: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:430: Warning: Image in text ./Tutorial/chapter_graphics.tex:430: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:430: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:430: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:459: Warning: Image in text ./Tutorial/chapter_graphics.tex:459: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:459: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:459: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:473: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:473: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:482: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:482: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:482: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:482: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:485: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:485: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:488: Warning: Undefined label: 'sec:gd_top_down' ./Tutorial/chapter_graphics.tex:564: Warning: Image in text ./Tutorial/chapter_graphics.tex:564: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:564: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:566: Warning: Image in text ./Tutorial/chapter_graphics.tex:566: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:566: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:591: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:591: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:596: Warning: Undefined citation: 'proux2002' ./Tutorial/chapter_graphics.tex:599: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:599: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:600: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:600: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:601: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:601: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:605: Warning: Undefined label: 'sec:efetch' ./Tutorial/chapter_graphics.tex:608: Warning: Undefined label: 'sec:SeqRecord-slicing' ./Tutorial/chapter_graphics.tex:610: Warning: Undefined label: 'sec:SeqRecord-reverse-complement' ./Tutorial/chapter_graphics.tex:728: Warning: Image in text ./Tutorial/chapter_graphics.tex:728: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:728: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:752: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:752: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:759: Warning: Undefined citation: 'proux2002' ./Tutorial/chapter_graphics.tex:841: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:841: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:843: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:843: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:843: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:843: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:843: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:873: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:873: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:874: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:874: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:874: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:874: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:875: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:875: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:876: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:876: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:890: Warning: Image in text ./Tutorial/chapter_graphics.tex:890: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:890: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:914: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:914: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:923: Warning: Image in text ./Tutorial/chapter_graphics.tex:923: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:923: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:953: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:953: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:954: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:954: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:1004: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:1004: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:1006: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:1006: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:1011: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:1011: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:1012: Warning: Undefined citation: 'jupe2012' ./Tutorial/chapter_graphics.tex:1035: Warning: line too long ./Tutorial/chapter_graphics.tex:1036: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:1036: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:1057: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:1057: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:1110: Warning: Image in text ./Tutorial/chapter_graphics.tex:1110: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:1125: Warning: line too long ./Tutorial/chapter_graphics.tex:1190: Warning: Image in text ./Tutorial/chapter_graphics.tex:1190: Warning: '_' occurring outside math mode ./Tutorial/chapter_kegg.tex:1: Warning: line too long ./Tutorial/chapter_kegg.tex:1: Warning: line too long ./Tutorial/chapter_kegg.tex:1: Warning: line too long ./Tutorial/chapter_kegg.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_kegg.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_kegg.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_kegg.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phenotype.tex:5: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phenotype.tex:5: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phenotype.tex:10: Warning: '_' occurring outside math mode ./Tutorial/chapter_phenotype.tex:16: Warning: '_' occurring outside math mode ./Tutorial/chapter_phenotype.tex:30: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phenotype.tex:30: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phenotype.tex:32: Warning: '_' occurring outside math mode ./Tutorial/chapter_phenotype.tex:231: Warning: Optional argument to \item in itemize environment ./Tutorial/chapter_phenotype.tex:233: Warning: Optional argument to \item in itemize environment ./Tutorial/chapter_phenotype.tex:235: Warning: Optional argument to \item in itemize environment ./Tutorial/chapter_cookbook.tex:1: Warning: line too long ./Tutorial/chapter_cookbook.tex:1: Warning: line too long ./Tutorial/chapter_cookbook.tex:1: Warning: line too long ./Tutorial/chapter_cookbook.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:22: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_cookbook.tex:55: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:55: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:55: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:55: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:58: Warning: Undefined label: 'sec:low-level-fasta-fastq' ./Tutorial/chapter_cookbook.tex:60: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:60: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:103: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:105: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:105: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:105: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:105: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:115: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:115: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:116: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:116: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:125: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:125: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:126: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:126: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:126: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:126: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:145: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:145: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:146: Warning: Undefined label: 'sec:Bio.SeqIO-and-StringIO' ./Tutorial/chapter_cookbook.tex:201: Warning: Undefined label: 'sec:translation' ./Tutorial/chapter_cookbook.tex:201: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:201: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:202: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:202: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:202: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:202: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:205: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:205: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:206: Warning: Undefined label: 'sec:SeqIO-reverse-complement' ./Tutorial/chapter_cookbook.tex:207: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:207: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:208: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:208: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:243: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:243: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:252: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:252: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:253: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:253: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:263: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:263: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:267: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:267: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:280: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:280: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:283: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:283: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:310: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:310: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:326: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:326: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:329: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:329: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:330: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:330: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:333: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:333: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:334: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:334: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:334: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:334: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:335: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:335: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:337: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:337: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:337: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:337: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:338: Warning: Undefined label: 'sec:seqio-index-getraw' ./Tutorial/chapter_cookbook.tex:357: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:357: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:357: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:357: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:359: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:359: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:391: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:391: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:391: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:391: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:397: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:397: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:439: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:439: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:442: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:442: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:443: Warning: Undefined label: 'sec:low-level-fasta-fastq' ./Tutorial/chapter_cookbook.tex:452: Warning: line too long ./Tutorial/chapter_cookbook.tex:454: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:454: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:456: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:456: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:457: Warning: Undefined label: 'sec:low-level-fasta-fastq' ./Tutorial/chapter_cookbook.tex:459: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:459: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:460: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:460: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:461: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:461: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:480: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:480: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:480: Warning: Undefined label: 'sec:SeqRecord-slicing' ./Tutorial/chapter_cookbook.tex:561: Warning: line too long ./Tutorial/chapter_cookbook.tex:593: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:593: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:595: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:595: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:643: Warning: Undefined label: 'sec:SeqIO-conversion' ./Tutorial/chapter_cookbook.tex:644: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:644: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:646: Warning: Undefined citation: 'cock2010' ./Tutorial/chapter_cookbook.tex:655: Warning: Undefined block in text mode: 'DIV' [class="equationcontainer"] ./Tutorial/chapter_cookbook.tex:657: Warning: Undefined block in text mode: 'SPAN' [class="equationnumber"] ./Tutorial/chapter_cookbook.tex:657: Warning: Undefined block in text mode: 'SPAN' [] ./Tutorial/chapter_cookbook.tex:657: Warning: Undefined block in text mode: 'DIV' [] ./Tutorial/chapter_cookbook.tex:675: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:675: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:686: Warning: Undefined block in text mode: 'DIV' [class="equationcontainer"] ./Tutorial/chapter_cookbook.tex:688: Warning: Undefined block in text mode: 'SPAN' [class="equationnumber"] ./Tutorial/chapter_cookbook.tex:688: Warning: Undefined block in text mode: 'SPAN' [] ./Tutorial/chapter_cookbook.tex:688: Warning: Undefined block in text mode: 'DIV' [] ./Tutorial/chapter_cookbook.tex:694: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:694: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:695: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:695: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:714: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:714: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:715: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:715: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:715: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:715: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:759: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:759: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:764: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:764: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:764: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:764: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:766: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:766: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:777: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:777: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:796: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:796: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:799: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:799: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:801: Warning: Undefined label: 'sec:SeqIO-index' ./Tutorial/chapter_cookbook.tex:804: Warning: line too long ./Tutorial/chapter_cookbook.tex:821: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:821: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:823: Warning: Undefined label: 'sec:SeqIO-index' ./Tutorial/chapter_cookbook.tex:825: Warning: Undefined label: 'sec:SeqIO-sort' ./Tutorial/chapter_cookbook.tex:826: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:826: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:839: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:839: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:839: Warning: Undefined label: 'sec:SeqIO-conversion' ./Tutorial/chapter_cookbook.tex:904: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:905: Warning: Undefined label: 'sec:translation' ./Tutorial/chapter_cookbook.tex:915: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:915: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:915: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:915: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1024: Warning: Undefined label: 'sec:gd_nice_example' ./Tutorial/chapter_cookbook.tex:1031: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1031: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1041: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1041: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1041: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_cookbook.tex:1042: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1042: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1053: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1056: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1056: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1094: Warning: Image in text ./Tutorial/chapter_cookbook.tex:1094: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1117: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1117: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1118: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1118: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1127: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1129: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1129: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1163: Warning: Image in text ./Tutorial/chapter_cookbook.tex:1163: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1211: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1242: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1242: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1265: Warning: Image in text ./Tutorial/chapter_cookbook.tex:1265: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1287: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1287: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1308: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1308: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1341: Warning: Image in text ./Tutorial/chapter_cookbook.tex:1341: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1341: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1363: Warning: line too long ./Tutorial/chapter_cookbook.tex:1364: Warning: line too long ./Tutorial/chapter_cookbook.tex:1369: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1369: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1391: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1391: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1397: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1397: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1398: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1398: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1412: Warning: Image in text ./Tutorial/chapter_cookbook.tex:1418: Warning: Undefined label: 'chapter:align' ./Tutorial/chapter_cookbook.tex:1421: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1425: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1425: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1425: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1425: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1425: Warning: Undefined label: 'chapter:align' ./Tutorial/chapter_cookbook.tex:1433: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1433: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1436: Warning: Undefined label: 'sec:consensus' ./Tutorial/chapter_cookbook.tex:1437: Warning: Undefined label: 'sec:pssm' ./Tutorial/chapter_cookbook.tex:1438: Warning: Undefined label: 'sec:getting_info_content' ./Tutorial/chapter_cookbook.tex:1439: Warning: Undefined label: 'sec:sub_matrix' ./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined label: 'sec:summary_info' ./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1451: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1451: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1453: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1453: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1484: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1484: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1491: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1491: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1511: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1511: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1513: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1513: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1528: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1528: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1538: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1538: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1565: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1565: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1565: Warning: Undefined label: 'sec:summary_info' ./Tutorial/chapter_cookbook.tex:1571: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1571: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1582: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1582: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1584: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1584: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1592: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1592: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1617: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1626: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1626: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1640: Warning: Undefined label: 'sec:align_clustal' ./Tutorial/chapter_cookbook.tex:1642: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1642: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1743: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1748: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1748: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:1748: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_testing.tex:1: Warning: line too long ./Tutorial/chapter_testing.tex:1: Warning: line too long ./Tutorial/chapter_testing.tex:1: Warning: line too long ./Tutorial/chapter_testing.tex:1: Warning: line too long ./Tutorial/chapter_testing.tex:1: Warning: line too long ./Tutorial/chapter_testing.tex:1: Warning: line too long ./Tutorial/chapter_testing.tex:5: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:5: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:34: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:34: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:48: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:48: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:55: Warning: Undefined label: 'sec:doctest' ./Tutorial/chapter_testing.tex:62: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:62: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:68: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:68: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:73: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:73: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:74: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:74: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:74: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:74: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:75: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:75: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:111: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:111: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:120: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:120: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:121: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:121: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:145: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:145: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:150: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:150: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:154: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:154: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:154: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:154: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:189: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:189: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:193: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:193: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:195: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:195: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:195: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:195: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:197: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:197: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:198: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:198: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:201: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:201: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:212: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:212: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:222: Warning: line too long ./Tutorial/chapter_testing.tex:275: Warning: line too long ./Tutorial/chapter_testing.tex:282: Warning: Undefined label: 'sec:doctest' ./Tutorial/chapter_testing.tex:284: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:284: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:297: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:297: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:301: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:301: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:311: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:311: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:313: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:313: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:318: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:318: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:319: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:319: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:354: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:354: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:355: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:355: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:371: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:371: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:373: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:373: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:389: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:389: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:400: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:400: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:401: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:401: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:402: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:402: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:403: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:403: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:403: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:403: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:404: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:404: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:407: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:407: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:409: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_testing.tex:409: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_contributing.tex:11: Warning: '_' occurring outside math mode ./Tutorial/chapter_contributing.tex:32: Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_contributing.tex:38: Warning: '_' occurring outside math mode ./Tutorial/chapter_contributing.tex:68: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_contributing.tex:68: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_contributing.tex:80: Warning: '_' occurring outside math mode ./Tutorial/chapter_contributing.tex:85: Warning: Undefined label: 'chapter:testing' ./Tutorial/chapter_contributing.tex:101: Warning: Undefined label: 'chapter:testing' ./Tutorial/chapter_appendix.tex:35: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_appendix.tex:35: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_appendix.tex:37: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_appendix.tex:37: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_appendix.tex:38: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_appendix.tex:38: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_appendix.tex:41: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_appendix.tex:41: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_appendix.tex:53: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_appendix.tex:53: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_appendix.tex:54: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_appendix.tex:54: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_appendix.tex:91: Warning: Undefined label: 'sec:SeqIO_compressed' ./Tutorial/chapter_appendix.tex:98: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_appendix.tex:98: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial.tex:126: Warning: line too long ./Tutorial.tex:137: Warning: Application of '\'' on 'e' failed ./Tutorial.tex:137: Warning: Application of '\'' on 'o' failed ./Tutorial.tex:141: Warning: Application of '\"' on 'u' failed ./Tutorial.tex:215: Warning: Application of '\"' on 'o' failed ./Tutorial.tex:215: Warning: Application of '\"' on 'u' failed Fixpoint reached in 2 step(s) pdflatex --shell-escape "\def\bpversion{1.80}\input{Tutorial}" This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdflatex) \write18 enabled. entering extended mode LaTeX2e <2022-11-01> patch level 1 L3 programming layer <2023-01-16> (./Tutorial.tex (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2022/07/02 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/preprint/fullpage.sty) (/usr/share/texmf/tex/latex/misc/hevea.sty (/usr/share/texlive/texmf-dist/tex/latex/comment/comment.sty Excluding comment 'comment') Excluding comment 'rawhtml' Excluding comment 'htmlonly') (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/minted/minted.sty (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty)) (/usr/share/texlive/texmf-dist/tex/latex/fvextra/fvextra.sty (/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty) (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty) (/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty) (/usr/share/texlive/texmf-dist/tex/latex/lineno/lineno.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/calc.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/shellesc.sty) (/usr/share/texlive/texmf-dist/tex/latex/ifplatform/ifplatform.sty (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty)) (/usr/share/texlive/texmf-dist/tex/generic/catchfile/catchfile.sty (/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty)) (/usr/share/texlive/texmf-dist/tex/generic/iftex/ifluatex.sty) (./Tutorial.w18) ) (/usr/share/texlive/texmf-dist/tex/generic/xstring/xstring.sty (/usr/share/texlive/texmf-dist/tex/generic/xstring/xstring.tex)) (/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 70. (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx))/usr/bin/pygmentize (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) No file Tutorial.aux. (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) Excluding 'htmlonly' comment. Excluding 'rawhtml' comment. [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map} <./images/biopython_logo.pdf>] No file Tutorial.toc. pdfTeX warning (ext4): destination with the same identifier (name{page.1}) has been already used, duplicate ignored \relax l.102 \include{Tutorial/chapter_introduction} [1] (./Tutorial/chapter_introduction.tex Chapter 1. [2] LaTeX Warning: Citation `cock2009' on page 3 undefined on input line 91. LaTeX Warning: Citation `chapman2000' on page 3 undefined on input line 95. LaTeX Warning: Citation `hamelryck2003a' on page 3 undefined on input line 96. LaTeX Warning: Citation `dehoon2004' on page 3 undefined on input line 97. LaTeX Warning: Citation `pritchard2006' on page 3 undefined on input line 98. LaTeX Warning: Citation `talevich2012' on page 3 undefined on input line 99. LaTeX Warning: Citation `cock2010' on page 3 undefined on input line 100. [3] Excluding 'rawhtml' comment. Underfull \hbox (badness 10000) in paragraph at lines 122--128 Underfull \hbox (badness 10000) in paragraph at lines 134--136 (./_minted-Tutorial/default.pygstyle) (./_minted-Tutorial/C3217FD04973F24516F5530BB525A22CBD02851C2FB632864165FCA4920 46548.pygtex) [4 <./images/biopython_logo_old.jpg>] LaTeX Warning: Reference `sec:seq-comparison' on page 5 undefined on input line 185. Overfull \hbox (2.99303pt too wide) in paragraph at lines 187--189 \OT1/cmr/m/n/10 Check the built in doc-strings (\OT1/cmtt/m/n/10 from Bio impor t SeqIO\OT1/cmr/m/n/10 , then \OT1/cmtt/m/n/10 help(SeqIO)\OT1/cmr/m/n/10 ), or see [][]$\OT1/cmtt/m/n/10 http : / / biopython . LaTeX Warning: Reference `sec:appendix-handles' on page 5 undefined on input li ne 191. [5]) [6] (./Tutorial/chapter_quick_start.tex Chapter 2. LaTeX Warning: Reference `chapter:cookbook' on page 7 undefined on input line 1 4. LaTeX Warning: Reference `chapter:advanced' on page 7 undefined on input line 1 4. LaTeX Warning: Reference `chapter:seq_objects' on page 7 undefined on input lin e 19. (./_minted-Tutorial/C083BA757ADC0A392BD8802D1351612CBD02851C2FB632864165FCA4920 46548.pygtex [7]) (./_minted-Tutorial/BCD1E3D53103B8919C8BBE66D33535ABBD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `chapter:seqio' on page 8 undefined on input line 45. LaTeX Warning: Reference `sec:sequence-parsing' on page 8 undefined on input li ne 65. LaTeX Warning: Reference `chapter:entrez' on page 8 undefined on input line 65. LaTeX Warning: Reference `chapter:uniprot' on page 8 undefined on input line 65 . LaTeX Warning: Reference `sec:align_clustal' on page 8 undefined on input line 65. [8] LaTeX Warning: Reference `chapter:seqio' on page 9 undefined on input line 72. LaTeX Warning: Reference `sec:connecting-with-biological-databases' on page 9 u ndefined on input line 79. (./_minted-Tutorial/AD9EF2BC42CEF4E413923F9BFFE1BE07669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/33F85FAC7266F854F2B0213346781855BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/57D5D2D450B93D59CC2D6708C6BA430BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9951EE2B2EB57108F1B91BF42B5EF26DBD02851C2FB632864165FCA4920 46548.pygtex [9]) (./_minted-Tutorial/D0C141F7F69A52FF8D2723831BF439F2BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `chapter:seqio' on page 10 undefined on input line 145 . LaTeX Warning: Reference `chapter:align' on page 10 undefined on input line 145 . LaTeX Warning: Reference `chapter:cookbook' on page 10 undefined on input line 150. LaTeX Warning: Reference `chapter:entrez' on page 10 undefined on input line 15 8. LaTeX Warning: Reference `chapter:uniprot' on page 10 undefined on input line 1 59. [10] LaTeX Warning: Reference `chapter:cookbook' on page 11 undefined on input line 169. ) [11] (./Tutorial/chapter_seq_objects.tex Chapter 3. LaTeX Warning: Reference `chapter:seq_annot' on page 12 undefined on input line 5. LaTeX Warning: Reference `chapter:seqio' on page 12 undefined on input line 5. (./_minted-Tutorial/048D805D0CE39D0271B0A9A9F6FA0B90BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CCFAD09A7C678CC6F23FB63113DD1EDCBD02851C2FB632864165FCA4920 46548.pygtex) [12] (./_minted-Tutorial/FD65D36A7B14289ADEAB241851842BCABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C0F44B540F3531194878FC29AF017902BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/739024CAA2FC886FEC674E3B4C3FD3A4BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:mutable-seq' on page 13 undefined on input line 8 6. (./_minted-Tutorial/EB307D8D2C6B186F102975D2F777C5C8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/504E820336D4D852A5104D8E97622504BD02851C2FB632864165FCA4920 46548.pygtex [13]) (./_minted-Tutorial/21058E2884DE0E2797798658CEC2E54FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6C027F180664948287C5ED0C06A70E36BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8900FA9A050CA74204F5DCB8D9386420BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5A43D1A8AC729BFB659D75BFD070C79ABD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:SeqRecord-format' on page 14 undefined on input l ine 155. LaTeX Warning: Reference `chapter:seqio' on page 14 undefined on input line 157 . (./_minted-Tutorial/732D927996C79742AC990312B3D6EEB0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/36BB9CB69ABA7149C7050E321F74C270BD02851C2FB632864165FCA4920 46548.pygtex [14]) (./_minted-Tutorial/14DC45CA9BEAFF3B8A49C8E43A9FF33CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4FC9049D1029A23D48B33F9D862ACC47BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E62329AC6ED4D8F7B1EF4988F8DBA19FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/008EC869056581873654FF9A8E92D394BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/457BF67E0722BB5B93A17BD27C0B6D8DBD02851C2FB632864165FCA4920 46548.pygtex [15]) (./_minted-Tutorial/21058E2884DE0E2797798658CEC2E54FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/34FD0122B81370E5F3563284D60CFF17BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:SeqIO-reverse-complement' on page 16 undefined on input line 278. (./_minted-Tutorial/A54827F8BB70B416D99923FF5088CCC0BD02851C2FB632864165FCA4920 46548.pygtex [16]) (./_minted-Tutorial/427B060556C1BB93F326E658CF6C8753BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/692203B43955DEEBA597180E090EBEBDBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0A4AF1735B84470B955325263082B386BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:seq-module-functions' on page 17 undefined on inp ut line 353. (./_minted-Tutorial/F7FFCC027B254744B7B47314F48923FEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/186028EBD7A9B4B4276808BC5B218A70BD02851C2FB632864165FCA4920 46548.pygtex [17]) (./_minted-Tutorial/2F42D08D321C7BC408E4704103B70F2EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/544C1E23D35FAC62FBE120AA24D6EF82BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A487EC21D16913E80A948528AA61CD64BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7BC83BB268F7BA2D207FDE001034CF98BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/59D2BC7361BC3147180163BF1D4DDE79BD02851C2FB632864165FCA4920 46548.pygtex [18]) (./_minted-Tutorial/087889BE640F25A1E1D26EB819B55990BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:SeqIO-translate' on page 19 undefined on input li ne 469. LaTeX Warning: Reference `sec:seq-module-functions' on page 19 undefined on inp ut line 475. (./_minted-Tutorial/C387354CBEC6317F42CD9F596E775BE0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A3542F02D57EFCE9A6BD62C8FAB75CE3BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F712265A78CB2524ABF9371BE2F3874DBD02851C2FB632864165FCA4920 46548.pygtex [19]) (./_minted-Tutorial/3A75E7306D7D2D81DE0C37038600A10ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/06DBC59F2EAD33E7A951888537876615BD02851C2FB632864165FCA4920 46548.pygtex) [20] (./_minted-Tutorial/4393B8540CDD633A481E29B1CF252CE6BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:seq-to-string' on page 21 undefined on input line 598. (./_minted-Tutorial/7F9F7641B195E2CACA3F77158DBE190CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/04626286E6AB345CB89BE7B7A049C338BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F2723D89FDBA794E82A8285BABB369CB669566ECC2CFEDC7429F829576A D0DC6.pygtex [21]) (./_minted-Tutorial/64147FAF6F5C5028B073B3C809EE3E84BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DFDB859800920408E228736AD921B5DFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D95D20C3283ADEDD76DAB3382BB1B040BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/AA99EB190DCB9061B7FD403ECDCEE451BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F5B125A1E250BEBA411CA3B2BBF3EDDDBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/39AA48793A64869F7458C1A2A0D69D2EBD02851C2FB632864165FCA4920 46548.pygtex [22]) (./_minted-Tutorial/29E9F3CE64EB99D132246C3633BA375CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/394CF49B3AAB621203EE87F2BD334CC4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3F2DB933A33BDAA3DB2299F2701B61CBBD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:seq-to-string' on page 23 undefined on input line 741. (./_minted-Tutorial/4307A980AB242F22FB1B0952E3FD37C0BD02851C2FB632864165FCA4920 46548.pygtex)) [23] [24] (./Tutorial/chapter_seq_annot.tex Chapter 4. LaTeX Warning: Reference `chapter:seq_objects' on page 25 undefined on input li ne 4. LaTeX Warning: Reference `chapter:seqio' on page 25 undefined on input line 4. (./_minted-Tutorial/032C91EF2474FD3535629DC0CDABC809BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `chapter:seq_objects' on page 25 undefined on input li ne 20. LaTeX Warning: Reference `chapter:seqio' on page 25 undefined on input line 20. LaTeX Warning: Reference `sec:FASTQ-filtering-example' on page 25 undefined on input line 33. [25] LaTeX Warning: Reference `sec:seq_features' on page 26 undefined on input line 37. LaTeX Warning: Reference `chapter:seqio' on page 26 undefined on input line 47. (./_minted-Tutorial/28ED5ED993E569AC59FDA480CD731BBCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/AD6AF21FB49ADADD3E9DF52EA341F92CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6A9404FB47549766BD16858F97A6D407BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B9321587EBA597104E435182128B200FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/22FC566F5A2B47EFD3D63327C15F7FC2BD02851C2FB632864165FCA4920 46548.pygtex [26]) (./_minted-Tutorial/510764EE0BB38AD6C688E71989677507669566ECC2CFEDC7429F829576A D0DC6.pygtex) LaTeX Warning: Reference `chapter:quick_start' on page 27 undefined on input li ne 130. LaTeX Warning: Reference `chapter:seqio' on page 27 undefined on input line 132 . (./_minted-Tutorial/885E3C393ABBD6448EFA8A6D8D849822BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D582F58715BB8D12B0A5A9CF9631A27CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C60AA1EB70D11A096523A07FC1BD2085BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7D4386614F3407AC9AFEDB894B0987D9669566ECC2CFEDC7429F829576A D0DC6.pygtex [27]) (./_minted-Tutorial/B659A3B495F4BF5A9945B83B9A29DC2BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/20D2783513E8123B155B9FE0B3FE7B4A669566ECC2CFEDC7429F829576A D0DC6.pygtex) LaTeX Warning: Reference `chapter:seqio' on page 28 undefined on input line 211 . (./_minted-Tutorial/86FA506E88E30EB82E7186A57112C98CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D582F58715BB8D12B0A5A9CF9631A27CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C9D6C80CD8B460806CB6E7C2935EA601BD02851C2FB632864165FCA4920 46548.pygtex [28]) (./_minted-Tutorial/332D9C95CC14B124A8528A76F4917ECEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/925BCB3D0BD30380832BA5F2C6367AD9BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D20F0AF7810B74883E42451F5810F926BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/47F0F8DD59EC4A71D5CA336E217F0C0DBD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:seq_features' on page 29 undefined on input line 275. LaTeX Warning: Reference `sec:locations' on page 29 undefined on input line 284 . LaTeX Warning: Reference `sec:locations' on page 29 undefined on input line 292 . [29] [30] (./_minted-Tutorial/AD47AD29D6F7927F9406BE5609676388BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A89E686BA7930FBF8AE5CCC27E1AC5BFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CD11055284C1F524585846BFB03F6EE8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1C597DC49857D56C7E140B1D795218F3BD02851C2FB632864165FCA4920 46548.pygtex [31]) (./_minted-Tutorial/EF871449F651FE5E7DFD84165065B14ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9ABE11BA111CDBEACB55DC5424AC66A1BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:locations' on page 32 undefined on input line 502 . (./_minted-Tutorial/D86C559003980DC8749AF92530435DFDBD02851C2FB632864165FCA4920 46548.pygtex) [32] (./_minted-Tutorial/1C0A562378DEEE8E210765437B3E1700BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C7BB516F80A4A8F5C291ABDF3B6E0B49BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C737C9C2EF139AD4F965B3AC1FF72C75BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/411A7DB0F7208D21C6099C86249233F3BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0C3ED75879971F09D72A92585654A32CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A4ED33BCBC94515EF1D3FF0CB0F2ACE9BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1432CF672342B0A065BD2202A12E3920BD02851C2FB632864165FCA4920 46548.pygtex [33]) (./_minted-Tutorial/3B61DDBFCC5B04C6BD9F6ED183CD312DBD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:seq-comparison' on page 34 undefined on input lin e 600. LaTeX Warning: Reference `sec:locations' on page 34 undefined on input line 608 . (./_minted-Tutorial/5039524AFDCC2184E0FA37B45448443DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/93B3AF8F7193FF3944CC29E4FE0F9689BD02851C2FB632864165FCA4920 46548.pygtex [34]) LaTeX Warning: Reference `chapter:seqio' on page 35 undefined on input line 648 . LaTeX Warning: Reference `sec:Bio.SeqIO-and-StringIO' on page 35 undefined on i nput line 651. (./_minted-Tutorial/B952BEC5DDC5176F8F8F8984196831F3BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D16AA28F327A9B07E6AE64737A6B2340BD02851C2FB632864165FCA4920 46548.pygtex [35]) (./_minted-Tutorial/C08741A8063662E3CF1313052B7EA7A4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/83934A12FA213409ADDBED937D121BEBBD02851C2FB632864165FCA4920 46548.pygtex [36]) (./_minted-Tutorial/7693A79AF1B5C3B342CEF51858B48A85BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C59A3BD3577D6DA7BB95528A68C9B311BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7FC68DDC3F22A92C79064A5F631D2457BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:SeqRecord-format' on page 37 undefined on input l ine 793. (./_minted-Tutorial/E4EE1174D845FF0CABBFC735D0B5DF82BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:FASTQ-slicing-off-primer' on page 37 undefined on input line 805. LaTeX Warning: Reference `sec:FASTQ-slicing-off-adaptor' on page 37 undefined o n input line 806. LaTeX Warning: Reference `chapter:seqio' on page 37 undefined on input line 819 . (./_minted-Tutorial/890A92414EE9EE5FB3B2F7B834307EDFBD02851C2FB632864165FCA4920 46548.pygtex [37]) (./_minted-Tutorial/CC2666A1113601FF5DADD7ED2118A3FEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E29BCA3E51B6B75E0E5EFF1718501669BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D20811F7EAA2FB2ED0A37B2C0F1B24D4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E92A933EB86A743F11CDB887CD2A9C1BBD02851C2FB632864165FCA4920 46548.pygtex [38]) (./_minted-Tutorial/675833B93A69F5DE13F680548E25EA3EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A8312A90F6B97A21EE1619F9A898ED36BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/68AB1E9E397375F82B6F3361E55900E7BD02851C2FB632864165FCA4920 46548.pygtex) [39] (./_minted-Tutorial/023FBCDB71B9572D8D436D0AA1193B63BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1B29C13B779A89B3DE705BA0061B8793BD02851C2FB632864165FCA4920 46548.pygtex)) [40] (./Tutorial/chapter_seqio.tex Chapter 5. LaTeX Warning: Reference `chapter:quick_start' on page 41 undefined on input li ne 4. LaTeX Warning: Reference `chapter:seq_annot' on page 41 undefined on input line 4. (./_minted-Tutorial/3F38D5012926DD7C810DA2383F53D498BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `chapter:seq_annot' on page 41 undefined on input line 12. LaTeX Warning: Reference `chapter:seq_objects' on page 41 undefined on input li ne 12. LaTeX Warning: Reference `sec:low-level-fasta-fastq' on page 41 undefined on in put line 14. LaTeX Warning: Reference `sec:SeqIO_Online' on page 41 undefined on input line 22. LaTeX Warning: Reference `sec:appendix-handles' on page 41 undefined on input l ine 22. (./_minted-Tutorial/CE17C15EEBC1BDC9846A29B8188EB6789543DFECA235A69AE23006BA05B 4EB70.pygtex [41]) LaTeX Warning: Reference `sec:sequence-parsing' on page 42 undefined on input l ine 43. (./_minted-Tutorial/357B0F655AFAF3808FD8EE23EE5009549543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/480025795249845BAA7F48D4A45ADB21BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:sequence-parsing-plus-pylab' on page 42 undefined on input line 68. (./_minted-Tutorial/F164035E9D5F8C01F84F5F95E2B166F19543DFECA235A69AE23006BA05B 4EB70.pygtex [42]) (./_minted-Tutorial/C82398A4A04383A063D2E648811230529543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/1A4F5B10F895EA1A0898B313C8FE3AED9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/665A7700DAC7A651C288CFBC04910736669566ECC2CFEDC7429F829576A D0DC6.pygtex) [43] LaTeX Warning: Reference `chapter:seq_annot' on page 44 undefined on input line 150. (./_minted-Tutorial/3FC3FD6D12B3257730F3B4F11F7F82E99543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/8C2F2A27559FC0864F47BBE543950C26669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/C1B7B447DBB266302BC82D7DBD1622219543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/3453EFD7B001ACCBD0126A13C98BAA4F9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/23C65980427B41C7D9E32947CD41FD829543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/36073AAEBADCD344208056C9868E001CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/32EC540B3F53C56F8F39A2A185A32CE6BD02851C2FB632864165FCA4920 46548.pygtex [44]) (./_minted-Tutorial/3B09F0463D35461C42D2272763E734519543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/16EB556A216CBBE3D3F735350EA21A2A9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/F1A3FE258B41FCC45D4A8272B13EC395669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/AD9EF2BC42CEF4E413923F9BFFE1BE07669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/58A82383AA9DEBBEEEC6694BA2DE777ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9562C263804C6DD613F075A435553A9FBD02851C2FB632864165FCA4920 46548.pygtex [45]) (./_minted-Tutorial/5654C63CA8B2C75821B4DD795E1D9C91BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:writing-sequence-files' on page 46 undefined on i nput line 306. (./_minted-Tutorial/1525A6F338DC70B7A056F15305A9579DBD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:appendix-handles' on page 46 undefined on input l ine 329. (./_minted-Tutorial/DCDC3EB1E5C136F423AC65A1907BE6B1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/23394A4616015FFE4619934E98424178BD02851C2FB632864165FCA4920 46548.pygtex [46]) (./_minted-Tutorial/48D36449ADA742065AC871DB512A14FFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7160C98DFF3E9F14B8FDC3EDEA5AAADEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1E26B09583F35CC794E34E0D3C822C09BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:SeqIO-index-bgzf' on page 47 undefined on input l ine 398. LaTeX Warning: Reference `sec:efetch' on page 47 undefined on input line 414. [47] (./_minted-Tutorial/A06B859656EACE1EB197B276B0CAD4769543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/5B68AB5634E46F0A59E5C238174AC4F0669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/AAC02B6C28E92C88B051BB2DE451DBD89543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/FECB9DCFA3C63121DB586752E4215990669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/CC27A8BEB077BCA7346A8D13F39867D79543DFECA235A69AE23006BA05B 4EB70.pygtex [48]) (./_minted-Tutorial/AE8667CEAACFF0F40839EE86774DD05D669566ECC2CFEDC7429F829576A D0DC6.pygtex) LaTeX Warning: Reference `chapter:entrez' on page 49 undefined on input line 50 4. LaTeX Warning: Reference `sec:entrez-guidelines' on page 49 undefined on input line 504. LaTeX Warning: Reference `chapter:uniprot' on page 49 undefined on input line 5 09. (./_minted-Tutorial/6467B5574DF68CEA13D016BEEC8841A49543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/3D2A207C38AC647D99F5A8861A9D1AA6669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/DDD2E1D663317F4FFB7F8B7F03E4989FBD02851C2FB632864165FCA4920 46548.pygtex [49]) LaTeX Warning: Reference `sec:seqio_todict' on page 50 undefined on input line 565. LaTeX Warning: Reference `sec:SeqIO-index' on page 50 undefined on input line 5 71. LaTeX Warning: Reference `sec:SeqIO-index-db' on page 50 undefined on input lin e 575. LaTeX Warning: Reference `sec:SeqIO-indexing-discussion' on page 50 undefined o n input line 578. LaTeX Warning: Reference `sec:SeqIO-index' on page 50 undefined on input line 5 88. (./_minted-Tutorial/2EE890D1737C8A159C79BA4FCA81BB03BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/77FD1FB1550DD72BE3E8CFAC5C21C7DFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/022009B5C6117EE88C29BE7A45D87CF6BD02851C2FB632864165FCA4920 46548.pygtex [50]) (./_minted-Tutorial/FE4CF732C73126A3874795838D95FAB5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E7420F7622CCC097E8ADA484A405A3C6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/07A24756D2FDD5E9B66DEB7412FC4D6E9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/7F04F15A8B73F26152ED44DB3C48528F669566ECC2CFEDC7429F829576A D0DC6.pygtex) LaTeX Warning: Reference `sec:fasta-parsing' on page 51 undefined on input line 661. (./_minted-Tutorial/55430EAFE498E385842834603E0B8C869543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/47CA5358E0862EF3920CC2BF888DBDB89543DFECA235A69AE23006BA05B 4EB70.pygtex [51]) (./_minted-Tutorial/A50FCDC5880666D012F0A802072B4AC5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D27A33312B4E81447304AAB2BAF2F6DC9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/11D55B86CA819707A4B89E7FDA2E6E83669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/74E272C92C546FD61FA6D3DA5C178893BD02851C2FB632864165FCA4920 46548.pygtex) [52] (./_minted-Tutorial/415024C641C8DA7A09117B3DFE240C78BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/487DCC9F44A2539C9B32C0122AEF4065BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5098CD053449CEC3C9C30C90A007A364BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:fastq-indexing' on page 53 undefined on input lin e 783. (./_minted-Tutorial/EEEF4ABAD66CE989F67C9E27EEDE95CCBD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:seqio-todict-functionkey' on page 53 undefined on input line 804. (./_minted-Tutorial/F6AFF5A59B0706E4973BC1656FBD2D669543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/C4099CB0613585FCCD5EA7D8198704CEBD02851C2FB632864165FCA4920 46548.pygtex [53]) Overfull \hbox (9.93459pt too wide) in paragraph at lines 848--853 \OT1/cmr/m/n/10 FTP site ([][]$\OT1/cmtt/m/n/10 ftp : / / ftp . uniprot . org / pub / databases / uniprot / current _ release / knowledgebase / complete / (./_minted-Tutorial/D52DA4EEEEE2BF0FBE89EE253714929DBD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:SeqIO-sort' on page 54 undefined on input line 86 6. Overfull \hbox (4.48064pt too wide) in paragraph at lines 891--894 []\OT1/cmr/m/n/10 As of Gen-Bank re-lease $210$, there are $38$ files mak-ing u p the vi-ral se-quences, \OT1/cmtt/m/n/10 gbvrl1.seq\OT1/cmr/m/n/10 , ..., \OT1 /cmtt/m/n/10 gbvrl38.seq\OT1/cmr/m/n/10 , (./_minted-Tutorial/D41A88D88AB398F0C3B719A5C7D017C144BBF456F55B5DC060035246D76 9EADB.pygtex [54]) (./_minted-Tutorial/B4D970E8C81930851D8639D77EC3E41044BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/7C4E0944FB13EC4E75DD6FC64900395ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C68CC3C9B3A505FB972706356D7F336FBD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:seqio-index-getraw' on page 55 undefined on input line 948. (./_minted-Tutorial/61AD507889ED86CFCEFC880BAF2A2777BD02851C2FB632864165FCA4920 46548.pygtex) [55] (./_minted-Tutorial/DC5117490176932EFB8A7F0E0DA450F6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/657D43328835FC01F9133F8BC964475D44BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/82CBCD9B9F23373D67D9D0D7D2CA363FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/36F8D0FD2B4ADF57AC4203A0C80C6471BD02851C2FB632864165FCA4920 46548.pygtex) [56] (./_minted-Tutorial/9CEF7BF9B2634ACBC930BA5EB6DD73429543DFECA235A69AE23006BA05B 4EB70.pygtex [57]) (./_minted-Tutorial/AC02E3950380715FC960C04EF317D69F9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/1C65F538FA7F22F7BB5183FC1553A0C6669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/935F773BF84C3BF326F4BA093FEC79D4669566ECC2CFEDC7429F829576A D0DC6.pygtex [58]) LaTeX Warning: Reference `sec:seqio-index-getraw' on page 59 undefined on input line 1189. (./_minted-Tutorial/C194E2231D844AE7D0223173D2A899919543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/10CB116B7358444BA68AFA046B5B84D59543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/29D12D495374A5A8C37AEB7083851DEABD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:SeqIO-fastq-conversion' on page 59 undefined on i nput line 1232. LaTeX Warning: Reference `sec:SeqIO-fasta-qual-conversion' on page 59 undefined on input line 1232. [59] LaTeX Warning: Reference `sec:seq-reverse-complement' on page 60 undefined on i nput line 1247. (./_minted-Tutorial/920133226A22EEB682D854077D7FB78FBD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:SeqRecord-reverse-complement' on page 60 undefine d on input line 1258. (./_minted-Tutorial/4EBA0A67E686E73FAA1A0EB27C260028BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C06224D76A18C126B27DFE55444AA3FDBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E381FF526AC999B71717F178C997F6B2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5F05AD4A17978E60C531612707D8F26ABD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:SeqIO-translate' on page 60 undefined on input li ne 1311. [60] (./_minted-Tutorial/D19467E367634413AE9EE17A62E5D9EA9543DFECA235A69AE23006BA05B 4EB70.pygtex) LaTeX Warning: Reference `sec:SeqRecord-format' on page 61 undefined on input l ine 1331. (./_minted-Tutorial/EDF3737891061C33EDE0FBFD16CCC63B9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/D1EAD55A1F8AD3DEAB82383A4F020F539543DFECA235A69AE23006BA05B 4EB70.pygtex) Overfull \hbox (19.46596pt too wide) in paragraph at lines 1349--1351 \OT1/cmr/m/n/10 Making a sin-gle call to [][]\OT1/cmtt/m/n/10 SeqIO.write(...) []\OT1/cmr/m/n/10 is also much quicker than mul-ti-ple calls to the [][]\OT1/cm tt/m/n/10 SeqRecord.format(...) [61] (./_minted-Tutorial/2F337ECD1F936D416FF9C5C6F41A02D7BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3337CD054623BAC21B6021E996EE0DFD9543DFECA235A69AE23006BA05B 4EB70.pygtex) Overfull \hbox (21.32593pt too wide) in paragraph at lines 1393--1397 []\OT1/cmr/m/n/10 Likewise, when pars-ing FASTQ files, in-ter-nally [][]\OT1/cm tt/m/n/10 Bio.SeqIO.parse() []\OT1/cmr/m/n/10 calls the low-level [][]\OT1/cmtt /m/n/10 FastqGeneralIterator (./_minted-Tutorial/D3AF6542680CA390CDA8C8DF87C693D3BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `chapter:cookbook' on page 62 undefined on input line 1412. (./_minted-Tutorial/D749A84299CF58E876E9A899069830DB9543DFECA235A69AE23006BA05B 4EB70.pygtex)) [62] (./Tutorial/chapter_align.tex Chapter 6. LaTeX Warning: Reference `sec:appendix-handles' on page 63 undefined on input l ine 31. LaTeX Warning: Reference `sec:AlignIO-count-argument' on page 63 undefined on i nput line 35. (./_minted-Tutorial/9CC7A6864E21FFDDB3F4D02F2870DF42669566ECC2CFEDC7429F829576A D0DC6.pygtex [63]) (./_minted-Tutorial/81FAFBAECB3A03B11080ECF19D4CCC80BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/31E7567531B3A1035700A1E555A47FC0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D2523B56ECD3F392CD3E37EEBE302AECBD02851C2FB632864165FCA4920 46548.pygtex [64]) LaTeX Warning: Reference `sec:alignment-format' on page 65 undefined on input l ine 113. (./_minted-Tutorial/AC12821BA0AEE8F48238EAC359A31077BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A6D29782988E1FB75F30F2D60AB93C4EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E48647CD11476AB33349258EA43C50F2669566ECC2CFEDC7429F829576A D0DC6.pygtex) [65] (./_minted-Tutorial/16CCFD1DA7A71D5F6D9A86870C560407BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C0B89B536EECC0E9CC886A8B4CC9713EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/EE5558D4A829B63692DC55F8215FD331669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/FA669D1E3279749AAAA27A72F3B44533669566ECC2CFEDC7429F829576A D0DC6.pygtex [66]) (./_minted-Tutorial/9119ACDDD7EFFD39008E7F98AB7BF756BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5C54BE5D00F2871BB58E36C383B3B4DE669566ECC2CFEDC7429F829576A D0DC6.pygtex) [67] (./_minted-Tutorial/CE4E385956165A535376F6D73447D3F7BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F55715342346472744E837C465922E6E669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/1B5E788850B45798FCA06125D5880A14669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/B913EFE8AC0AC995AF3DCCAC856FF020669566ECC2CFEDC7429F829576A D0DC6.pygtex [68]) (./_minted-Tutorial/5F9DFDCFBF42A04D6BD31E8E9638DA57BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/BDB62F4C6418AA14588B7DBEA69D61C5669566ECC2CFEDC7429F829576A D0DC6.pygtex) [69] (./_minted-Tutorial/A8D0C008D3D8E2CB96D91B2A5FF2D318BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9458BC75C22971F0F7F09C79C7D6AFE0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/FEF99AFE39529F3F1A5EFC7A23714477669566ECC2CFEDC7429F829576A D0DC6.pygtex [70]) Overfull \hbox (5.54102pt too wide) in paragraph at lines 434--435 \OT1/cmr/m/n/10 ever you can't do that when your records come from a gen-er-a-t or/iterator. There-fore the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write() LaTeX Warning: Reference `sec:SeqIO-conversion' on page 71 undefined on input l ine 444. Overfull \hbox (39.68698pt too wide) in paragraph at lines 442--447 [][]\OT1/cmtt/m/n/10 Bio.AlignIO.parse() []\OT1/cmr/m/n/10 and then save them u s-ing the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write() []\OT1/cmr/m/n/10 -- or just use the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.convert() (./_minted-Tutorial/9776F24C4F96F850E549BEF997E4D18CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D8256B42DA32121F3B83617DD03F4024BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DA108466F70572EEAE2D54AEA4C156A1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8FD10ACD641F4427B35E96F33B44479F669566ECC2CFEDC7429F829576A D0DC6.pygtex [71]) (./_minted-Tutorial/ACC9FF1F2F025F77815D96DC3115B7DFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7E530BB128C8AE6BCF7BCE91DD4AF189669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/C17F8CD5F33DB6EB328532E02ADD1FE6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C02EB78C9555A4FEE4954D77162ACF99669566ECC2CFEDC7429F829576A D0DC6.pygtex [72]) (./_minted-Tutorial/74D8F602592BD3646F12A04951B2C44CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CB14E2060AF38515C129AB5808537F169543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/E78F5A80C222A5B2777910FED4F43F56669566ECC2CFEDC7429F829576A D0DC6.pygtex [73]) (./_minted-Tutorial/4D0AF4A40C449D27FF181EC477C63CE6BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:SeqRecord-format' on page 74 undefined on input l ine 633. (./_minted-Tutorial/2590B11C695B984E246A0A91734F786CBD02851C2FB632864165FCA4920 46548.pygtex) [74] (./_minted-Tutorial/508710FC1759BFFED598544DEC99BC0DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/886094CE2C1CAC714387144709D5A47ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6DC12DBE1D4FD44E7395C66258B5EAC9BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CAC16111FAD8C2E739F6D7C04A986BF0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A4149E9BEF55B5853014A59A3CBBFBE5BD02851C2FB632864165FCA4920 46548.pygtex [75]) (./_minted-Tutorial/8327145320A3BCB412D977F6683B71A2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1E096B06E33D157FFE18E045579F838CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C7331D522D75BB7830A1364BC3B71692BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C45FE25766D82D1C4A245CBB9A77DB00BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C0937EED558D842CEA8E3DB9514C6E59BD02851C2FB632864165FCA4920 46548.pygtex [76]) LaTeX Warning: Reference `sec:SeqRecord-addition' on page 77 undefined on input line 813. (./_minted-Tutorial/8EC03E9C8500D05C6439AC85123A9253BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/AE857C14E4731CC6F6EBA53051460097BD02851C2FB632864165FCA4920 46548.pygtex) [77] (./_minted-Tutorial/F88E003F9A4A95A929AA549FA710239CBD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:subs_mat_ex' on page 78 undefined on input line 8 92. (./_minted-Tutorial/523928538FA511A925EC995B1803BD16BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:pairwise' on page 78 undefined on input line 913. [78] LaTeX Warning: Reference `chapter:seqio' on page 79 undefined on input line 917 . (./_minted-Tutorial/CD47D1913C82182C164BD47DA4715282BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:emboss-needle-water' on page 79 undefined on inpu t line 947. (./_minted-Tutorial/E7AA94166BAA5F4CBB44EF4336F3E893BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B49F47BF4F2EB4093BDE51E631C63064BD02851C2FB632864165FCA4920 46548.pygtex) [79] (./_minted-Tutorial/230B4706E315BD2F2A44F2EBCB37A442BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C11A66992B6C74B61F5A0BE7757AF3BCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/EAE190D91CC491562308EE568F986368BD02851C2FB632864165FCA4920 46548.pygtex [80]) (./_minted-Tutorial/6256254C5A7DFD21185291C77133BFDFBD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `chapter:phylo' on page 81 undefined on input line 109 3. (./_minted-Tutorial/FC96AF22EDD72BC4AC2EE47EBAA6B045BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E941CFC951CAE25312D9A5CAC9B27425BD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (8.40039pt too wide) in paragraph at lines 1126--1130 []\OT1/cmr/m/n/10 By de-fault MUS-CLE will out-put the align-ment as a FASTA fi le (us-ing gapped se-quences). The [][]\OT1/cmtt/m/n/10 Bio.AlignIO (./_minted-Tutorial/EA6A02999040945446E72AC6A00E56D8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/106ED62B0CFC10E7D5BC6CFC9CE003BDBD02851C2FB632864165FCA4920 46548.pygtex [81]) (./_minted-Tutorial/4D75AC9EDD74C466535F1EC4944833F7BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/14F1F3BAF80772F5999B0773C02432E7BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A261B9E9E2D4EB3C1DF5131C6F739998BD02851C2FB632864165FCA4920 46548.pygtex [82]) (./_minted-Tutorial/E2B86D066966C8BA13EEEF614D3E7454BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E87BDA1F176DA567A757DBA0231BC5BABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6BF1884F2D94AF8D067A2A20A9A41E2CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F551ABCEBB0043257A807C76B9D81B5CBD02851C2FB632864165FCA4920 46548.pygtex [83]) (./_minted-Tutorial/37B6E52C66902FA821D4B0E80172CE74BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:appendix-handles' on page 84 undefined on input l ine 1317. (./_minted-Tutorial/0BA045AD7DFE0F0F3DD972F3E2C40BA1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/482576AF06E80D82290535FF7857A240BD02851C2FB632864165FCA4920 46548.pygtex) [84] (./_minted-Tutorial/5D3CCD84BC2EC46BF5FD98E7A3FC7266669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/D9565472E525C9F2B734FC37A70D258E669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/39152F199CEBB3375366F2E947824519BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/256B036DA9C3EDBC9EE41E2E52FDE1ADBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DC6CF8B5CDDD2C32E2052C03AF385674BD02851C2FB632864165FCA4920 46548.pygtex [85]) (./_minted-Tutorial/CEE035FF629B69F7D6B6351C1DCE2493BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DF151703751D72BD556402B910190A87BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/004029547AAB1172AF2684D2CA89EA88BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Citation `durbin1998' on page 86 undefined on input line 1492. (./_minted-Tutorial/554024580088332FAF0EA9296BACE82EBD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:pairwise-aligner' on page 86 undefined on input l ine 1505. [86] (./_minted-Tutorial/419ECEB266819C8DCC38EB3E1DC3E361BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/143B9D317680E51D3A6E5641208720CABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6CCC707502EDD92E9C355854215BF885BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0A4B1939051DE630E53C7151447C8DD4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/2B6197C314840AD3EC15C56F366120C5BD02851C2FB632864165FCA4920 46548.pygtex [87]) LaTeX Warning: Citation `waterman1987' on page 88 undefined on input line 1578. (./_minted-Tutorial/E5E00F47BD7A0C8BC5F8818526283868BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:pairwise-substitution-scores' on page 88 undefine d on input line 1608. LaTeX Warning: Reference `sec:pairwise-affine-gapscores' on page 88 undefined o n input line 1608. LaTeX Warning: Reference `sec:pairwise-general-gapscores' on page 88 undefined on input line 1608. LaTeX Warning: Reference `sec:pairwise-basic' on page 88 undefined on input lin e 1609. LaTeX Warning: Reference `sec:pairwise-affine-gapscores' on page 88 undefined o n input line 1612. LaTeX Warning: Reference `sec:pairwise-general-gapscores' on page 88 undefined on input line 1613. (./_minted-Tutorial/52B42D5819C8EC5D57A21AE60D28F6CEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5F566D907B2F88621EC4175F1F17AE04BD02851C2FB632864165FCA4920 46548.pygtex) [88] LaTeX Warning: Citation `altschul1990' on page 89 undefined on input line 1639. LaTeX Warning: Reference `sec:pairwise-affine-gapscores' on page 89 undefined o n input line 1639. (./_minted-Tutorial/0FE96E337A3BA73D52896D46E2E233DCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/434D41043E1630324FA64E8B55B90BD5BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Citation `altschul1990' on page 89 undefined on input line 1668. (./_minted-Tutorial/48453D528762FF183499778647AF218BBD02851C2FB632864165FCA4920 46548.pygtex [89]) (./_minted-Tutorial/BD86EE3248811DE8FD9DE8ED02397A39BD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (76.42714pt too wide) in paragraph at lines 1707--1711 []\OT1/cmr/m/n/10 By de-fault, [][]\OT1/cmtt/m/n/10 aligner.substitution_matrix []\OT1/cmr/m/n/10 is [][]\OT1/cmtt/m/n/10 None[]\OT1/cmr/m/n/10 . The at-tribu tes [][]\OT1/cmtt/m/n/10 aligner.match_score []\OT1/cmr/m/n/10 and [][]\OT1/cmt t/m/n/10 aligner.mismatch_score Overfull \hbox (47.73264pt too wide) in paragraph at lines 1707--1711 []\OT1/cmr/m/n/10 are ig-nored if [][]\OT1/cmtt/m/n/10 aligner.substitution_mat rix []\OT1/cmr/m/n/10 is not [][]\OT1/cmtt/m/n/10 None[]\OT1/cmr/m/n/10 . Set-t ing [][]\OT1/cmtt/m/n/10 aligner.match_score []\OT1/cmr/m/n/10 or [][]\OT1/cmtt /m/n/10 aligner.mismatch_score LaTeX Warning: `h' float specifier changed to `ht'. LaTeX Warning: Reference `table:align-meta-attributes' on page 90 undefined on input line 1772. Overfull \hbox (32.852pt too wide) in paragraph at lines 1776--1820 [][] (./_minted-Tutorial/DCCEE6D592009E7B8E7DE81563D8D4CEBD02851C2FB632864165FCA4920 46548.pygtex [90]) [91] [92] (./_minted-Tutorial/98D9A5E0CD47E306CA0DA2AFE878514ABD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:pairwise-examples' on page 93 undefined on input line 1908. [93] (./_minted-Tutorial/FBB2100548FA74FADE3EAE28A2DE1911BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5C9DFA2EBF75572BAC340EC89D69B3D4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B788F0FBC120E74A47922EA232EB8671BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/504D01562B8D0E8E16B44A19B5FCD5EFBD02851C2FB632864165FCA4920 46548.pygtex [94]) (./_minted-Tutorial/DE91DA6F7C30BDD779CED0A91AB75DAFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A59C6CF4854355E98CC312686998A38BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3D37B0AE7B982968C1F24FD3EAA535EBBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5214A9AAFC8A40430707E3A6B6DC0D01BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/32985CB8E0884A44019C3AD3006E3F9FBD02851C2FB632864165FCA4920 46548.pygtex [95]) (./_minted-Tutorial/0758643069FF669538B9540ECD26C94CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0BDC838410673E955B3534CCCB8AC77FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/385490B66B3AC742DD6257196C784FE2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/BF27E9BF2471340998870C4A34296592BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A072B421EFC519E90AA0A540338E8E4EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C5780017603AFBC3BB3E9F52ED6688C59543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/76E331C5187C259B69198E91FC4AD112BD02851C2FB632864165FCA4920 46548.pygtex [96]) (./_minted-Tutorial/BF7EA4D0E316F88B3A609CF62C6CD357BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A564D138D2F52B4E2858B9D14814966BBD02851C2FB632864165FCA4920 46548.pygtex [97]) (./_minted-Tutorial/68A0723415861BAD8A4809FC33D4A2EEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/66AABFA387595237A8CE2518915213F8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B15E737F9393063B641148640673D991BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/EB25FB90F1A09B5CEE3428AFC4487B46BD02851C2FB632864165FCA4920 46548.pygtex [98]) (./_minted-Tutorial/EACCEA5889A222FB9830265E6A8DACB9BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/874975627BAB24A36A35FD4C633D246DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/35E64D230C4D7DA7362D8F8BA278ABB5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B0937117DDA6BB67D133C99E550AD5BDBD02851C2FB632864165FCA4920 46548.pygtex [99]) (./_minted-Tutorial/9C81CE609C3C74FF6DDE53A3528FDA3ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/AF515AF157FE4840A244030AD4DCE3A7BD02851C2FB632864165FCA4920 46548.pygtex [100]) (./_minted-Tutorial/C8046F75BC00F97BFBB444E7FCFDE7BABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9249A0A01E1025FA8711414C0E36841FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D1BAA37DF09A601FA4C6F2BEF162C3E0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/52868B2F44504455E4969FEF2614B63BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/433C9892AE287F36B57A8A95FE75AB94BD02851C2FB632864165FCA4920 46548.pygtex) [101] (./_minted-Tutorial/E7E68A8851DEEE300947A0531513417DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/60C347B45B5A049CB5B00A20D29DEF65BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1498327D070D6F98AC2E3DB39EAA1733BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Citation `kent2002' on page 102 undefined on input line 2424. (./_minted-Tutorial/6502BA65433924876427DBB6013C1003BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DE6EBD36098288038E8FFA4A045EC8FDBD02851C2FB632864165FCA4920 46548.pygtex [102]) (./_minted-Tutorial/B66E52A450DAB10C11EF0A5303F7F66EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8791CE2DDF360A2EB13DED7B355F1012BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/ED55B2BAF04247D4F10E951590AA5077BD02851C2FB632864165FCA4920 46548.pygtex [103]) (./_minted-Tutorial/779C61444C54C1736794F4E11B0E326DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9FF41FE72E025C3EC8E41470B268E105BD02851C2FB632864165FCA4920 46548.pygtex [104]) (./_minted-Tutorial/779CE460F4F768A71E6F35DDB7FDFA77BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9EF49B98A62C70CD81126514DF796600BD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (19.80069pt too wide) in paragraph at lines 2612--2613 \OT1/cmr/m/n/10 In this ex-am-ple, the to-tal num-ber of op-ti-mal align-ments is huge (more than $4 \OMS/cmsy/m/n/10 ^^B \OT1/cmr/m/n/10 10[]$), and call-ing [][]\OT1/cmtt/m/n/10 len(alignments) (./_minted-Tutorial/F89522EF58FB067C6521C367C7134716BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/76A8D90A1791A7B42DD5E6329FCCBE20BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/399250FB2BC395588B8004ACD928BE9CBD02851C2FB632864165FCA4920 46548.pygtex [105]) (./_minted-Tutorial/882BD2544386DECA236BF25C7DD64857BD02851C2FB632864165FCA4920 46548.pygtex [106]) (./_minted-Tutorial/22FCA15B328DDB0383F97012E3C1FA70BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Citation `schneider2005' on page 107 undefined on input line 272 5. LaTeX Warning: Reference `sec:substitution_matrices' on page 107 undefined on i nput line 2725. (./_minted-Tutorial/DA98355B1CF48169F9C82F2DD1F86A29BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/13D646E6B49807044DBDC43707A09846BD02851C2FB632864165FCA4920 46548.pygtex [107]) (./_minted-Tutorial/467CA50C36874E405E988587FEC07686BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E4398C5237FE7113BC5A8DE3B0E138A6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E827958137C7E69DAEDB0C4151298E62BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A94C18D2207C354646F831D57FD85B35BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/801A90831A5799E3FF1FC0A5E721F4F2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4329189CC201D756D0770BD7596DF0D8BD02851C2FB632864165FCA4920 46548.pygtex [108]) (./_minted-Tutorial/C7C0911CDDC1913791B1BD1EDA0EC55FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F13283947C7FDCA9456A70797E029A73BD02851C2FB632864165FCA4920 46548.pygtex [109]) (./_minted-Tutorial/AAF53200644F4F68779FB844730087D3BD02851C2FB632864165FCA4920 46548.pygtex [110]) (./_minted-Tutorial/FCBF8AC8128D86DFE3607A8465EC034BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/96A1DC106863D5F4D96B9200B7B5BE06BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7323803F0E90CDA6FB16D10E868318BBBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/FBFC10402209A281F117C1A7C3D2057DBD02851C2FB632864165FCA4920 46548.pygtex [111]) (./_minted-Tutorial/04CF4E50F88DE1F6947064E1188A1BABBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/88E3C6FE8CD1E52180656649B61F8CBBBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3352A1628AB7C0D638BB368952D0DEDCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/842D73F66680850822D006857AE71FE7BD02851C2FB632864165FCA4920 46548.pygtex) [112] (./_minted-Tutorial/FAF36BBB1FEE777074E1CB3B06F18C8ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6B4057929CCF1526CF34FF943CFE3135BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E0AB5DB602ED615A4FA228E22B0CC4F2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5E9D6563DE4DEF6BBF8840F7693212F4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7C466424D72F09AE5AACA884161416F9BD02851C2FB632864165FCA4920 46548.pygtex [113]) (./_minted-Tutorial/F3DBACE95BC0B45F9EEF5BC8C67DEB0ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CC9E9C07C5DC6BDB4071B2A0EA825278BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/55D34AF6272FC77B12E7D4DD16884A6BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A5A764AD6E5C1A70216D27249F680093BD02851C2FB632864165FCA4920 46548.pygtex [114]) (./_minted-Tutorial/54EF0A3F068FF357EC3C51C6E1172A57BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1E78F0FD7A0E228935EE2D650C9315ECBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CEB2F5A09DE2611D752331C16E5BE61FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/007A62C4B86AFB9385A7D86241664707BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E19493E35A1B212412F37B3A7079D5ADBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0B051755682044B54FDC8CE728FD23B5669566ECC2CFEDC7429F829576A D0DC6.pygtex [115]) (./_minted-Tutorial/659317FF2415828FBE0F4505ECB5B4E5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/60D893638743BD147116D13E00593D6CBD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Citation `altschul1990' on page 116 undefined on input line 3282 . (./_minted-Tutorial/FC6687367D9EC6B1C018CE84CA30555D669566ECC2CFEDC7429F829576A D0DC6.pygtex [116]) (./_minted-Tutorial/9AD9216297281F0858F16EA5C03B98AFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CB8FA536E934FA2DC233E7FF52DEAED4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/14104DE21243051DA2E8D004C5D1A9EDBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3C42B04C08C3B07CABB6D2D7AE1F1B6DBD02851C2FB632864165FCA4920 46548.pygtex [117]) LaTeX Warning: Citation `henikoff1992' on page 118 undefined on input line 3354 . LaTeX Warning: Citation `dayhoff1978' on page 118 undefined on input line 3354. (./_minted-Tutorial/A6E4A89F3F3E07605D5B2BD57C7671CABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1795B10D0BABDD4E83A8B6EBE5DAF8CDBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/691C9A3D9A1EB52FAECF7E4C91F03BE9BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Citation `schneider2005' on page 118 undefined on input line 337 9. (./_minted-Tutorial/9A7868CC2484B4CFB34F94E7549F2519BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:pairwise' on page 118 undefined on input line 339 1. (/usr/share/texlive/texmf-dist/tex/latex/base/omlcmr.fd) (./_minted-Tutorial/A7706714F4982C826867A73C2B665ED0BD02851C2FB632864165FCA4920 46548.pygtex) [118] (./_minted-Tutorial/44E2C06C8661B128385CD75A7E7608AABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F120EF3444F3192D48657B4E52407017BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9AC50DD22A56E4DC2B26465D89DE35EABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CFB7E0A19AF729834746B283E60F2091BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7DA73F8FE9E6D95C2255220886791B5DBD02851C2FB632864165FCA4920 46548.pygtex [119]) (./_minted-Tutorial/E9F207F5DA488246642864EBF9EA466DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/15FD2886E49804AE97038F2733592C71BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1D1D98CF394058EA9EB8F6FA3B0DB75ABD02851C2FB632864165FCA4920 46548.pygtex [120])) [121] (./Tutorial/chapter_blast.tex Chapter 7. LaTeX Warning: Reference `chapter:searchio' on page 122 undefined on input line 18. Overfull \hbox (5.71313pt too wide) in paragraph at lines 45--46 []\OT1/cmr/m/n/10 NCBI guide-lines, from [][]$\OT1/cmtt/m/n/10 https : / / blas t . ncbi . nlm . nih . gov / Blast . cgi ? CMD = Web & PAGE _ TYPE = BlastDocs & [122] (./_minted-Tutorial/A6D333F851BCB09A0C02030C1BC37AB1BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:parsing-blast' on page 123 undefined on input lin e 73. (./_minted-Tutorial/69F91830197D9990EA9A0BD7D074EE21BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CF5D749C3878C5A1FD3C8C63CA51FD08BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/00F087159F0534545C0B7288838BEF0EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8A150C3E431DF572EF74B2B19AB15AF8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/2FDF7B3FB3DC9B4B3C157122F78C3F4EBD02851C2FB632864165FCA4920 46548.pygtex [123]) LaTeX Warning: Reference `chapter:seqio' on page 124 undefined on input line 13 3. LaTeX Warning: Reference `sec:parsing-blast' on page 124 undefined on input lin e 138. (./_minted-Tutorial/0E750E34F5C53FAE26988AF1CDC7FBC6BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:parsing-blast' on page 124 undefined on input lin e 160. (./_minted-Tutorial/C9558BD802C8764E46CF73625C14C204BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:parsing-blast' on page 124 undefined on input lin e 169. LaTeX Warning: Reference `sec:running-www-blast' on page 124 undefined on input line 178. [124] LaTeX Warning: Reference `sec:alignment-tools' on page 125 undefined on input l ine 206. (./_minted-Tutorial/21FCFA3232935EE0DF07988BE50D1AEF44BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/88BD5D9B190061FD4FD34D2573EE4792BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:parsing-blast' on page 125 undefined on input lin e 241. [125] LaTeX Warning: Reference `sec:running-www-blast' on page 126 undefined on input line 287. LaTeX Warning: Reference `sec:running-local-blast' on page 126 undefined on inp ut line 289. LaTeX Warning: Reference `sec:appendix-handles' on page 126 undefined on input line 304. (./_minted-Tutorial/CF5D749C3878C5A1FD3C8C63CA51FD08BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C9558BD802C8764E46CF73625C14C204BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/16EEC09BFB431080BCE9C5E6ADA5DAA9BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E34865BFB20F9D165069B84AE5218004BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `chapter:seqio' on page 126 undefined on input line 34 0. LaTeX Warning: Reference `chapter:align' on page 126 undefined on input line 34 0. (./_minted-Tutorial/E0F63513A18DD0126288BC98B9F40394BD02851C2FB632864165FCA4920 46548.pygtex [126]) (./_minted-Tutorial/A614B982013DB6EC38FCADD82303A8BEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DD49CD888784736545A3066AC257FBFFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B7DE908D2BB5BA4FD1BB179810D8D238BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/16EEC09BFB431080BCE9C5E6ADA5DAA9BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/68259DF5B1930070C029D5A72D891A36BD02851C2FB632864165FCA4920 46548.pygtex [127]) (./_minted-Tutorial/0C1E2B9A587BB44A7E19E83A4E5B1924669566ECC2CFEDC7429F829576A D0DC6.pygtex) LaTeX Warning: Reference `fig:blastrecord' on page 128 undefined on input line 452. Excluding 'htmlonly' comment. LaTeX Warning: Reference `fig:psiblastrecord' on page 128 undefined on input li ne 468. Excluding 'htmlonly' comment. LaTeX Warning: Float too large for page by 32.27644pt on input line 481. ) [128] [129 <./images/BlastRecord.png>] [130 <./images/PSIBlastRecord.png>] (./Tutorial/chapter_searchio.tex Chapter 8. (./_minted-Tutorial/6D0EADF658E662CBA394834EFAC7346E669566ECC2CFEDC7429F829576A D0DC6.pygtex) [131] Overfull \hbox (2.9019pt too wide) in paragraph at lines 85--93 [][][]\OT1/cmtt/m/n/10 HSPFragment[]\OT1/cmr/m/n/10 , to rep-re-sent a sin-gle con-tigu-ous align-ment be-tween query and hit se-quences. [][]\OT1/cmtt/m/n/10 HSPFragment Overfull \hbox (8.43927pt too wide) in paragraph at lines 105--107 [][][]\OT1/cmtt/m/n/10 parse []\OT1/cmr/m/n/10 is used for search out-put files with mul-ti-ple queries and re-turns a gen-er-a-tor that yields [][]\OT1/cmtt/ m/n/10 QueryResult (./_minted-Tutorial/0EF47CD31A1F702FF10BD5C95E6D18FCBD02851C2FB632864165FCA4920 46548.pygtex [132]) (./_minted-Tutorial/BCDD1F95C8585B3C70DE9C1280B51955BD02851C2FB632864165FCA4920 46548.pygtex [133]) (./_minted-Tutorial/7A12FEF8445FE62A62C651C8B4EC163FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/362861C831165FEA5413E0240053CD89BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/40227DD719AAD22E8DC2923BF43CE327BD02851C2FB632864165FCA4920 46548.pygtex [134]) (./_minted-Tutorial/FD9C81C098491598DBFB6208173BB575BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/87D36F7AE3CBC4EDC6FCCFDE0173412CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CA24D00985B075C56E7C71A246E439FFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DE8A481953AA0F7BD7A99C0E281AD1A0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E7AA701BE1D007CE77D402E8CBFC777ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/906546E8B6F7831A0E7C5FC93AA56A03BD02851C2FB632864165FCA4920 46548.pygtex) [135] (./_minted-Tutorial/0B914838010D3E86EC368E1702EB7253BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E4688DCAB619DBEB784ED0D836D1E619BD02851C2FB632864165FCA4920 46548.pygtex [136]) (./_minted-Tutorial/DDECA9EB99D9FA38003A52C176593072BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/578CBF904F35965EECFEC1FA694F0752BD02851C2FB632864165FCA4920 46548.pygtex [137]) (./_minted-Tutorial/C0EB7D270F64704BA5AF848A21AACD64BD02851C2FB632864165FCA4920 46548.pygtex) [138] (./_minted-Tutorial/84848AABE250EF05E85067B2CD3275B8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A2EA3A12F7596A64ECEE374A9C53499ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E7A6E47CCC64E8FADF02D1CDC6246863BD02851C2FB632864165FCA4920 46548.pygtex) [139] (./_minted-Tutorial/A3385B945E43CC076FFA693B27681F05BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DAAFD2AAF126ED8D7284764B561B5E2BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4B4824DE2ED3215F02082987EE573577BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/61406D58E5F7C40FD0A0280DCAA66B46BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/BF77764978D907008BC936FD2A5FCD95BD02851C2FB632864165FCA4920 46548.pygtex [140]) (./_minted-Tutorial/CE618F26D70602D511E57E53CD880444BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DE23F71CD74CF7717D38AD01C1E1C787BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `chapter:seq_annot' on page 141 undefined on input lin e 739. Overfull \hbox (27.24287pt too wide) in paragraph at lines 743--745 []\OT1/cmr/m/n/10 It should not sur-prise you now that the [][]\OT1/cmtt/m/n/10 HSP []\OT1/cmr/m/n/10 ob-ject has an [][]\OT1/cmtt/m/n/10 alignment []\OT1/cmr /m/n/10 prop-erty which is a [][]\OT1/cmtt/m/n/10 MultipleSeqAlignment (./_minted-Tutorial/338C616C7128C3DB7FFD516F5C2BDA12BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1195D6861E887568107FA7F463EA9BBABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/31F43A46088F6D2E63B39857A3536909BD02851C2FB632864165FCA4920 46548.pygtex [141]) (./_minted-Tutorial/16771935702D6A2A9762A80A621013D8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/046FE550C51B323D1E952A27E126FE19BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A55E467518B2E0F936A232F0970B1037BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6D69D310788199FBA6E8A5BF5CAB2021BD02851C2FB632864165FCA4920 46548.pygtex [142]) (./_minted-Tutorial/2C71B4AE1F4F9990447491C6C291ABC2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/FD7ECFDD9D017B829A54C995FEE42EEDBD02851C2FB632864165FCA4920 46548.pygtex [143]) (./_minted-Tutorial/3AD8335853E972C8E62AAF79CF0A3D33BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/758BAC7574A59544686354199D20892CBD02851C2FB632864165FCA4920 46548.pygtex) [144] (./_minted-Tutorial/7A63CB5E786CCE052981F7DD10653DA9BD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (14.20721pt too wide) in paragraph at lines 1055--1059 \OT1/cmr/m/n/10 func-tion re-turns a gen-er-a-tor ob-ject that yields a [][]\OT 1/cmtt/m/n/10 QueryResult []\OT1/cmr/m/n/10 ob-ject in each it-er-a-tion. Like [][]\OT1/cmtt/m/n/10 Bio.SearchIO.read[]\OT1/cmr/m/n/10 , (./_minted-Tutorial/DC4E434DA5B851CF1E22BD3608A311F4BD02851C2FB632864165FCA4920 46548.pygtex) [145] LaTeX Warning: Reference `sec:SeqIO-index' on page 146 undefined on input line 1089. Overfull \hbox (20.13245pt too wide) in paragraph at lines 1087--1092 []\OT1/cmr/m/n/10 In this case, the ideal choice would be to in-dex the file us -ing [][]\OT1/cmtt/m/n/10 Bio.SearchIO.index []\OT1/cmr/m/n/10 or [][]\OT1/cmtt /m/n/10 Bio.SearchIO.index_db[]\OT1/cmr/m/n/10 . (./_minted-Tutorial/0AB25750C7D89E832295045C60D6B8C4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DFACFE04880AE0CA2E8E32ABDC9E9868BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/51F256FC56FFFAE1F1E84A4EFC5BAE55BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5BCEFFE3DBB7A0AE4FD5D950731D72DEBD02851C2FB632864165FCA4920 46548.pygtex) [146] Overfull \hbox (11.82602pt too wide) in paragraph at lines 1167--1170 []\OT1/cmr/m/n/10 Finally, [][]\OT1/cmtt/m/n/10 Bio.SearchIO []\OT1/cmr/m/n/10 also pro-vides a [][]\OT1/cmtt/m/n/10 convert []\OT1/cmr/m/n/10 func-tion, whic h is sim-ply a short-cut for [][]\OT1/cmtt/m/n/10 Bio.SearchIO.parse (./_minted-Tutorial/BDE985FA3ADA6B0D37013C3D5F37C176BD02851C2FB632864165FCA4920 46548.pygtex)) [147] (./Tutorial/chapter_entrez.tex Chapter 9. [148] LaTeX Warning: Reference `sec:entrez-specialized-parsers' on page 149 undefined on input line 21. (./_minted-Tutorial/95F72AA1E59C898262005610BC25A6BABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/320E9A38F759168BA03B078BD9CC013BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DAEC2235DDE454C09ECEB0DF4CD26FB5BD02851C2FB632864165FCA4920 46548.pygtex) [149] LaTeX Warning: Reference `sec:entrez-webenv' on page 150 undefined on input lin e 60. LaTeX Warning: Reference `sec:BioSQL' on page 150 undefined on input line 63. (./_minted-Tutorial/7692669934D8ED6DEE1B8B6684745421BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4E8E7490F3E1B9120A0B1B53C024FA36BD02851C2FB632864165FCA4920 46548.pygtex [150]) (./_minted-Tutorial/C21F612C84412948C9890ED976F536B0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7E05622F86D5C6456282864B1095B19CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/846A93AAA063B5CBA3EDEF3D5FC8C008BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/03DD15474BC34E37527B593FC22220FCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7B7AA3167A6472C6C33ACA91F8E88FACBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/82DFC9B19D35F2D9482DE6B365FC35F6BD02851C2FB632864165FCA4920 46548.pygtex [151]) (./_minted-Tutorial/01D9FCC3424FD0B497241E81D2FE83C6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F74B27B285F0D0CC7E69CABE07232C68BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:efetch' on page 152 undefined on input line 216. LaTeX Warning: Reference `sec:entrez-einfo' on page 152 undefined on input line 220. (./_minted-Tutorial/83C7791C8A9F82BA61AD4B1644D50277BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:efetch' on page 152 undefined on input line 236. [152] (./_minted-Tutorial/3B6409EA2F4B25B8F136CE97DC95E8C4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/53F668B0CE9069489F6D35B114D072B1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/49E5F2A1DFC2444E5A673AD6C6E3F19FBD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:entrez-webenv' on page 153 undefined on input lin e 299. [153] (./_minted-Tutorial/96245EB54DC7A4475CD270566892BAE4BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:SeqIO_GenBank_Online' on page 154 undefined on in put line 325. LaTeX Warning: Reference `sec:efetch' on page 154 undefined on input line 325. (./_minted-Tutorial/AA26452EC447FD01D35D14B1CE4F3147BD02851C2FB632864165FCA4920 46548.pygtex [154] [155]) LaTeX Warning: Reference `chapter:seqio' on page 156 undefined on input line 41 9. (./_minted-Tutorial/042DA7A7135DAEF797FB2EE6170C3B6DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/11417087354B0B78128E27B0162F48D59543DFECA235A69AE23006BA05B 4EB70.pygtex [156]) (./_minted-Tutorial/51CC2C09DB95235CA19612EAFF65F487BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:entrez-specialized-parsers' on page 157 undefined on input line 481. LaTeX Warning: Reference `sec:entrez-webenv' on page 157 undefined on input lin e 483. (./_minted-Tutorial/01919CABECEE21D3FA5A6B7A01CCCB5EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0DD80468D8C175A94BC63142BD16EF1DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/414E52C4377A1D0E6A428B032A7756FDBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6109D29005C5EC9FAE01CDFBE62EF008BD02851C2FB632864165FCA4920 46548.pygtex [157]) (./_minted-Tutorial/A0ED7F47BA117071BA21263E7AF6DB27BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3C5A1B892E98E1E6E8C179B5F465500ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/68622353B578A611D2F621023E3C4BD1BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:elink-citations' on page 158 undefined on input l ine 565. LaTeX Warning: Reference `sec:entrez_example_genbank' on page 158 undefined on input line 571. (./_minted-Tutorial/7455566FBE10CCFD5236DF65992A9F70BD02851C2FB632864165FCA4920 46548.pygtex [158]) (./_minted-Tutorial/6E7EC19AB4E894FD7BECB47DC082FC38BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E02371BEF7596435E8F90267E0362E0944BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/8A1D9304F979E03817FD393E44DC722ABD02851C2FB632864165FCA4920 46548.pygtex [159]) (./_minted-Tutorial/2B17732B358EE5D871A248019977CF38669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/2186E927D5A018F8950E8A7D0F734E71669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/DDE0AA7C839DD601590297B5D523D03BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1516062A6E16A043D5996183E67DEB86669566ECC2CFEDC7429F829576A D0DC6.pygtex) [160] (./_minted-Tutorial/08B5AC3C9DEAD2E377FE070B35391F0BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/898885F88FEAC697F30E8E063D95F24D669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/8BFD5A5D2A0A2DB21DA15E3F1719D3F6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B89E703729CE0DB5EB3456180292FA1B669566ECC2CFEDC7429F829576A D0DC6.pygtex [161]) (./_minted-Tutorial/06D29A54CBCE7E9BEC9B02AF3737953FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/115C0D8716DAB358EAFF936486F27AB9BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:SeqIO_GenBank_Online' on page 162 undefined on in put line 780. LaTeX Warning: Reference `sec:efetch' on page 162 undefined on input line 780. [162] (./_minted-Tutorial/9BFD2F013E1A1D8756C2BFF5B3706AAD669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/9D66917D850D2EF232ECFE32D0F8D1CEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/474ACCF7269CF6DA8C1148E094B63C80BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/265BCBE09451F85D4BB86E81E6F3D4E1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/077B6C28FFFD9E8EB72387BF7F1D9BF1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/41118C19A2E462F9721E8AB1E52AAFC3BD02851C2FB632864165FCA4920 46548.pygtex [163]) (./_minted-Tutorial/8D1D071E3CA3DD9187A6F2C35836C58ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9E297F3C90950B761CCB974F597BCC12BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/30DFAED5DDA7DA75BB6A3BF0F0C12D75BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E07A958FADB74CD60F7086FF6319E277BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:entrez-webenv' on page 164 undefined on input lin e 902. [164] (./_minted-Tutorial/55E8C5FCC00AEE8A4E1D892ACA95C2BCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/473B4163A14D626D6B7A08A26A0A1266BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4802D221A3EBE7AAC3E07CB05144CA27BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F7C9857DB48F3111F31BB49EC39F2019669566ECC2CFEDC7429F829576A D0DC6.pygtex [165]) (./_minted-Tutorial/650077A39F2D52831A52D045B184B624BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/17E5085C64881C08DC82C2B5573291F2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/076325C16F7C56460228C73B3147DF7A9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/2018A02508D4B36EF0217BE478D18CE1BD02851C2FB632864165FCA4920 46548.pygtex) [166] (./_minted-Tutorial/67F7BC27D166185C4B7B9A9F270ACDA5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F01452391D049758B3588D8F37184AA19543DFECA235A69AE23006BA05B 4EB70.pygtex) LaTeX Warning: Reference `sec:orchids' on page 167 undefined on input line 1072 . (./_minted-Tutorial/04D54F815C5EFA53EF9010776D1AA07EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D46819E08D3CDD954897218A7EB7C8C0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/57648E2674FE9BB727770109CA65C71ABD02851C2FB632864165FCA4920 46548.pygtex [167]) (./_minted-Tutorial/676B968CE2CF2F3AEF6899757E020B1EBD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:entrez-webenv' on page 168 undefined on input lin e 1115. (./_minted-Tutorial/8778F0F3798A99FE0C3840234CAC2B5BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/FAD1D32BBD3E6FC5FE31DBBF8029928ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/85AA5F6E67E515A70F5F0A4D9A0548C0669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/24D6870F7CF00B7F93EF1F55424D4AD0BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:orchids' on page 168 undefined on input line 1161 . [168] (./_minted-Tutorial/964257041BEB9E732FF9A943209BD6EDBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/600193D5D5D44162E61A3CAB40448426BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E963D1B8D3330FC994CC39110B642038BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/574A29DDA761C1725F490FB0F1CD4EEFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6FD15C01D270A661A77854FF78F033B8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5845916CE276A61945EF5849B982E8A0BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:entrez-webenv' on page 169 undefined on input lin e 1216. (./_minted-Tutorial/8905908F46BA67CB99A3360F253875C5BD02851C2FB632864165FCA4920 46548.pygtex [169]) (./_minted-Tutorial/4DA8ECCF1EA4588537B571B9F46E13A1BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:entrez-webenv' on page 170 undefined on input lin e 1251. LaTeX Warning: Reference `sec:SeqIO_GenBank_Online' on page 170 undefined on in put line 1258. LaTeX Warning: Reference `sec:entrez-webenv' on page 170 undefined on input lin e 1259. (./_minted-Tutorial/714497BD693AE1BF76AD1C44D3A43F2FBD02851C2FB632864165FCA4920 46548.pygtex [170]) (./_minted-Tutorial/824F6600A92AA40841D5D9A4C2EDC5FDBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A3EC6E0F9D852E0B8DED607938A72797BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E8FC03C2B925F09D2849BD1DDCBB3848BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `chapter:seqio' on page 171 undefined on input line 13 11. (./_minted-Tutorial/A137A30778671FFE0F193EED7A8819D7BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3D76169664531538D144C55FFC33571BBD02851C2FB632864165FCA4920 46548.pygtex [171]) LaTeX Warning: Reference `sec:entrez-guidelines' on page 172 undefined on input line 1335. LaTeX Warning: Reference `sec:entrez-webenv' on page 172 undefined on input lin e 1336. (./_minted-Tutorial/D49E38D9D1357F6225DB42AC5AD5ED7EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CC6CFA7B6751FFF8C74660FCC40D3C45BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0D86B77B8C40BC4335F18EE35CB93649BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/37575ADC7CF832C14B5854633F9C88D8BD02851C2FB632864165FCA4920 46548.pygtex) [172] LaTeX Warning: Reference `sec:entrez-search-fetch-genbank' on page 173 undefine d on input line 1396. (./_minted-Tutorial/5E81FD2679BB8BC4F82244B31C22C477BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:entrez_example_genbank' on page 173 undefined on input line 1418. (./_minted-Tutorial/7212F8F4D805E6009D8612AB61498E24BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B038E9BC100BB2A231E2B4BF11B0330CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3256378680D2E01A0D283817FC4F9633BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1E93113A22D275DCF1ED22A91F77D5749543DFECA235A69AE23006BA05B 4EB70.pygtex [173]) (./_minted-Tutorial/4F9D9C998FB1DECE2FBF932B39921FFA9543DFECA235A69AE23006BA05B 4EB70.pygtex [174]) LaTeX Warning: Reference `sec:entrez-and-medline' on page 175 undefined on inpu t line 1507. LaTeX Warning: Reference `sec:elink' on page 175 undefined on input line 1512. (./_minted-Tutorial/43EC7DBFBCAE4E8B197BA170F7FE7CB2BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:entrez-webenv' on page 175 undefined on input lin e 1537. (./_minted-Tutorial/5F55F80E3D84EDCE0B63B5BCEC4E927ABD02851C2FB632864165FCA4920 46548.pygtex)) [175] (./Tutorial/chapter_uniprot.tex Chapter 10. LaTeX Warning: Reference `sec:SeqIO_ExPASy_and_SwissProt' on page 176 undefined on input line 12. (./_minted-Tutorial/DC3FD651AB93A0CE9D668FE4206D1A86BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DD1C7AE6EB54A3133F3D58EE95B3A668BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/BB844FCBFB442A424E4ED0D244DD6768BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:expasy_swissprot' on page 176 undefined on input line 37. (./_minted-Tutorial/930B60BD569CAAF368B0E614553F3030BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:SeqIO_ExPASy_and_SwissProt' on page 176 undefined on input line 45. [176] (./_minted-Tutorial/ADCE00FC778B0EA886D44F1AA6519182BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3D3E040F0C8AAE9BF46C3D89DB934669BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C65ED72167AAF5D5730D19463FD69228BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CFBCB7DFF63857026EF72107C91C4D14BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D965DDAA766509A8449374C475416C06BD02851C2FB632864165FCA4920 46548.pygtex [177]) (./_minted-Tutorial/747E2FE5A2594F5385BB7437A4517918BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8837CDE38481CF679BB33997916F09ABBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9E15781AA166AC63C2DF3BCF25628224669566ECC2CFEDC7429F829576A D0DC6.pygtex [178]) (./_minted-Tutorial/956383F4066B9E093C9D2E3843CA0220BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/BA8B23CD43F97133B0CE8ECD0A9462AA669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/8B296BCFBFAA7137B45E8CB899424BE4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C2EF087C5641CFFF6A40A4396FE9307BBD02851C2FB632864165FCA4920 46548.pygtex [179]) (./_minted-Tutorial/9AB12EEC55BEE868B932EF7EF12109CEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6E2B75EC45BA35CA8C7799FFAFE69A4DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1DE080CE5283B4D334F81719880190E2BD02851C2FB632864165FCA4920 46548.pygtex) [180] (./_minted-Tutorial/6ED198EEC186F92A098C5692A874CF5B669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/F4AB180AFE85CC09CE3F73EE547FC783BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B1A88EF3A17DB1FA7EC5A60B27A37BF9BD02851C2FB632864165FCA4920 46548.pygtex [181]) (./_minted-Tutorial/454E46BC171F751C15F6A295F2284AB7BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8DCADA174B7DBC35827913027E1507B4BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:orchids' on page 182 undefined on input line 345. (./_minted-Tutorial/20DD2D91201FBA08EE81FE73D557B622BD02851C2FB632864165FCA4920 46548.pygtex [182]) Overfull \hbox (24.29903pt too wide) in paragraph at lines 365--366 []\OT1/cmr/m/n/10 If the ac-ces-sion num-ber you pro-vided to [][]\OT1/cmtt/m/n /10 ExPASy.get_sprot_raw []\OT1/cmr/m/n/10 does not ex-ist, then [][]\OT1/cmtt/ m/n/10 SwissProt.read(handle) (./_minted-Tutorial/30A3D5D1EA4F73DD0984EDFDDAF9090CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/950511DA0658C1A2824DF92F06F34BE8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6A833CD3DDDD6A4CCF169D082C63D87DBD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (65.93893pt too wide) in paragraph at lines 409--410 []\OT1/cmr/m/n/10 The same func-tion can be used to re-trieve a Prosite doc-u-m en-ta-tion record and parse it into a [][]\OT1/cmtt/m/n/10 Bio.ExPASy.Prodoc.Re cord (./_minted-Tutorial/DF2DA17EFC0F6336210C74066809B753BD02851C2FB632864165FCA4920 46548.pygtex) [183] (./_minted-Tutorial/9457A436D281E066D350873A88476E59BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5C1399E579A6AA8D432E509AE441C2AEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7528F52197E46B376DB12FB34672D7A8669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/64ACD8E8EC2C5F323A9D84639080EBCBBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C8BC3187BF8F96BDF009A2CA8A95A3C3BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4323DBBD15E176599A70095217F377E7BD02851C2FB632864165FCA4920 46548.pygtex [184]) (./_minted-Tutorial/0B895A7CD7770AD5152A902E24E86169BD02851C2FB632864165FCA4920 46548.pygtex)) [185] (./Tutorial/chapter_pdb.tex Chapter 11. (./_minted-Tutorial/D779A8F555F6BCC207B905D5D6C22853BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/946CAECCFDBF1349958F40A0FC03463FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/2FDED7F9BEF9EA1F5CE28B11996ED43DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/05714E0F28AC6B36B176161D8A9FA84DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3D3953EF520FE9546FC19DB705E69085BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E37E6F74461E0075B61AF24790D37C71BD02851C2FB632864165FCA4920 46548.pygtex [186]) (./_minted-Tutorial/32D78458130807D5C8DD536942BA7388BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B49437C8CCF1C8D72B8DBA0CFE1DCB35BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A7F199DA98E2BD66B92177EFD14AA59ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/57A82B690A435E6AD7DAD62778DB8231BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:problem_structures' on page 187 undefined on inpu t line 84. (./_minted-Tutorial/3AABC2CB1B50E66D5DBACF20EF52245ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C79D210A6D0E5501910FFF311063879EBD02851C2FB632864165FCA4920 46548.pygtex) [187] (./_minted-Tutorial/41FC845107E552AB47AA881B90236E18BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B41B5BFD7D85ED4E7E70DA059AE1D176BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/36AD36AC9E663BF06BB871053927CDF0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1BBCC7F8F1756C270C4D99E9F943A024BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4AD3361A8DEC1848967C5C4904CBAA6BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D8411ECFB826F8858D5702457B0FB9A5BD02851C2FB632864165FCA4920 46548.pygtex) [188] (./_minted-Tutorial/684AC0ECE33D6BA84F0409CE669AB136BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C85B5FA2C9BF8127C2FEFF62553FECECBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/05AAA27695D5E74A2F0C892230E4EFA4BD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (13.022pt too wide) in paragraph at lines 262--264 \OT1/cmr/m/n/10 The over-all lay-out of a \OT1/cmtt/m/n/10 Structure \OT1/cmr/m /n/10 ob-ject fol-lows the so-called SM-CRA (Struc-ture/Model/Chain/Residue/Ato m) [189] LaTeX Warning: Reference `fig:smcra' on page 190 undefined on input line 275. LaTeX Warning: Reference `sec:problem_structures' on page 190 undefined on inpu t line 284. Excluding 'htmlonly' comment. (./_minted-Tutorial/DCB043864D9F8E2B59DEBF1784B30CDCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B6B956752D54554859CB3FC041890BD7BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/958010CCD8250B2A6D359F037738B54EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/69627B7F3108FCBC466F45AE8D24D979BD02851C2FB632864165FCA4920 46548.pygtex) [190] [191 <./images/smcra.png (PNG copy)>] (./_minted-Tutorial/13774A78311C8B2B99285E3D509AD855BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/EC253507D414D1E9DDE9BC5CAF6BC78CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/69D3F9059506073A988980B78CEAB247BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5A42A68287048A843E1066F2E2727622BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/22421A9A4B194CFEBFABE1E2DDFC8A12BD02851C2FB632864165FCA4920 46548.pygtex) [192] LaTeX Warning: Reference `sec:hetero_problems' on page 193 undefined on input l ine 421. (./_minted-Tutorial/8A579A2F82E38AFC725C7AD02B2F5D57BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C4346C691565244D87DFA5ED26B512E3BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:point_mutations' on page 193 undefined on input l ine 466. (./_minted-Tutorial/38F92E91F7EF83579513DC2A23D231DCBD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:disordered_atoms' on page 193 undefined on input line 483. [193] (./_minted-Tutorial/35E34E333445AAAA4E33570211335BA5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A2470AECC1DA459F7A1ACC68FCD911B1BD02851C2FB632864165FCA4920 46548.pygtex [194]) (./_minted-Tutorial/874F41EC8F1C0D727A004EAEFDC88098BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/94A9BE470837AFDA4B8581B79BB12492BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `fig:smcra' on page 195 undefined on input line 610. (./_minted-Tutorial/76657140082404C594EE786B642215C3BD02851C2FB632864165FCA4920 46548.pygtex [195]) LaTeX Warning: Reference `fig:smcra' on page 196 undefined on input line 657. (./_minted-Tutorial/17EB0A1D2812B68E199CC00449B9254CBD02851C2FB632864165FCA4920 46548.pygtex) [196] (./_minted-Tutorial/D94A742238FBA8E89BB46038CDBDEB90BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0BFD7EDA2178705DA7C24F4D3735823EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/73DA0F97AF01C85175F4AF2DFAE2C6B7BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7E80E6D2D75417229F3B2B705315B128BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/618AFB68C3893C2A344D3A532D9BD99ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/82DD3285068398C1A65910EDE1BE970CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0799FD26AFF50D33D257B86E8D3E40B3BD02851C2FB632864165FCA4920 46548.pygtex [197]) (./_minted-Tutorial/2857EE83D7FCEE22018F0C0AD63239E0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/365D7E5A27BEEE6ED9265079DF231899BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0B35B80BBDE5AE1373CAE9105C01A624BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/BDCD0910528B95EADEE1C7C6BD40AD3CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3A499902396CBA88B311EE3A93BC2663BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B2412D9441598FCD30172739CB3CCA39BD02851C2FB632864165FCA4920 46548.pygtex [198]) (./_minted-Tutorial/728242DAC9077785511462C5CD16E667BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/866FA21894DE0E73CE09F7F50E59FDC5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D6328A6D8E47F7B8E9530D396E8ED50DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/2CF9B1EBC15ECA1536AFA86FAF01899BBD02851C2FB632864165FCA4920 46548.pygtex [199]) (./_minted-Tutorial/F412BF266412BEC93BB127CA53AB4D0CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A73938953B2223965D08B528F27C56E8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B33389074760A02AC27316E67DAAB073BD02851C2FB632864165FCA4920 46548.pygtex [200]) Overfull \hbox (42.26714pt too wide) in paragraph at lines 956--960 \OT1/cmr/m/n/10 breaks and dis-or-dered residues and atoms as de-scribed above are han-dled cor-rectly. \OT1/cmtt/m/n/10 structure[]rebuild[]test(entity) LaTeX Warning: Reference `table:ic-attribs' on page 201 undefined on input line 973. Overfull \hbox (3.8904pt too wide) in paragraph at lines 976--996 [][] [201] LaTeX Warning: Citation `golub1989' on page 202 undefined on input line 1018. (./_minted-Tutorial/10F60558792DABA08CE906FCD09A993CBD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Citation `hamelryck2005' on page 202 undefined on input line 104 6. LaTeX Warning: Command \r invalid in math mode on input line 1049. (./_minted-Tutorial/10BEDFA26FE20B8B11FC832131C1705EBD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `table:DSSP-codes' on page 202 undefined on input line 1081. LaTeX Warning: Reference `sec:residue_depth' on page 202 undefined on input lin e 1121. [202] (./_minted-Tutorial/12DBC9D94FB0B4B78A481C6C111C6709BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/895E3343902EFB0E5475667B01C4B691BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Citation `hamelryck2003a' on page 203 undefined on input line 11 72. [203] [204] (./_minted-Tutorial/7A6D5A10ECC42BAFEE724455549BCB15BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D5B0F5228C1E7FAD0C7AB40AEFF6B6A9BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/2810A7579DC6FE011D31E2F074471A74BD02851C2FB632864165FCA4920 46548.pygtex [205]) (./_minted-Tutorial/D9D0B8746EBF14CF4BE7DA480D9ECD5DBD02851C2FB632864165FCA4920 46548.pygtex) [206] LaTeX Warning: Citation `hamelryck2003b' on page 207 undefined on input line 13 83. LaTeX Warning: Citation `majumdar2005' on page 207 undefined on input line 1384 . ) [207] (./Tutorial/chapter_popgen.tex Chapter 12. (./_minted-Tutorial/E5F1866C3CBB485B8C06B62764ACFBB29543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/331BEE386F268F55DE217F54E27EAB6B9543DFECA235A69AE23006BA05B 4EB70.pygtex) [208] (./_minted-Tutorial/6CD64A1F591B16F512F7EB6B68E5B3FC9543DFECA235A69AE23006BA05B 4EB70.pygtex)) [209] (./Tutorial/chapter_phylo.tex Chapter 13. LaTeX Warning: Citation `talevich2012' on page 210 undefined on input line 9. (./_minted-Tutorial/8F8EFC1C83277AE6C5B5A259FAAC5671669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/4914B4679D1C933D9AD76E95F18CE15844BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/3D758844BE2A5D4414B741470EDE8C24BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/719B0C758B666CDEEB2B250C2143A4ADBD02851C2FB632864165FCA4920 46548.pygtex [210]) (./_minted-Tutorial/8698B66B622D8A91E7706D889D5F35DDBD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `fig:phylo-simple-draw' on page 211 undefined on input line 96. (./_minted-Tutorial/6621A01BB423374C8FC608E267D0EA7DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/87517FEF82BFE1AB8D89A83F4DC5E8B9BD02851C2FB632864165FCA4920 46548.pygtex) Excluding 'htmlonly' comment. (./_minted-Tutorial/6C5156DAD460519324A5B7657B301B5DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1836031BC83AA94C8906762F613E6CBABD02851C2FB632864165FCA4920 46548.pygtex) [211] (./_minted-Tutorial/D0A75FB8C1C791E4AA80420B93F216A8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/FEC6C2CB5FA0AFCFE00D995BD3642FF2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/2B435DC3041611A5D6A663B437ADB1ADBD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (25.13162pt too wide) in paragraph at lines 182--185 []\OT1/cmr/m/n/10 Let's tar-get the most re-cent com-mon an-ces-tor (MRCA) of t he nodes named ``E'' and ``F''. The [][]\OT1/cmtt/m/n/10 common_ancestor (./_minted-Tutorial/29624A9666C9430AABADF395148BBF27BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D0F05D42BA0A9BC594EEDB16319A972DBD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `fig:phylo-color-draw' on page 212 undefined on input line 201. (./_minted-Tutorial/87517FEF82BFE1AB8D89A83F4DC5E8B9BD02851C2FB632864165FCA4920 46548.pygtex [212 <./images/phylo-simple-draw.png>]) Excluding 'htmlonly' comment. (./_minted-Tutorial/D713148814BA75DCDEB1C77B12674D9BBD02851C2FB632864165FCA4920 46548.pygtex [213 <./images/phylo-color-draw.png>]) (./_minted-Tutorial/69333D76AA5D97D8BF9E95DEECEEE2B1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/456F5679DCD4FF740E7A110889D86573BD02851C2FB632864165FCA4920 46548.pygtex [214]) (./_minted-Tutorial/2B3BFA62F3A778E4818959ED3E8AD3EEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/08F738B2988883F2B3BAD96FA439AD7CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8C7F4AB58CCB44E2FF66E36A26E59F55BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/00BD91C09868B2B26E32B5FB41A2583CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A1E441205EAE188E6F4319753E3982D3BD02851C2FB632864165FCA4920 46548.pygtex [215]) (./_minted-Tutorial/C3E382424C6F17EF8DB95D08D8AC9FEEBD02851C2FB632864165FCA4920 46548.pygtex) Excluding 'htmlonly' comment. [216 <./images/phylo-draw-example.p ng>] Overfull \hbox (19.85507pt too wide) in paragraph at lines 479--486 \OT1/cmr/m/n/10 For ex-am-ple, in a tree with clade names Foo1, Foo2 and Foo3, [][]\OT1/cmtt/m/n/10 tree.find_clades({"name": "Foo1"}) [217] Overfull \hbox (13.48741pt too wide) in paragraph at lines 534--537 []\OT1/cmr/m/n/10 Find each clade con-tain-ing a match-ing el-e-ment. That is, find each el-e-ment as with [][]\OT1/cmtt/m/n/10 find_elements[]\OT1/cmr/m/n/10 , [218] (./_minted-Tutorial/6AAB725DBD2E5B7C5FD79A9A16536BF69543DFECA235A69AE23006BA05B 4EB70.pygtex) [219] Overfull \hbox (15.04868pt too wide) in paragraph at lines 703--707 []\OT1/cmr/m/n/10 Below is an ex-am-ple on how to use a python script to in-ter -act with PhyML ([][]$\OT1/cmtt/m/n/10 http : / / www . atgc-[]montpellier . (./_minted-Tutorial/20AACD5E58630D4B64529F3A1ACD8119BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/EB4CA3626331FD00CE50FECC3590095BBD02851C2FB632864165FCA4920 46548.pygtex) [220] (./_minted-Tutorial/0702C9875263768417DD3ED2EF78755EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C395044A3DB827E8D2E36BA5259475D2BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:PhyloXML' on page 221 undefined on input line 823 . [221]) [222] (./Tutorial/chapter_motifs.tex Chapter 14. LaTeX Warning: Reference `sec:links' on page 223 undefined on input line 8. (./_minted-Tutorial/9344D5588F066D22473BF4F77E39E1F3BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/AB934E1AD357BE20BA1F223A29AE486ABD02851C2FB632864165FCA4920 46548.pygtex [223]) (./_minted-Tutorial/A7AAAF382950D3CAD77D17E6B6489D03BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CEBDE9089C5A4F125D8DD8D4E6ACD9C4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9293BA115F68336B4D0213D24C96AE75BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/BFC042DE8B1588B2D23A8510A608989CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5F3B74C4B4D1FF3D387E6F57F726D177BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0517D975CF92331B81AF837F9D257173BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C66E35936EA68A132264FDF63F70A42ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/86717C2BCE65F41FCDB8652763165857BD02851C2FB632864165FCA4920 46548.pygtex [224]) (./_minted-Tutorial/8572965E772BA3D97A5ACAB64A3CEA2BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0CFCBF886B5144440F79F61243192022BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/176227E746894D602FF7231BCB8E5F21BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Citation `cornish1985' on page 225 undefined on input line 165. LaTeX Warning: Citation `cavener1987' on page 225 undefined on input line 166. (./_minted-Tutorial/02A6CF1EA94D619AE2B9428BDA4531C5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/EDCE72CAE83814FFFF4AE6A97CBB2476BD02851C2FB632864165FCA4920 46548.pygtex) [225] (./_minted-Tutorial/C6095CA0913B3D01D81200EBA18DE7FA669566ECC2CFEDC7429F829576A D0DC6.pygtex [226]) (./_minted-Tutorial/2CAEA4D1EDEE84068D05546A212DB0C6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CD1D7AEBB145784C9665DAA472D55CE2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/30EDED7029501226C973943BBA0D1ECDBD02851C2FB632864165FCA4920 46548.pygtex [227]) (./_minted-Tutorial/5C8E141CD14F7220B986B96A3E564D14669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/95F985CC0D974FEE28E0B2667232BA3FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E778DA34B5EC9B33527CC22435275C76BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D11003572C5456D15CB1BF6CD74B860EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CD308858A86E4C77FD58BD7CFCB2EF92669566ECC2CFEDC7429F829576A D0DC6.pygtex [228]) (./_minted-Tutorial/4910FFD3FDCDF743F7F37BE10B04F706BD02851C2FB632864165FCA4920 46548.pygtex [229]) (./_minted-Tutorial/AF4CF0FDC0B4EBF46401E9953A293EF5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7D8B23E400A55050254232F7CA2CC9E1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0E771A916EB510C91DEEBFC8201442DCBD02851C2FB632864165FCA4920 46548.pygtex [230]) (./_minted-Tutorial/1C14559B3C7AC9C35B84F1518D8088FDBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/46FF514D13E6C4030C26EC4EFF8CFAFDBD02851C2FB632864165FCA4920 46548.pygtex [231]) (./_minted-Tutorial/8E9A5519710E4288CC6DA45EFD61B3AEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/47B231A79951117DFE8D7B369F5A0EDEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CF5314A9EF9BBFFA32CFF87ADC53C378BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/FD7EDF217AC860547FAAC456716F6D6BBD02851C2FB632864165FCA4920 46548.pygtex [232]) LaTeX Warning: Citation `bailey1994' on page 233 undefined on input line 542. (./_minted-Tutorial/7EC0366BAB057E95DD30855AF8AD06F8669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/805B769BEA8271618919879EBC73D6AB669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/AD271A766709EB68A386A406C3E3DCB0669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/3C12150A1943B695BB045865F0A87E44669566ECC2CFEDC7429F829576A D0DC6.pygtex [233]) (./_minted-Tutorial/95318595464A829C3F1A431E3C76909FBD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (13.10551pt too wide) in paragraph at lines 603--606 \OT1/cmr/m/n/10 The [][]\OT1/cmtt/m/n/10 motifs.parse []\OT1/cmr/m/n/10 com-man d reads the com-plete file di-rectly, so you can close the file af-ter call-ing [][]\OT1/cmtt/m/n/10 motifs.parse[]\OT1/cmr/m/n/10 . (./_minted-Tutorial/147DE2DA7F37C2A5A1C1344033AB8B84BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/36E981BB5EF7EC3A1829EC830B0AF9C2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/22F78F0EFBBBF61FA3DB5795B5820CD7BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F87F681AD46E2F9ABF3B87ADA8B1EFB6BD02851C2FB632864165FCA4920 46548.pygtex [234]) (./_minted-Tutorial/CB1A766DCCC9D440884673396E012053BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Citation `matys2003' on page 235 undefined on input line 688. (./_minted-Tutorial/64B1E8E30714DF156170A704E0AF9B9E669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/744EE283B3B7A72BE718EF244D782CA7669566ECC2CFEDC7429F829576A D0DC6.pygtex [235]) (./_minted-Tutorial/BCCDFDD968CCC98039C6D6F4886917C1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/2F48F226FED2AEC7A54EAA6C769060B9BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9D8413811B6BC75226431D501B682BD9BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4293959D98D2DC2DC0CE6CA72DFD5D5CBD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `table:transfaccodes' on page 236 undefined on input l ine 772. LaTeX Warning: `h' float specifier changed to `ht'. [236] (./_minted-Tutorial/86BE687BF0F504548CFBA35246A755EFBD02851C2FB632864165FCA4920 46548.pygtex [237]) (./_minted-Tutorial/21510EFF9B5DA96F8CCEE8DFB8F26406BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7B5EBBADDB3E7B53C5C4AED82E42FFC4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0B25C484239457B0395121E60BF51495BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F8B39433E243DA74D8945D4CCEE70605BD02851C2FB632864165FCA4920 46548.pygtex [238]) (./_minted-Tutorial/46C8C36973CB3D67D276A48C8EA6FEE0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/99B6E6DD45FE4AED26044A4FD1A68C74BD02851C2FB632864165FCA4920 46548.pygtex [239]) (./_minted-Tutorial/001DF21D4EE824968A1A6CCAE41948EBBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5CBFAEFFA194A41048B5DAFCF4C98812BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E2EC88874CB26E442AD8A92E3073E225BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/176227E746894D602FF7231BCB8E5F21BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B9A36F2FAD2C11328984E7BBD1033E48BD02851C2FB632864165FCA4920 46548.pygtex [240]) (./_minted-Tutorial/31F98B5F648636905472A89ADB4396EABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6E38B20582EF8FBF09C0864F13C6172DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D36079E59E9C6C6FCEFB62B1C38D03DCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/949879BACF1AC9FDD5E01F1FDF5D0C7BBD02851C2FB632864165FCA4920 46548.pygtex [241]) (./_minted-Tutorial/CEF4EF7AD2559AA1A840E9E5F4F1E33EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8A4D3A313CCE21054A332F39A60F4F8DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8AC6389F07C07315B68A4843F8EC4A81BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CD7B5AA933F3E10D95D901D3BB5DA161BD02851C2FB632864165FCA4920 46548.pygtex) [242] (./_minted-Tutorial/21D3336F2855CBE535339D390FE18E25BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/33B5E369AD9661A05C861A5AE12A5092BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A80C26CD370CE20C0095D5E8948B4CA2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/34B3515117C70C6DAC332384F14FD0D0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6EC91D6C707FE27D0D4D730403C86073BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B3D49921528F0B11F6E5813C6062BEC5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3712C0CA690A1E7FF72D1693AABFE970BD02851C2FB632864165FCA4920 46548.pygtex [243]) (./_minted-Tutorial/4F50929124655BC08B3D6057B14984E5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DA79BC51C090F498913A417759345DF4BD02851C2FB632864165FCA4920 46548.pygtex [244]) (./_minted-Tutorial/4B2423E325126B67BF464F894752E322BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/25136DD7F6E2BE72E81866FB3F2A41C9BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/50111CA97C115B1826E19F91E69CE8BFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9E8A7295F5BEF290E7F4283BD7261603BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D5F089B3901176BD3F7658EA70DA2473BD02851C2FB632864165FCA4920 46548.pygtex [245]) (./_minted-Tutorial/753220AB94A0DA3FD9F8379D30465A7ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/35B38D8BFFB75E06C84D419CF8CBB21BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A6DBEC036FAC23CE4697722B836743C1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DF57AC6C176D67E4A7B147371D11BA16BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B593C755A27EDDCAF56E94C0930898D3BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/53BF343E6B63B739979E29182E1485D3BD02851C2FB632864165FCA4920 46548.pygtex) [246] (./_minted-Tutorial/868ABF9ABD2736A12F423306646D7706BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/912C817861E626118AB2FA06F12910B6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/62D830B5536F542C80973708E7B78A26BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4A6B49E72A96FB6AC93E0E280B4F4472669566ECC2CFEDC7429F829576A D0DC6.pygtex) [247] (./_minted-Tutorial/F99AB908B88D7B819F597C02D259A52BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CB4926B7151E97486270449C8F84AB41BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/852A3852541269829CE5DF380357F2CCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/AC8B7A8ADEC6FEB0B1260E665CF238B6BD02851C2FB632864165FCA4920 46548.pygtex) [248]) [249] (./Tutorial/chapter_cluster.tex Chapter 15. LaTeX Warning: Citation `dehoon2004' on page 250 undefined on input line 6. LaTeX Warning: Citation `lecuyer1988' on page 250 undefined on input line 30. LaTeX Warning: Citation `kachitvichyanukul1988' on page 250 undefined on input line 30. [250] [251] [252] LaTeX Warning: Citation `snedecor1989' on page 253 undefined on input line 154. [253] (./_minted-Tutorial/C7B59059E3AE6CDE790EFE6EB0ED4140BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:distancefunctions' on page 254 undefined on input line 183. (./_minted-Tutorial/C2B72A7408C7DF74DFCEBE0485997287BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/425EDAA643B5AA9589F3EEE601735827BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/50B5971EFCF22FCC4E1302DB2D0A25009543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/293084E63EA5C0E01F325A4DD59469C0BD02851C2FB632864165FCA4920 46548.pygtex [254]) Overfull \hbox (78.60634pt too wide) in paragraph at lines 245--246 \OT1/cmr/m/n/10 men-sions of these ar-rays are $[]$ if [][]\OT1/cmtt/m/n/10 tra nspose []\OT1/cmr/m/n/10 is [][]\OT1/cmtt/m/n/10 0[]\OT1/cmr/m/n/10 , or $[]$ (./_minted-Tutorial/05DC01C08B8EDF71F86E3C3A9C28EB34BD02851C2FB632864165FCA4920 46548.pygtex) [255] LaTeX Warning: Reference `sec:distancefunctions' on page 256 undefined on input line 278. [256] (./_minted-Tutorial/A4A28B5A443208DEAB3B4D76AA3B762EBD02851C2FB632864165FCA4920 46548.pygtex) [257] LaTeX Warning: Reference `sec:distancefunctions' on page 258 undefined on input line 346. (./_minted-Tutorial/C286E2777B917B774560CBDC7CF92626BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D04E097D8E8C4C039FEC20FA103CED189543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/36EF8931044EF448BC70F722AFADB43D9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/805B33438269C932AC54C0DAB5A3D7AC9543DFECA235A69AE23006BA05B 4EB70.pygtex) [258] [259] Overfull \hbox (16.73593pt too wide) in paragraph at lines 423--424 [][]\OT1/cmtt/m/n/10 distance []\OT1/cmr/m/n/10 is the dis-tance be-tween them. The items be-ing clus-tered are num-bered from 0 to $[]$, (./_minted-Tutorial/015798D317E9D8732518AFD186C997CABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A27E6BF4EEB8E8B1C239049267861739BD02851C2FB632864165FCA4920 46548.pygtex) [260] (./_minted-Tutorial/81E4060E427D22B8F0C63B69EEC10A2ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B8D2A546EC4941692F427A363193FBDEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A54EF6455421EFDFA1F63EB361CD74F6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8975A4CCBC4C6138C302117E04F203ADBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/636486BB1CF700F6391685224211BE22BD02851C2FB632864165FCA4920 46548.pygtex) [261] (./_minted-Tutorial/6EFE1AC811BF16FF597EBE3E25BD2F72BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F8E41E59FD44DADEB3740B0C0ED17D41BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1B924FC8FA13A8B73C1C9E6EF8895055BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:distancefunctions' on page 262 undefined on input line 556. (./_minted-Tutorial/77B32E49165B4345FFCA9FACF597BEEBBD02851C2FB632864165FCA4920 46548.pygtex [262]) (./_minted-Tutorial/D04E097D8E8C4C039FEC20FA103CED189543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/36EF8931044EF448BC70F722AFADB43D9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/805B33438269C932AC54C0DAB5A3D7AC9543DFECA235A69AE23006BA05B 4EB70.pygtex) LaTeX Warning: Citation `kohonen1997' on page 263 undefined on input line 600. LaTeX Warning: Citation `tamayo1999' on page 263 undefined on input line 600. [263] (./_minted-Tutorial/E542C07D0131DF56A89D92F80416C175BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:distancefunctions' on page 264 undefined on input line 647. [264] Overfull \hbox (106.77225pt too wide) in paragraph at lines 654--656 \OT1/cmr/m/n/10 An ar-ray with di-men-sions $[]$ if rows are be-ing clus-tered, or $[]$ LaTeX Warning: Citation `yeung2001' on page 265 undefined on input line 660. LaTeX Warning: Citation `golub1971' on page 265 undefined on input line 668. (./_minted-Tutorial/7476A2D5F9D3A46EE00108837901FAEABD02851C2FB632864165FCA4920 46548.pygtex) [265] (./_minted-Tutorial/0420D397BA03971C0079F52E55FEABABBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8D3928D79091BFFA7AFB6D6F35A52C7CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4D59CC328F454A26A4BE9F91740D961CBD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (25.39864pt too wide) in paragraph at lines 739--750 [] [266] [267] (./_minted-Tutorial/EFB8602799AD543446B386107A8147F7BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:distancefunctions' on page 268 undefined on input line 802. LaTeX Warning: Reference `sec:distancematrix' on page 268 undefined on input li ne 805. (./_minted-Tutorial/43B30B527C3A2D8148F25CA143719CAFBD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:clustercentroids' on page 268 undefined on input line 823. (./_minted-Tutorial/C77F1ABB31C6A53C1626E0E0B34BB0FCBD02851C2FB632864165FCA4920 46548.pygtex) [268] LaTeX Warning: Reference `sec:distancefunctions' on page 269 undefined on input line 846. (./_minted-Tutorial/1F3E2EFB988F2639C701A920B547241DBD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:distancefunctions' on page 269 undefined on input line 871. (./_minted-Tutorial/3CAD921471DA4CA4441D02558CD1F2E0BD02851C2FB632864165FCA4920 46548.pygtex [269]) LaTeX Warning: Reference `sec:distancefunctions' on page 270 undefined on input line 900. (./_minted-Tutorial/1A863BDE3A5754AA2C865F2A82DA8504BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:distancefunctions' on page 270 undefined on input line 922. [270] Overfull \hbox (106.77225pt too wide) in paragraph at lines 929--931 \OT1/cmr/m/n/10 An ar-ray with di-men-sions $[]$ if rows are be-ing clus-tered, or $[]$ (./_minted-Tutorial/A39469F362670EDC6C7E8FD9FDF412C4BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Citation `hihara2001' on page 271 undefined on input line 954. (./_minted-Tutorial/12B5F20EFF78F0E8FE505D45A9786D70BD02851C2FB632864165FCA4920 46548.pygtex [271]) (./_minted-Tutorial/E6C8D570402CFDDB43A6AE5A198BCF58BD02851C2FB632864165FCA4920 46548.pygtex)) Overfull \hbox (26.21434pt too wide) in paragraph at lines 986--116 []\OT1/cmr/m/n/10 This will cre-ate the files [][]\OT1/cmtt/m/n/10 cyano_result _K_G2_A2.cdt[]\OT1/cmr/m/n/10 , [][]\OT1/cmtt/m/n/10 cyano_result_K_G2.kgg[]\OT 1/cmr/m/n/10 , and [][]\OT1/cmtt/m/n/10 cyano_result_K_A2.kag[]\OT1/cmr/m/n/10 . [272] (./Tutorial/chapter_learning.tex Chapter 16. [273] LaTeX Warning: Reference `eq:OP' on page 274 undefined on input line 40. LaTeX Warning: Reference `eq:NOP' on page 274 undefined on input line 40. LaTeX Warning: Reference `table:training' on page 274 undefined on input line 7 5. (./_minted-Tutorial/A66CDD6792A98054D498A97A3A920D4DBD02851C2FB632864165FCA4920 46548.pygtex [274]) (./_minted-Tutorial/390D9013E6AF7385E3C5A71EC44014AABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9153ABDB5D850EC42F344B9B42C10E4FBD02851C2FB632864165FCA4920 46548.pygtex [275]) (./_minted-Tutorial/183EBB0903E699FF7289E5FDA71CB096BD02851C2FB632864165FCA4920 46548.pygtex [276]) LaTeX Warning: Reference `eq:OP' on page 277 undefined on input line 197. LaTeX Warning: Reference `eq:NOP' on page 277 undefined on input line 197. (./_minted-Tutorial/7E494FD25838EE4C9E476EBA48BDF0CEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B53BAB1CC7569CE8ADFECF2CFC02D402BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0201F5A7D34B6F74CAF2C8723DA28C0ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/906DB90E50544D69A8A7FA2703E3A012BD02851C2FB632864165FCA4920 46548.pygtex [277]) LaTeX Warning: Reference `eq:OP' on page 278 undefined on input line 261. LaTeX Warning: Reference `eq:NOP' on page 278 undefined on input line 261. LaTeX Warning: Reference `eq:OP' on page 278 undefined on input line 263. LaTeX Warning: Reference `eq:NOP' on page 278 undefined on input line 263. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 267. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 267. LaTeX Warning: Reference `sec:LogisticRegression' on page 278 undefined on inpu t line 273. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 275. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 275. LaTeX Warning: Reference `table:training' on page 278 undefined on input line 2 77. (./_minted-Tutorial/AE2B91C0366D79644B870EB1EB9436E6BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:LogisticRegressionTraining' on page 278 undefined on input line 285. [278] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 287. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 287. (./_minted-Tutorial/B35CDBE12860937BD1F854583E7BA595BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B38BF6A3D910590D450B331A075B723CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E59729DAB9242AE915A0943E44B8DF9BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/AEF267C3082CB68394DCEE656CEB2FC1BD02851C2FB632864165FCA4920 46548.pygtex [279]) (./_minted-Tutorial/A38355D92EE3DC8D96655428C0CEDC15BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A586FFDD9483C890754DBE5DFC420710BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8F9899A476407D923F0AEB91D4FF3D35BD02851C2FB632864165FCA4920 46548.pygtex [280])) [281] (./Tutorial/chapter_graphics.tex Chapter 17. LaTeX Warning: Citation `pritchard2006' on page 282 undefined on input line 18. LaTeX Warning: Citation `toth2006' on page 282 undefined on input line 28. LaTeX Warning: Citation `vanderauwera2009' on page 282 undefined on input line 31. LaTeX Warning: Reference `chapter:seq_annot' on page 282 undefined on input lin e 36. LaTeX Warning: Reference `chapter:seqio' on page 282 undefined on input line 36 . [282] LaTeX Warning: Reference `chapter:seqio' on page 283 undefined on input line 64 . (./_minted-Tutorial/775A7C8BD2C1E8942CA7A717928F51A09543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/997BE59EDA00B2D427337713C8A7E3D99543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/684A3C9C1713469B78289C6B9952D8169543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/F1FF3DF6D6F3CDAA260F74B59EE3502F9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/864F43F6883D29AB2276A3D7B4C4B0359543DFECA235A69AE23006BA05B 4EB70.pygtex) Excluding 'htmlonly' comment. LaTeX Warning: Reference `fig:plasmid_linear' on page 283 undefined on input li ne 136. (./_minted-Tutorial/F52EB727435E5F7D4D3C22DD13755CA79543DFECA235A69AE23006BA05B 4EB70.pygtex [283]) Excluding 'htmlonly' comment. LaTeX Warning: Reference `fig:plasmid_circular' on page 284 undefined on input line 167. (./_minted-Tutorial/68BE5A2D2503535D27E3B265B36AB36E9543DFECA235A69AE23006BA05B 4EB70.pygtex [284 <./images/plasmid_linear.png (PNG copy)>]) LaTeX Warning: Reference `sec:seq_features' on page 285 undefined on input line 220. [285 <./images/plasmid_circular.png (PNG copy)>] (./_minted-Tutorial/ECF4549C3ED9BED5D89616D96689FF279543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/F6FC21242AEF7E7CBB38249DA932A7359543DFECA235A69AE23006BA05B 4EB70.pygtex) Excluding 'htmlonly' comment. LaTeX Warning: Reference `fig:gd_sigil_labels' on page 286 undefined on input l ine 260. (./_minted-Tutorial/E9061B00D3D1F94D19518B622458CA8B9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/869D4007B198B35A03870134DB69E5F29543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/83AFE18710C133D7AFEBCF65D9D3D8509543DFECA235A69AE23006BA05B 4EB70.pygtex [286]) Excluding 'htmlonly' comment. LaTeX Warning: Reference `fig:gd_sigil_labels' on page 287 undefined on input l ine 330. LaTeX Warning: Reference `sec:gd_features_without_seqfeatures' on page 287 unde fined on input line 339. LaTeX Warning: Reference `sec:gd_feature_captions' on page 287 undefined on inp ut line 339. LaTeX Warning: Reference `sec:gd_features_without_seqfeatures' on page 287 unde fined on input line 339. LaTeX Warning: Reference `sec:gd_feature_captions' on page 287 undefined on inp ut line 339. LaTeX Warning: Reference `sec:gd_nice_example' on page 287 undefined on input l ine 345. (./_minted-Tutorial/7767B7CE8DD842D17DB77A8BF9691B949543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/B7F9EB41E9BA682D9273C414D13CA80C9543DFECA235A69AE23006BA05B 4EB70.pygtex [287] [288 <./images/GD_sigil_labels.png (PNG copy)>]) Excluding 'htmlonly' comment. LaTeX Warning: Reference `fig:gd_sigils' on page 289 undefined on input line 38 7. Excluding 'htmlonly' comment. LaTeX Warning: Reference `sec:gd_sigils' on page 289 undefined on input line 40 3. (./_minted-Tutorial/6EE3865BBB66BBD15ABFD7BAE73F8FEB9543DFECA235A69AE23006BA05B 4EB70.pygtex) Excluding 'htmlonly' comment. LaTeX Warning: Reference `fig:gd_sigil_arrow_shafts' on page 289 undefined on i nput line 434. LaTeX Warning: Reference `sec:gd_arrow_sigils' on page 289 undefined on input l ine 439. (./_minted-Tutorial/74C150D1D11511477A4CD9DC0CD7863A9543DFECA235A69AE23006BA05B 4EB70.pygtex) Excluding 'htmlonly' comment. LaTeX Warning: Reference `fig:gd_sigil_arrow_heads' on page 289 undefined on in put line 463. LaTeX Warning: Reference `sec:gd_arrow_sigils' on page 289 undefined on input l ine 468. (./_minted-Tutorial/2216BF82E557F1E99146777612D2BA8F9543DFECA235A69AE23006BA05B 4EB70.pygtex) LaTeX Warning: Reference `sec:gd_top_down' on page 289 undefined on input line 488. (./_minted-Tutorial/67B3F646AA5F8690151428081229D39B9543DFECA235A69AE23006BA05B 4EB70.pygtex [289] [290 <./images/GD_sigils.png>] [291 <./images/GD_sigil_arrow _shafts.png>] [292 <./images/GD_sigil_arrow_heads.png>] [293]) Excluding 'htmlonly' comment. LaTeX Warning: Reference `fig:plasmid_linear_nice' on page 294 undefined on inp ut line 570. LaTeX Warning: Reference `fig:plasmid_circular_nice' on page 294 undefined on i nput line 571. LaTeX Warning: Reference `sec:gd_nice_example' on page 294 undefined on input l ine 577. LaTeX Warning: Reference `sec:gd_nice_example' on page 294 undefined on input l ine 577. LaTeX Warning: Reference `sec:gd_nice_example' on page 294 undefined on input l ine 585. LaTeX Warning: Reference `sec:gd_nice_example' on page 294 undefined on input l ine 585. LaTeX Warning: Citation `proux2002' on page 294 undefined on input line 596. LaTeX Warning: Reference `sec:efetch' on page 294 undefined on input line 605. LaTeX Warning: Reference `sec:SeqRecord-slicing' on page 294 undefined on input line 608. LaTeX Warning: Reference `sec:SeqRecord-reverse-complement' on page 294 undefin ed on input line 610. [294 <./images/plasmid_linear_nice.png (PNG copy)>] [295 <./images/plasmid_circ ular_nice.png>] (./_minted-Tutorial/7CAF22FEDE98A6B9B7990010CA8709DC9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/FA676816242752C9FE9F5EB12D4DAA899543DFECA235A69AE23006BA05B 4EB70.pygtex [296]) (./_minted-Tutorial/7926619D7609A591C404A01B2A99177A9543DFECA235A69AE23006BA05B 4EB70.pygtex [297]) Excluding 'htmlonly' comment. LaTeX Warning: Reference `fig:three_track_simple' on page 298 undefined on inpu t line 732. LaTeX Warning: Reference `sec:gd_multiple_tracks' on page 298 undefined on inpu t line 739. LaTeX Warning: Reference `sec:gd_multiple_tracks' on page 298 undefined on inpu t line 739. LaTeX Warning: Citation `proux2002' on page 298 undefined on input line 759. (./_minted-Tutorial/A2465D4E8908256A31684D5DDE7DA1119543DFECA235A69AE23006BA05B 4EB70.pygtex [298 <./images/three_track_simple.png>]) (./_minted-Tutorial/347EB36A3001532221DDF6C29AA04AFB9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/F46F39DD7A8EC7B20CD42ACF6EFD18409543DFECA235A69AE23006BA05B 4EB70.pygtex [299]) (./_minted-Tutorial/2CF2D2FC7E96B3F426F22452724A4C289543DFECA235A69AE23006BA05B 4EB70.pygtex) Overfull \hbox (2.65141pt too wide) in paragraph at lines 873--879 []\OT1/cmr/m/n/10 There are sev-eral im-por-tant pieces to this code. First the [][]\OT1/cmtt/m/n/10 GenomeDiagram []\OT1/cmr/m/n/10 ob-ject has a [][]\OT1/cm tt/m/n/10 cross_track_links Excluding 'htmlonly' comment. LaTeX Warning: Reference `fig:three_track_cl' on page 300 undefined on input li ne 894. LaTeX Warning: Reference `sec:gd_cross_links' on page 300 undefined on input li ne 901. LaTeX Warning: Reference `sec:gd_cross_links' on page 300 undefined on input li ne 901. Excluding 'htmlonly' comment. LaTeX Warning: Reference `fig:three_track_cl2' on page 300 undefined on input l ine 927. LaTeX Warning: Reference `sec:gd_cross_links' on page 300 undefined on input li ne 934. LaTeX Warning: Reference `sec:gd_cross_links' on page 300 undefined on input li ne 934. [300] [301 <./images/three_track_cl.png>] [302 <./images/three_track_cl2a.png>] (./_minted-Tutorial/F9FFB9659EC22BC166AEB6F7284149779543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/A9695DE54C455E13B400269BF9F424FE9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/F545B5C3D394029AA34E76D27DC2DBAF9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/3BACFFDF9009929D690C44BF09EFB67F9543DFECA235A69AE23006BA05B 4EB70.pygtex) LaTeX Warning: Citation `jupe2012' on page 303 undefined on input line 1012. (./_minted-Tutorial/0AC11BF466D4AA0B0536F05378BEC9CC9543DFECA235A69AE23006BA05B 4EB70.pygtex [303] [304 <./images/simple_chrom.pdf> <./images/tRNA_chrom.pdf>]) (./_minted-Tutorial/F5380F7F462C2A51219D9EF8994C192C9543DFECA235A69AE23006BA05B 4EB70.pygtex [305]) Excluding 'htmlonly' comment. LaTeX Warning: Reference `fig:simplechromosome' on page 306 undefined on input line 1114. (./_minted-Tutorial/7B75AD289117B9F25E36C48BBFCB0A759543DFECA235A69AE23006BA05B 4EB70.pygtex [306]) Excluding 'htmlonly' comment. LaTeX Warning: Reference `fig:simplechromosome' on page 307 undefined on input line 1194. ) [307] (./Tutorial/chapter_kegg.tex Chapter 18. (./_minted-Tutorial/27731B46F813E809C1F5AB60C050CD4ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4FAF7CA55B5CBF29D4D0569020062C71BD02851C2FB632864165FCA4920 46548.pygtex) [308] (./_minted-Tutorial/39B217C0E81B95398ED4BBC9D1B0F5CCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D9724C7E513E9BF6FDCCF6A64359AD4B9543DFECA235A69AE23006BA05B 4EB70.pygtex [309]) (./_minted-Tutorial/64868CEDE925B08BA4840E27792F9C95669566ECC2CFEDC7429F829576A D0DC6.pygtex)) [310] (./Tutorial/chapter_phenotype.tex Chapter 19. (./_minted-Tutorial/252224E77AA1520CEA1F05EB2C082F8DBD02851C2FB632864165FCA4920 46548.pygtex) [311] (./_minted-Tutorial/1742F69ECDDF3F5D15E6B5DBFEFA9721BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4835A2D15014EC539B36FCA111ABBB44BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/FD6100DF6B4884776EB70DBE176DB081BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/943877B8F1F5B9C773FB1AA7B24E159EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0BDF372B652AEF5EA570E28DA8244BF8BD02851C2FB632864165FCA4920 46548.pygtex [312]) (./_minted-Tutorial/BE8D8FA0E8D3D6C871BF41D7B5DEB51DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/290D0631491AEE7E10A3CE09C85D7206BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/EA2967473FD2864501AEB5123E3D579DBD02851C2FB632864165FCA4920 46548.pygtex [313]) (./_minted-Tutorial/AEDB3BBBBA5C2503EDA86617E0872188BD02851C2FB632864165FCA4920 46548.pygtex [314]) (./_minted-Tutorial/43A346E75A27D33FDB3F346C240E06E6BD02851C2FB632864165FCA4920 46548.pygtex)) [315] (./Tutorial/chapter_cookbook.tex Chapter 20. LaTeX Warning: Reference `chapter:seqio' on page 316 undefined on input line 22 . (./_minted-Tutorial/D080533227BF139CB7F7C56D06E7D6EB9543DFECA235A69AE23006BA05B 4EB70.pygtex [316]) LaTeX Warning: Reference `sec:low-level-fasta-fastq' on page 317 undefined on i nput line 58. (./_minted-Tutorial/CA0835D76EF6887731674D8AB555091B9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/1F5CA35662EA2CAC7BDBA9D33CDB13A0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A3BD1DBCF883DB2E1DD394B912E57164BD02851C2FB632864165FCA4920 46548.pygtex) [317] (./_minted-Tutorial/C6B2C783E94EA95E84DF3F108F727AD4BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:Bio.SeqIO-and-StringIO' on page 318 undefined on input line 146. (./_minted-Tutorial/EC0DF654B46A2F2CE5F2C795E0321ED29543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/19A3D00CDA3CDDA100F55F41BCAAF54F9543DFECA235A69AE23006BA05B 4EB70.pygtex [318]) LaTeX Warning: Reference `sec:translation' on page 319 undefined on input line 201. LaTeX Warning: Reference `sec:SeqIO-reverse-complement' on page 319 undefined o n input line 206. (./_minted-Tutorial/FF8E30AFA718C8DC6288D5C9AD354F649543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/019E169CFF67EC7D891D6A02396470619543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/9CFE18F499906D88CC2737F15500C03B9543DFECA235A69AE23006BA05B 4EB70.pygtex [319]) (./_minted-Tutorial/C2311B95BFB64D51B766D16ACEF028DD9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/D6A48411D1CBD21E55ABF85BFBC655419543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/7448CA91BF0AA6E19C1517B6DE4087939543DFECA235A69AE23006BA05B 4EB70.pygtex) LaTeX Warning: Reference `sec:seqio-index-getraw' on page 320 undefined on inpu t line 338. [320] (./_minted-Tutorial/C3FBD2FC664129F7A578076AD05E79D99543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/38576C78990D3D95691E2AC6EB80ABA29543DFECA235A69AE23006BA05B 4EB70.pygtex) [321] (./_minted-Tutorial/D08928CA73DF435476A35E8ADF6418319543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/D51441AC892832CAA5031DFFA5F354509543DFECA235A69AE23006BA05B 4EB70.pygtex) LaTeX Warning: Reference `sec:low-level-fasta-fastq' on page 322 undefined on i nput line 443. LaTeX Warning: Reference `sec:low-level-fasta-fastq' on page 322 undefined on i nput line 457. Overfull \hbox (5.83499pt too wide) in paragraph at lines 454--458 \OT1/cmr/m/n/10 mat (e.g. FASTA files). How-ever, for large FASTQ files it woul d be faster the low-level [][]\OT1/cmtt/m/n/10 FastqGeneralIterator (./_minted-Tutorial/AB16E58608A2F17CC79E6929557208879543DFECA235A69AE23006BA05B 4EB70.pygtex [322]) Overfull \hbox (4.57849pt too wide) in paragraph at lines 475--477 \OT1/cmr/m/n/10 That should find $13819$ reads from \OT1/cmtt/m/n/10 SRR014849. fastq \OT1/cmr/m/n/10 and save them to a new FASTQ file, \OT1/cmtt/m/n/10 with[ ]primer.fastq\OT1/cmr/m/n/10 . LaTeX Warning: Reference `sec:SeqRecord-slicing' on page 323 undefined on input line 480. (./_minted-Tutorial/6D336A88208F39729D1A90FF60CB5EBD9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/2C62FFE33ECD45881AC7A8296BCCA5569543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/7E077104A49653CA66AAC778C604E64A9543DFECA235A69AE23006BA05B 4EB70.pygtex [323]) (./_minted-Tutorial/ECD311074B098CDA38E7451A88AC0F9C9543DFECA235A69AE23006BA05B 4EB70.pygtex) [324] (./_minted-Tutorial/CC6E723850600015A2C6BAC6C88F89159543DFECA235A69AE23006BA05B 4EB70.pygtex) LaTeX Warning: Reference `sec:SeqIO-conversion' on page 325 undefined on input line 643. LaTeX Warning: Citation `cock2010' on page 325 undefined on input line 646. [325] (./_minted-Tutorial/1E88A30624397E1FA5202CD67F078C319543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/55F15E0B4613AC1B2AC177DC407373679543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/C6B1FCFF3C4616196F6CE060D97D2587BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7B877C459BB3438E40CD76B614F605B69543DFECA235A69AE23006BA05B 4EB70.pygtex [326]) (./_minted-Tutorial/C47681A25A04F989A9657602F996D5B59543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/20E6EE0734FD2ED211933BE632478CAB9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/BF6F632251CC051592D2BE57B36A38A09543DFECA235A69AE23006BA05B 4EB70.pygtex) LaTeX Warning: Reference `sec:SeqIO-index' on page 327 undefined on input line 801. (./_minted-Tutorial/C8587EE0D03D0937B88179912FC3582EBD02851C2FB632864165FCA4920 46548.pygtex [327]) LaTeX Warning: Reference `sec:SeqIO-index' on page 328 undefined on input line 823. LaTeX Warning: Reference `sec:SeqIO-sort' on page 328 undefined on input line 8 25. LaTeX Warning: Reference `sec:SeqIO-conversion' on page 328 undefined on input line 839. (./_minted-Tutorial/7F8C2BBB4F26A8E6A0FD7BCC41E2BB80BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/FCE533CC3550AB6D1B3C6F6ED53E0CEBBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/37A86DCC1F181ADAA1855D9EBC303BAC44BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/474B445E26A3CD55A1BA5820E4D03C7DBD02851C2FB632864165FCA4920 46548.pygtex [328]) LaTeX Warning: Reference `sec:translation' on page 329 undefined on input line 905. (./_minted-Tutorial/DDBEEE137CB936CA422E560A63FB97B8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B802763B27D7694A759DB2EBF16EF098BD02851C2FB632864165FCA4920 46548.pygtex) [329] (./_minted-Tutorial/EE9671DEE2B114F544A5881F074C33B29543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/5A7FB5AC8923F9582CAE20A770A63052669566ECC2CFEDC7429F829576A D0DC6.pygtex [330]) LaTeX Warning: Reference `sec:gd_nice_example' on page 331 undefined on input l ine 1024. LaTeX Warning: Reference `chapter:seqio' on page 331 undefined on input line 10 41. (./_minted-Tutorial/8F229FE70B397EEE7D48ECD1D5BAD1CCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/71434DB3B51372DFED40CEB6F06647B79543DFECA235A69AE23006BA05B 4EB70.pygtex [331]) Excluding 'htmlonly' comment. LaTeX Warning: Reference `fig:seq-len-hist' on page 332 undefined on input line 1109. Overfull \hbox (4.00363pt too wide) in paragraph at lines 1117--1120 []\OT1/cmr/m/it/10 Tip: \OT1/cmr/m/n/10 Rather than us-ing [][]\OT1/cmtt/m/n/10 pylab.show() []\OT1/cmr/m/n/10 to show the plot in a win-dow, you can also use [][]\OT1/cmtt/m/n/10 pylab.savefig(...) (./_minted-Tutorial/798776F436EA559BACD9C305C09973919543DFECA235A69AE23006BA05B 4EB70.pygtex [332 <./images/hist_plot.png>]) (./_minted-Tutorial/CB78AD94DFE82ADBAF348C0EC1D261CD9543DFECA235A69AE23006BA05B 4EB70.pygtex) Excluding 'htmlonly' comment. LaTeX Warning: Reference `fig:seq-gc-plot' on page 333 undefined on input line 1177. LaTeX Warning: Reference `fig:nuc-dot-plot' on page 333 undefined on input line 1191. Excluding 'htmlonly' comment. [333 <./images/gc_plot.png>] (./_minted-Tutorial/6E0DA723E11A7B9CA8E2353A984B5DF79543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/80A47C8780CE3021D53829563E8166569543DFECA235A69AE23006BA05B 4EB70.pygtex [334 <./images/dot_plot.png>]) (./_minted-Tutorial/9574E55C4A182E2A0201DF18689F52F49543DFECA235A69AE23006BA05B 4EB70.pygtex) Excluding 'htmlonly' comment. LaTeX Warning: Reference `fig:nuc-dot-plot' on page 335 undefined on input line 1269. (./_minted-Tutorial/24C65C38DAD936B7AA15C7ED02EA36B39543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/6655B5CD97C33186A22E6897501301FF9543DFECA235A69AE23006BA05B 4EB70.pygtex [335]) (./_minted-Tutorial/7727E7020AA1BDC4C2A426B7590C20AD9543DFECA235A69AE23006BA05B 4EB70.pygtex) Excluding 'htmlonly' comment. LaTeX Warning: Reference `fig:nuc-dot-plot-scatter' on page 336 undefined on in put line 1345. [336 <./images/dot_plot_scatter.png>] (./_minted-Tutorial/601CCA4B782F1DA528DB81B0248031959543DFECA235A69AE23006BA05B 4EB70.pygtex) LaTeX Warning: Reference `fig:paired-end-qual-plot' on page 337 undefined on in put line 1406. Excluding 'htmlonly' comment. LaTeX Warning: Reference `chapter:align' on page 337 undefined on input line 14 18. LaTeX Warning: Reference `chapter:align' on page 337 undefined on input line 14 25. (./_minted-Tutorial/9D2779E6D02C00C016A7A73A452EBC739543DFECA235A69AE23006BA05B 4EB70.pygtex) LaTeX Warning: Reference `sec:consensus' on page 337 undefined on input line 14 36. LaTeX Warning: Reference `sec:pssm' on page 337 undefined on input line 1437. [337] LaTeX Warning: Reference `sec:getting_info_content' on page 338 undefined on in put line 1438. LaTeX Warning: Reference `sec:sub_matrix' on page 338 undefined on input line 1 439. LaTeX Warning: Reference `sec:summary_info' on page 338 undefined on input line 1445. (./_minted-Tutorial/06CAA397021B5D0CD904B7CF0209DCA39543DFECA235A69AE23006BA05B 4EB70.pygtex) [338 <./images/SRR001666.png>] (./_minted-Tutorial/16711B0A63F93BBACAF3C86CFFB7BEFA669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/96EC77291C119EF69670ACDB1C35CE21669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/6C14F4F0692168BA7165351C706B643D9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/E686FC2D122CF1560FAF4512CD53777F9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/E09A8EBF1B7CB9F831FC2D9DA48145359543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/E598995EF885D7803642E8685DCB8F90669566ECC2CFEDC7429F829576A D0DC6.pygtex) Overfull \hbox (49.0755pt too wide) in paragraph at lines 1528--1529 []\OT1/cmr/m/n/10 You can ac-cess any el-e-ment of the PSSM by sub-script-ing l ike [][]\OT1/cmtt/m/n/10 your_pssm[sequence_number][residue_count_name][]\OT1/c mr/m/n/10 . (./_minted-Tutorial/7F027F6FD8E839F99A1077399D9B8EFFBD02851C2FB632864165FCA4920 46548.pygtex [339]) LaTeX Warning: Reference `sec:summary_info' on page 340 undefined on input line 1565. (./_minted-Tutorial/25AF2FA7C23EEF982CD3578DCB5300659543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/7662755469082A25B2A4B53656D96A409543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/EA8748814B0C57E7E4D7F8619D00D0439543DFECA235A69AE23006BA05B 4EB70.pygtex [340]) (./_minted-Tutorial/99476F758194110AC0ED8AAAFD8ECB7C9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/504DC4F75F719CFF95C5294B2961C973BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:align_clustal' on page 341 undefined on input lin e 1640. (./_minted-Tutorial/486C8450148EF1EADB63A41AB9A896FABD02851C2FB632864165FCA4920 46548.pygtex [341]) (./_minted-Tutorial/DD48495FAB2341AA078121E9286C0717BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DE31628D815724B7B422A1012BAA0C37BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5740381D1C5E453AC66BA80B49407915BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/19B054992CCA481AA19D78F9C6DD93BFBD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (13.15053pt too wide) in paragraph at lines 1703--1704 \OT1/cmr/m/n/10 two [][]\OT1/cmtt/m/n/10 residue_frequencies []\OT1/cmr/m/n/10 val-ues mul-ti-plied with each other. For ex-am-ple, [][]\OT1/cmtt/m/n/10 expec ted_frequencies[^^MD^^M, ^^ME^^M] (./_minted-Tutorial/40ECF2E139F38209730D3B02B624EF74BD02851C2FB632864165FCA4920 46548.pygtex [342]) (./_minted-Tutorial/8965C8E87A0A43ECCE216C12F7DE7A4FBD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `chapter:seqio' on page 343 undefined on input line 17 48. ) [343] (./Tutorial/chapter_testing.tex Chapter 21. (./_minted-Tutorial/867AD481B37AFD4F1A17FC0F2F42FCAE44BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/E8078015A2C53794A733DDC875BD062144BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/754EBE4BCCE307413E74F18728530D0444BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/E40D6903CCE8EA230C75C80B7C2D907344BBF456F55B5DC060035246D76 9EADB.pygtex) LaTeX Warning: Reference `sec:doctest' on page 344 undefined on input line 55. (./_minted-Tutorial/7A0DBB9735CDAA1699A6FA164701062F44BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/BC243371043473AEE20C23FF0FABFF0D44BBF456F55B5DC060035246D76 9EADB.pygtex) Overfull \hbox (39.35472pt too wide) in paragraph at lines 73--77 []\OT1/cmr/m/n/10 Tests based on Python's stan-dard [][]\OT1/cmtt/m/n/10 unitte st []\OT1/cmr/m/n/10 frame-work will [][]\OT1/cmtt/m/n/10 import unittest []\OT 1/cmr/m/n/10 and then de-fine [][]\OT1/cmtt/m/n/10 unittest.TestCase [344] (./_minted-Tutorial/9373056942403CCACDB96B0F438E4B64669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/2A1F0B8D037B993D748BF652420448ED44BBF456F55B5DC060035246D76 9EADB.pygtex [345]) (./_minted-Tutorial/61465735FDB5BC7ADF12D7A4628FC9A79543DFECA235A69AE23006BA05B 4EB70.pygtex) [346] (./_minted-Tutorial/826F7B9143F73D7CFCAB00906377DAB99543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/B1E279D3993E4775FBE4555B6DD342AD44BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/313C740A73E814DA220EB71149FE706E9543DFECA235A69AE23006BA05B 4EB70.pygtex [347]) (./_minted-Tutorial/99DA0A53F2BD41D9D1BCE2B0332444F444BBF456F55B5DC060035246D76 9EADB.pygtex) LaTeX Warning: Reference `sec:doctest' on page 348 undefined on input line 282. (./_minted-Tutorial/4916E014295B56C6CDDB3C287542DA299543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/1B0AB11BDA71CF4763A5A4A8B82977119543DFECA235A69AE23006BA05B 4EB70.pygtex [348]) (./_minted-Tutorial/7A0DBB9735CDAA1699A6FA164701062F44BBF456F55B5DC060035246D76 9EADB.pygtex) [349] (./_minted-Tutorial/3E57444149EF1ACC12DA2995F5B0345644BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/DD3A1A642CB850F292FC934F9336EC4344BBF456F55B5DC060035246D76 9EADB.pygtex)) [350] (./Tutorial/chapter_contributing.tex Chapter 22. LaTeX Warning: Reference `chapter:cookbook' on page 351 undefined on input line 32. [351] (./_minted-Tutorial/7713FA97EA16E9508BA3E6B94494492544BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/61D19A91BF1A1F95030292E40EF87A3644BBF456F55B5DC060035246D76 9EADB.pygtex) LaTeX Warning: Reference `chapter:testing' on page 352 undefined on input line 85. LaTeX Warning: Reference `chapter:testing' on page 352 undefined on input line 101. [352]) [353] (./Tutorial/chapter_appendix.tex Chapter 23. (./_minted-Tutorial/109DA6882E9B770A79B0E47E5D014D32BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D8DF7F2BE4A1010E81F7C5AD3A4628599543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/268983882DD871BC94F164D025D08B429543DFECA235A69AE23006BA05B 4EB70.pygtex [354]) (./_minted-Tutorial/940D9D0165FD2273E52C2D203CE26C429543DFECA235A69AE23006BA05B 4EB70.pygtex) LaTeX Warning: Reference `sec:SeqIO_compressed' on page 355 undefined on input line 91. (./_minted-Tutorial/4B521F4803AD1FD3B86D09A2ECD5A203BD02851C2FB632864165FCA4920 46548.pygtex)) [355] [356] [357] [358] (./Tutorial.aux (./Tutorial/chapter_introduction.aux) (./Tutorial/chapter_quick_start.aux) (./Tutorial/chapter_seq_objects.aux) (./Tutorial/chapter_seq_annot.aux) (./Tutorial/chapter_seqio.aux) (./Tutorial/chapter_align.aux) (./Tutorial/chapter_blast.aux) (./Tutorial/chapter_searchio.aux) (./Tutorial/chapter_entrez.aux) (./Tutorial/chapter_uniprot.aux) (./Tutorial/chapter_pdb.aux) (./Tutorial/chapter_popgen.aux) (./Tutorial/chapter_phylo.aux) (./Tutorial/chapter_motifs.aux) (./Tutorial/chapter_cluster.aux) (./Tutorial/chapter_learning.aux) (./Tutorial/chapter_graphics.aux) (./Tutorial/chapter_kegg.aux) (./Tutorial/chapter_phenotype.aux) (./Tutorial/chapter_cookbook.aux) (./Tutorial/chapter_testing.aux) (./Tutorial/chapter_contributing.aux) (./Tutorial/chapter_appendix.aux)) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcrm1000 mkdir: cannot create directory ‘././sbuild-nonexistent’: Permission denied mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcrm1000 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm1000.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymb.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [27] [29]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txgen.mf Ok [100] [109] [98] [99] [108]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymbol.mf Ok [13] [18] [21] [22] [23] [24] [25] [26] [28] [31] [32] [36] [39] [44] [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] [96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txromod.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrsuper.mf Ok [185] [178] [179] [170] [186]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrfract.mf Ok [188] [189] [190]) ) ) ) (some charht values had to be adjusted by as much as 0.06943pt) Font metrics written on tcrm1000.tfm. Output written on tcrm1000.600gf (128 characters, 23548 bytes). Transcript written on tcrm1000.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/tcrm1000.600pk: successfully generated. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. Package rerunfilecheck Warning: File `Tutorial.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information) < /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb> Output written on Tutorial.pdf (359 pages, 2459747 bytes). Transcript written on Tutorial.log. pdflatex --shell-escape "\def\bpversion{1.80}\input{Tutorial}" This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdflatex) \write18 enabled. entering extended mode LaTeX2e <2022-11-01> patch level 1 L3 programming layer <2023-01-16> (./Tutorial.tex (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2022/07/02 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/preprint/fullpage.sty) (/usr/share/texmf/tex/latex/misc/hevea.sty (/usr/share/texlive/texmf-dist/tex/latex/comment/comment.sty Excluding comment 'comment') Excluding comment 'rawhtml' Excluding comment 'htmlonly') (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/minted/minted.sty (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty)) (/usr/share/texlive/texmf-dist/tex/latex/fvextra/fvextra.sty (/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty) (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty) (/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty) (/usr/share/texlive/texmf-dist/tex/latex/lineno/lineno.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/calc.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/shellesc.sty) (/usr/share/texlive/texmf-dist/tex/latex/ifplatform/ifplatform.sty (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty)) (/usr/share/texlive/texmf-dist/tex/generic/catchfile/catchfile.sty (/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty)) (/usr/share/texlive/texmf-dist/tex/generic/iftex/ifluatex.sty) (./Tutorial.w18) ) (/usr/share/texlive/texmf-dist/tex/generic/xstring/xstring.sty (/usr/share/texlive/texmf-dist/tex/generic/xstring/xstring.tex)) (/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 70. (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx))/usr/bin/pygmentize (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./Tutorial.aux (./Tutorial/chapter_introduction.aux) (./Tutorial/chapter_quick_start.aux) (./Tutorial/chapter_seq_objects.aux) (./Tutorial/chapter_seq_annot.aux) (./Tutorial/chapter_seqio.aux) (./Tutorial/chapter_align.aux LaTeX Warning: Label `sec:pairwise-general-gapscores' multiply defined. ) (./Tutorial/chapter_blast.aux) (./Tutorial/chapter_searchio.aux) (./Tutorial/chapter_entrez.aux) (./Tutorial/chapter_uniprot.aux) (./Tutorial/chapter_pdb.aux) (./Tutorial/chapter_popgen.aux) (./Tutorial/chapter_phylo.aux) (./Tutorial/chapter_motifs.aux) (./Tutorial/chapter_cluster.aux) (./Tutorial/chapter_learning.aux) (./Tutorial/chapter_graphics.aux) (./Tutorial/chapter_kegg.aux) (./Tutorial/chapter_phenotype.aux) (./Tutorial/chapter_cookbook.aux) (./Tutorial/chapter_testing.aux) (./Tutorial/chapter_contributing.aux) (./Tutorial/chapter_appendix.aux)) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (./Tutorial.out) (./Tutorial.out) Excluding 'htmlonly' comment. Excluding 'rawhtml' comment. [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.m ap} <./images/biopython_logo.pdf>] (./Tutorial.toc pdfTeX warning (ext4): destination with the same identifier (name{page.1}) has been already used, duplicate ignored \relax l.39 ...tions and locations}{30}{subsection.4.3.2} % [1] [2] [3] [4] [5] [6] [7]) [8] (./Tutorial/chapter_introduction.tex Chapter 1. [9] [10] Excluding 'rawhtml' comment. Underfull \hbox (badness 10000) in paragraph at lines 122--128 Underfull \hbox (badness 10000) in paragraph at lines 134--136 (./_minted-Tutorial/default.pygstyle) (./_minted-Tutorial/C3217FD04973F24516F5530BB525A22CBD02851C2FB632864165FCA4920 46548.pygtex) [11 <./images/biopython_logo_old.jpg>] Overfull \hbox (2.99303pt too wide) in paragraph at lines 187--189 \OT1/cmr/m/n/10 Check the built in doc-strings (\OT1/cmtt/m/n/10 from Bio impor t SeqIO\OT1/cmr/m/n/10 , then \OT1/cmtt/m/n/10 help(SeqIO)\OT1/cmr/m/n/10 ), or see [][]$\OT1/cmtt/m/n/10 http : / / biopython . [12]) [13] (./Tutorial/chapter_quick_start.tex Chapter 2. LaTeX Warning: Reference `chapter:advanced' on page 14 undefined on input line 14. (./_minted-Tutorial/C083BA757ADC0A392BD8802D1351612CBD02851C2FB632864165FCA4920 46548.pygtex [14]) (./_minted-Tutorial/BCD1E3D53103B8919C8BBE66D33535ABBD02851C2FB632864165FCA4920 46548.pygtex) [15] (./_minted-Tutorial/AD9EF2BC42CEF4E413923F9BFFE1BE07669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/33F85FAC7266F854F2B0213346781855BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/57D5D2D450B93D59CC2D6708C6BA430BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9951EE2B2EB57108F1B91BF42B5EF26DBD02851C2FB632864165FCA4920 46548.pygtex [16]) (./_minted-Tutorial/D0C141F7F69A52FF8D2723831BF439F2BD02851C2FB632864165FCA4920 46548.pygtex) [17]) [18] (./Tutorial/chapter_seq_objects.tex Chapter 3. (./_minted-Tutorial/048D805D0CE39D0271B0A9A9F6FA0B90BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CCFAD09A7C678CC6F23FB63113DD1EDCBD02851C2FB632864165FCA4920 46548.pygtex) [19] (./_minted-Tutorial/FD65D36A7B14289ADEAB241851842BCABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C0F44B540F3531194878FC29AF017902BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/739024CAA2FC886FEC674E3B4C3FD3A4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/EB307D8D2C6B186F102975D2F777C5C8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/504E820336D4D852A5104D8E97622504BD02851C2FB632864165FCA4920 46548.pygtex [20]) (./_minted-Tutorial/21058E2884DE0E2797798658CEC2E54FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6C027F180664948287C5ED0C06A70E36BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8900FA9A050CA74204F5DCB8D9386420BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5A43D1A8AC729BFB659D75BFD070C79ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/732D927996C79742AC990312B3D6EEB0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/36BB9CB69ABA7149C7050E321F74C270BD02851C2FB632864165FCA4920 46548.pygtex [21]) (./_minted-Tutorial/14DC45CA9BEAFF3B8A49C8E43A9FF33CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4FC9049D1029A23D48B33F9D862ACC47BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E62329AC6ED4D8F7B1EF4988F8DBA19FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/008EC869056581873654FF9A8E92D394BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/457BF67E0722BB5B93A17BD27C0B6D8DBD02851C2FB632864165FCA4920 46548.pygtex [22]) (./_minted-Tutorial/21058E2884DE0E2797798658CEC2E54FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/34FD0122B81370E5F3563284D60CFF17BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A54827F8BB70B416D99923FF5088CCC0BD02851C2FB632864165FCA4920 46548.pygtex [23]) (./_minted-Tutorial/427B060556C1BB93F326E658CF6C8753BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/692203B43955DEEBA597180E090EBEBDBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0A4AF1735B84470B955325263082B386BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F7FFCC027B254744B7B47314F48923FEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/186028EBD7A9B4B4276808BC5B218A70BD02851C2FB632864165FCA4920 46548.pygtex [24]) (./_minted-Tutorial/2F42D08D321C7BC408E4704103B70F2EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/544C1E23D35FAC62FBE120AA24D6EF82BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A487EC21D16913E80A948528AA61CD64BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7BC83BB268F7BA2D207FDE001034CF98BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/59D2BC7361BC3147180163BF1D4DDE79BD02851C2FB632864165FCA4920 46548.pygtex [25]) (./_minted-Tutorial/087889BE640F25A1E1D26EB819B55990BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C387354CBEC6317F42CD9F596E775BE0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A3542F02D57EFCE9A6BD62C8FAB75CE3BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F712265A78CB2524ABF9371BE2F3874DBD02851C2FB632864165FCA4920 46548.pygtex [26]) (./_minted-Tutorial/3A75E7306D7D2D81DE0C37038600A10ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/06DBC59F2EAD33E7A951888537876615BD02851C2FB632864165FCA4920 46548.pygtex) [27] (./_minted-Tutorial/4393B8540CDD633A481E29B1CF252CE6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7F9F7641B195E2CACA3F77158DBE190CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/04626286E6AB345CB89BE7B7A049C338BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F2723D89FDBA794E82A8285BABB369CB669566ECC2CFEDC7429F829576A D0DC6.pygtex [28]) (./_minted-Tutorial/64147FAF6F5C5028B073B3C809EE3E84BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DFDB859800920408E228736AD921B5DFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D95D20C3283ADEDD76DAB3382BB1B040BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/AA99EB190DCB9061B7FD403ECDCEE451BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F5B125A1E250BEBA411CA3B2BBF3EDDDBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/39AA48793A64869F7458C1A2A0D69D2EBD02851C2FB632864165FCA4920 46548.pygtex [29]) (./_minted-Tutorial/29E9F3CE64EB99D132246C3633BA375CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/394CF49B3AAB621203EE87F2BD334CC4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3F2DB933A33BDAA3DB2299F2701B61CBBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4307A980AB242F22FB1B0952E3FD37C0BD02851C2FB632864165FCA4920 46548.pygtex)) [30] [31] (./Tutorial/chapter_seq_annot.tex Chapter 4. (./_minted-Tutorial/032C91EF2474FD3535629DC0CDABC809BD02851C2FB632864165FCA4920 46548.pygtex) [32] (./_minted-Tutorial/28ED5ED993E569AC59FDA480CD731BBCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/AD6AF21FB49ADADD3E9DF52EA341F92CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6A9404FB47549766BD16858F97A6D407BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B9321587EBA597104E435182128B200FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/22FC566F5A2B47EFD3D63327C15F7FC2BD02851C2FB632864165FCA4920 46548.pygtex [33]) (./_minted-Tutorial/510764EE0BB38AD6C688E71989677507669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/885E3C393ABBD6448EFA8A6D8D849822BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D582F58715BB8D12B0A5A9CF9631A27CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C60AA1EB70D11A096523A07FC1BD2085BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7D4386614F3407AC9AFEDB894B0987D9669566ECC2CFEDC7429F829576A D0DC6.pygtex [34]) (./_minted-Tutorial/B659A3B495F4BF5A9945B83B9A29DC2BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/20D2783513E8123B155B9FE0B3FE7B4A669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/86FA506E88E30EB82E7186A57112C98CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D582F58715BB8D12B0A5A9CF9631A27CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C9D6C80CD8B460806CB6E7C2935EA601BD02851C2FB632864165FCA4920 46548.pygtex [35]) (./_minted-Tutorial/332D9C95CC14B124A8528A76F4917ECEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/925BCB3D0BD30380832BA5F2C6367AD9BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D20F0AF7810B74883E42451F5810F926BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/47F0F8DD59EC4A71D5CA336E217F0C0DBD02851C2FB632864165FCA4920 46548.pygtex) [36] [37] (./_minted-Tutorial/AD47AD29D6F7927F9406BE5609676388BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A89E686BA7930FBF8AE5CCC27E1AC5BFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CD11055284C1F524585846BFB03F6EE8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1C597DC49857D56C7E140B1D795218F3BD02851C2FB632864165FCA4920 46548.pygtex [38]) (./_minted-Tutorial/EF871449F651FE5E7DFD84165065B14ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9ABE11BA111CDBEACB55DC5424AC66A1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D86C559003980DC8749AF92530435DFDBD02851C2FB632864165FCA4920 46548.pygtex) [39] (./_minted-Tutorial/1C0A562378DEEE8E210765437B3E1700BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C7BB516F80A4A8F5C291ABDF3B6E0B49BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C737C9C2EF139AD4F965B3AC1FF72C75BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/411A7DB0F7208D21C6099C86249233F3BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0C3ED75879971F09D72A92585654A32CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A4ED33BCBC94515EF1D3FF0CB0F2ACE9BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1432CF672342B0A065BD2202A12E3920BD02851C2FB632864165FCA4920 46548.pygtex [40]) (./_minted-Tutorial/3B61DDBFCC5B04C6BD9F6ED183CD312DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5039524AFDCC2184E0FA37B45448443DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/93B3AF8F7193FF3944CC29E4FE0F9689BD02851C2FB632864165FCA4920 46548.pygtex [41]) (./_minted-Tutorial/B952BEC5DDC5176F8F8F8984196831F3BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D16AA28F327A9B07E6AE64737A6B2340BD02851C2FB632864165FCA4920 46548.pygtex [42]) (./_minted-Tutorial/C08741A8063662E3CF1313052B7EA7A4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/83934A12FA213409ADDBED937D121BEBBD02851C2FB632864165FCA4920 46548.pygtex [43]) (./_minted-Tutorial/7693A79AF1B5C3B342CEF51858B48A85BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C59A3BD3577D6DA7BB95528A68C9B311BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7FC68DDC3F22A92C79064A5F631D2457BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E4EE1174D845FF0CABBFC735D0B5DF82BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/890A92414EE9EE5FB3B2F7B834307EDFBD02851C2FB632864165FCA4920 46548.pygtex [44]) (./_minted-Tutorial/CC2666A1113601FF5DADD7ED2118A3FEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E29BCA3E51B6B75E0E5EFF1718501669BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D20811F7EAA2FB2ED0A37B2C0F1B24D4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E92A933EB86A743F11CDB887CD2A9C1BBD02851C2FB632864165FCA4920 46548.pygtex [45]) (./_minted-Tutorial/675833B93A69F5DE13F680548E25EA3EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A8312A90F6B97A21EE1619F9A898ED36BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/68AB1E9E397375F82B6F3361E55900E7BD02851C2FB632864165FCA4920 46548.pygtex) [46] (./_minted-Tutorial/023FBCDB71B9572D8D436D0AA1193B63BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1B29C13B779A89B3DE705BA0061B8793BD02851C2FB632864165FCA4920 46548.pygtex)) [47] (./Tutorial/chapter_seqio.tex Chapter 5. (./_minted-Tutorial/3F38D5012926DD7C810DA2383F53D498BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CE17C15EEBC1BDC9846A29B8188EB6789543DFECA235A69AE23006BA05B 4EB70.pygtex [48]) (./_minted-Tutorial/357B0F655AFAF3808FD8EE23EE5009549543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/480025795249845BAA7F48D4A45ADB21BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F164035E9D5F8C01F84F5F95E2B166F19543DFECA235A69AE23006BA05B 4EB70.pygtex [49]) (./_minted-Tutorial/C82398A4A04383A063D2E648811230529543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/1A4F5B10F895EA1A0898B313C8FE3AED9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/665A7700DAC7A651C288CFBC04910736669566ECC2CFEDC7429F829576A D0DC6.pygtex) [50] (./_minted-Tutorial/3FC3FD6D12B3257730F3B4F11F7F82E99543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/8C2F2A27559FC0864F47BBE543950C26669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/C1B7B447DBB266302BC82D7DBD1622219543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/3453EFD7B001ACCBD0126A13C98BAA4F9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/23C65980427B41C7D9E32947CD41FD829543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/36073AAEBADCD344208056C9868E001CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/32EC540B3F53C56F8F39A2A185A32CE6BD02851C2FB632864165FCA4920 46548.pygtex [51]) (./_minted-Tutorial/3B09F0463D35461C42D2272763E734519543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/16EB556A216CBBE3D3F735350EA21A2A9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/F1A3FE258B41FCC45D4A8272B13EC395669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/AD9EF2BC42CEF4E413923F9BFFE1BE07669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/58A82383AA9DEBBEEEC6694BA2DE777ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9562C263804C6DD613F075A435553A9FBD02851C2FB632864165FCA4920 46548.pygtex [52]) (./_minted-Tutorial/5654C63CA8B2C75821B4DD795E1D9C91BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1525A6F338DC70B7A056F15305A9579DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DCDC3EB1E5C136F423AC65A1907BE6B1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/23394A4616015FFE4619934E98424178BD02851C2FB632864165FCA4920 46548.pygtex [53]) (./_minted-Tutorial/48D36449ADA742065AC871DB512A14FFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7160C98DFF3E9F14B8FDC3EDEA5AAADEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1E26B09583F35CC794E34E0D3C822C09BD02851C2FB632864165FCA4920 46548.pygtex) [54] (./_minted-Tutorial/A06B859656EACE1EB197B276B0CAD4769543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/5B68AB5634E46F0A59E5C238174AC4F0669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/AAC02B6C28E92C88B051BB2DE451DBD89543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/FECB9DCFA3C63121DB586752E4215990669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/CC27A8BEB077BCA7346A8D13F39867D79543DFECA235A69AE23006BA05B 4EB70.pygtex [55]) (./_minted-Tutorial/AE8667CEAACFF0F40839EE86774DD05D669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/6467B5574DF68CEA13D016BEEC8841A49543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/3D2A207C38AC647D99F5A8861A9D1AA6669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/DDD2E1D663317F4FFB7F8B7F03E4989FBD02851C2FB632864165FCA4920 46548.pygtex [56]) (./_minted-Tutorial/2EE890D1737C8A159C79BA4FCA81BB03BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/77FD1FB1550DD72BE3E8CFAC5C21C7DFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/022009B5C6117EE88C29BE7A45D87CF6BD02851C2FB632864165FCA4920 46548.pygtex [57]) (./_minted-Tutorial/FE4CF732C73126A3874795838D95FAB5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E7420F7622CCC097E8ADA484A405A3C6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/07A24756D2FDD5E9B66DEB7412FC4D6E9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/7F04F15A8B73F26152ED44DB3C48528F669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/55430EAFE498E385842834603E0B8C869543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/47CA5358E0862EF3920CC2BF888DBDB89543DFECA235A69AE23006BA05B 4EB70.pygtex [58]) (./_minted-Tutorial/A50FCDC5880666D012F0A802072B4AC5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D27A33312B4E81447304AAB2BAF2F6DC9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/11D55B86CA819707A4B89E7FDA2E6E83669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/74E272C92C546FD61FA6D3DA5C178893BD02851C2FB632864165FCA4920 46548.pygtex) [59] (./_minted-Tutorial/415024C641C8DA7A09117B3DFE240C78BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/487DCC9F44A2539C9B32C0122AEF4065BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5098CD053449CEC3C9C30C90A007A364BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/EEEF4ABAD66CE989F67C9E27EEDE95CCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F6AFF5A59B0706E4973BC1656FBD2D669543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/C4099CB0613585FCCD5EA7D8198704CEBD02851C2FB632864165FCA4920 46548.pygtex [60]) Overfull \hbox (9.93459pt too wide) in paragraph at lines 848--853 \OT1/cmr/m/n/10 FTP site ([][]$\OT1/cmtt/m/n/10 ftp : / / ftp . uniprot . org / pub / databases / uniprot / current _ release / knowledgebase / complete / (./_minted-Tutorial/D52DA4EEEEE2BF0FBE89EE253714929DBD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (4.48064pt too wide) in paragraph at lines 891--894 []\OT1/cmr/m/n/10 As of Gen-Bank re-lease $210$, there are $38$ files mak-ing u p the vi-ral se-quences, \OT1/cmtt/m/n/10 gbvrl1.seq\OT1/cmr/m/n/10 , ..., \OT1 /cmtt/m/n/10 gbvrl38.seq\OT1/cmr/m/n/10 , (./_minted-Tutorial/D41A88D88AB398F0C3B719A5C7D017C144BBF456F55B5DC060035246D76 9EADB.pygtex [61]) (./_minted-Tutorial/B4D970E8C81930851D8639D77EC3E41044BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/7C4E0944FB13EC4E75DD6FC64900395ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C68CC3C9B3A505FB972706356D7F336FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/61AD507889ED86CFCEFC880BAF2A2777BD02851C2FB632864165FCA4920 46548.pygtex) [62] (./_minted-Tutorial/DC5117490176932EFB8A7F0E0DA450F6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/657D43328835FC01F9133F8BC964475D44BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/82CBCD9B9F23373D67D9D0D7D2CA363FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/36F8D0FD2B4ADF57AC4203A0C80C6471BD02851C2FB632864165FCA4920 46548.pygtex) [63] (./_minted-Tutorial/9CEF7BF9B2634ACBC930BA5EB6DD73429543DFECA235A69AE23006BA05B 4EB70.pygtex [64]) (./_minted-Tutorial/AC02E3950380715FC960C04EF317D69F9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/1C65F538FA7F22F7BB5183FC1553A0C6669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/935F773BF84C3BF326F4BA093FEC79D4669566ECC2CFEDC7429F829576A D0DC6.pygtex [65]) (./_minted-Tutorial/C194E2231D844AE7D0223173D2A899919543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/10CB116B7358444BA68AFA046B5B84D59543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/29D12D495374A5A8C37AEB7083851DEABD02851C2FB632864165FCA4920 46548.pygtex) [66] (./_minted-Tutorial/920133226A22EEB682D854077D7FB78FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4EBA0A67E686E73FAA1A0EB27C260028BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C06224D76A18C126B27DFE55444AA3FDBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E381FF526AC999B71717F178C997F6B2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5F05AD4A17978E60C531612707D8F26ABD02851C2FB632864165FCA4920 46548.pygtex) [67] (./_minted-Tutorial/D19467E367634413AE9EE17A62E5D9EA9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/EDF3737891061C33EDE0FBFD16CCC63B9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/D1EAD55A1F8AD3DEAB82383A4F020F539543DFECA235A69AE23006BA05B 4EB70.pygtex) Overfull \hbox (19.46596pt too wide) in paragraph at lines 1349--1351 \OT1/cmr/m/n/10 Making a sin-gle call to [][]\OT1/cmtt/m/n/10 SeqIO.write(...) []\OT1/cmr/m/n/10 is also much quicker than mul-ti-ple calls to the [][]\OT1/cm tt/m/n/10 SeqRecord.format(...) [68] (./_minted-Tutorial/2F337ECD1F936D416FF9C5C6F41A02D7BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3337CD054623BAC21B6021E996EE0DFD9543DFECA235A69AE23006BA05B 4EB70.pygtex) Overfull \hbox (21.32593pt too wide) in paragraph at lines 1393--1397 []\OT1/cmr/m/n/10 Likewise, when pars-ing FASTQ files, in-ter-nally [][]\OT1/cm tt/m/n/10 Bio.SeqIO.parse() []\OT1/cmr/m/n/10 calls the low-level [][]\OT1/cmtt /m/n/10 FastqGeneralIterator (./_minted-Tutorial/D3AF6542680CA390CDA8C8DF87C693D3BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D749A84299CF58E876E9A899069830DB9543DFECA235A69AE23006BA05B 4EB70.pygtex)) [69] (./Tutorial/chapter_align.tex Chapter 6. (./_minted-Tutorial/9CC7A6864E21FFDDB3F4D02F2870DF42669566ECC2CFEDC7429F829576A D0DC6.pygtex [70]) (./_minted-Tutorial/81FAFBAECB3A03B11080ECF19D4CCC80BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/31E7567531B3A1035700A1E555A47FC0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D2523B56ECD3F392CD3E37EEBE302AECBD02851C2FB632864165FCA4920 46548.pygtex [71]) (./_minted-Tutorial/AC12821BA0AEE8F48238EAC359A31077BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A6D29782988E1FB75F30F2D60AB93C4EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E48647CD11476AB33349258EA43C50F2669566ECC2CFEDC7429F829576A D0DC6.pygtex) [72] (./_minted-Tutorial/16CCFD1DA7A71D5F6D9A86870C560407BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C0B89B536EECC0E9CC886A8B4CC9713EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/EE5558D4A829B63692DC55F8215FD331669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/FA669D1E3279749AAAA27A72F3B44533669566ECC2CFEDC7429F829576A D0DC6.pygtex [73]) (./_minted-Tutorial/9119ACDDD7EFFD39008E7F98AB7BF756BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5C54BE5D00F2871BB58E36C383B3B4DE669566ECC2CFEDC7429F829576A D0DC6.pygtex) [74] (./_minted-Tutorial/CE4E385956165A535376F6D73447D3F7BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F55715342346472744E837C465922E6E669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/1B5E788850B45798FCA06125D5880A14669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/B913EFE8AC0AC995AF3DCCAC856FF020669566ECC2CFEDC7429F829576A D0DC6.pygtex [75]) (./_minted-Tutorial/5F9DFDCFBF42A04D6BD31E8E9638DA57BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/BDB62F4C6418AA14588B7DBEA69D61C5669566ECC2CFEDC7429F829576A D0DC6.pygtex) [76] (./_minted-Tutorial/A8D0C008D3D8E2CB96D91B2A5FF2D318BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9458BC75C22971F0F7F09C79C7D6AFE0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/FEF99AFE39529F3F1A5EFC7A23714477669566ECC2CFEDC7429F829576A D0DC6.pygtex [77]) Overfull \hbox (5.54102pt too wide) in paragraph at lines 434--435 \OT1/cmr/m/n/10 ever you can't do that when your records come from a gen-er-a-t or/iterator. There-fore the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write() Overfull \hbox (39.68698pt too wide) in paragraph at lines 442--447 [][]\OT1/cmtt/m/n/10 Bio.AlignIO.parse() []\OT1/cmr/m/n/10 and then save them u s-ing the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write() []\OT1/cmr/m/n/10 -- or just use the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.convert() (./_minted-Tutorial/9776F24C4F96F850E549BEF997E4D18CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D8256B42DA32121F3B83617DD03F4024BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DA108466F70572EEAE2D54AEA4C156A1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8FD10ACD641F4427B35E96F33B44479F669566ECC2CFEDC7429F829576A D0DC6.pygtex [78]) (./_minted-Tutorial/ACC9FF1F2F025F77815D96DC3115B7DFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7E530BB128C8AE6BCF7BCE91DD4AF189669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/C17F8CD5F33DB6EB328532E02ADD1FE6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C02EB78C9555A4FEE4954D77162ACF99669566ECC2CFEDC7429F829576A D0DC6.pygtex [79]) (./_minted-Tutorial/74D8F602592BD3646F12A04951B2C44CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CB14E2060AF38515C129AB5808537F169543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/E78F5A80C222A5B2777910FED4F43F56669566ECC2CFEDC7429F829576A D0DC6.pygtex [80]) (./_minted-Tutorial/4D0AF4A40C449D27FF181EC477C63CE6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/2590B11C695B984E246A0A91734F786CBD02851C2FB632864165FCA4920 46548.pygtex) [81] (./_minted-Tutorial/508710FC1759BFFED598544DEC99BC0DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/886094CE2C1CAC714387144709D5A47ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6DC12DBE1D4FD44E7395C66258B5EAC9BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CAC16111FAD8C2E739F6D7C04A986BF0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A4149E9BEF55B5853014A59A3CBBFBE5BD02851C2FB632864165FCA4920 46548.pygtex [82]) (./_minted-Tutorial/8327145320A3BCB412D977F6683B71A2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1E096B06E33D157FFE18E045579F838CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C7331D522D75BB7830A1364BC3B71692BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C45FE25766D82D1C4A245CBB9A77DB00BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C0937EED558D842CEA8E3DB9514C6E59BD02851C2FB632864165FCA4920 46548.pygtex [83]) (./_minted-Tutorial/8EC03E9C8500D05C6439AC85123A9253BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/AE857C14E4731CC6F6EBA53051460097BD02851C2FB632864165FCA4920 46548.pygtex) [84] (./_minted-Tutorial/F88E003F9A4A95A929AA549FA710239CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/523928538FA511A925EC995B1803BD16BD02851C2FB632864165FCA4920 46548.pygtex) [85] (./_minted-Tutorial/CD47D1913C82182C164BD47DA4715282BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E7AA94166BAA5F4CBB44EF4336F3E893BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B49F47BF4F2EB4093BDE51E631C63064BD02851C2FB632864165FCA4920 46548.pygtex) [86] (./_minted-Tutorial/230B4706E315BD2F2A44F2EBCB37A442BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C11A66992B6C74B61F5A0BE7757AF3BCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/EAE190D91CC491562308EE568F986368BD02851C2FB632864165FCA4920 46548.pygtex [87]) (./_minted-Tutorial/6256254C5A7DFD21185291C77133BFDFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/FC96AF22EDD72BC4AC2EE47EBAA6B045BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E941CFC951CAE25312D9A5CAC9B27425BD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (8.40039pt too wide) in paragraph at lines 1126--1130 []\OT1/cmr/m/n/10 By de-fault MUS-CLE will out-put the align-ment as a FASTA fi le (us-ing gapped se-quences). The [][]\OT1/cmtt/m/n/10 Bio.AlignIO (./_minted-Tutorial/EA6A02999040945446E72AC6A00E56D8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/106ED62B0CFC10E7D5BC6CFC9CE003BDBD02851C2FB632864165FCA4920 46548.pygtex [88]) (./_minted-Tutorial/4D75AC9EDD74C466535F1EC4944833F7BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/14F1F3BAF80772F5999B0773C02432E7BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A261B9E9E2D4EB3C1DF5131C6F739998BD02851C2FB632864165FCA4920 46548.pygtex [89]) (./_minted-Tutorial/E2B86D066966C8BA13EEEF614D3E7454BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E87BDA1F176DA567A757DBA0231BC5BABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6BF1884F2D94AF8D067A2A20A9A41E2CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F551ABCEBB0043257A807C76B9D81B5CBD02851C2FB632864165FCA4920 46548.pygtex [90]) (./_minted-Tutorial/37B6E52C66902FA821D4B0E80172CE74BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0BA045AD7DFE0F0F3DD972F3E2C40BA1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/482576AF06E80D82290535FF7857A240BD02851C2FB632864165FCA4920 46548.pygtex) [91] (./_minted-Tutorial/5D3CCD84BC2EC46BF5FD98E7A3FC7266669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/D9565472E525C9F2B734FC37A70D258E669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/39152F199CEBB3375366F2E947824519BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/256B036DA9C3EDBC9EE41E2E52FDE1ADBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DC6CF8B5CDDD2C32E2052C03AF385674BD02851C2FB632864165FCA4920 46548.pygtex [92]) (./_minted-Tutorial/CEE035FF629B69F7D6B6351C1DCE2493BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DF151703751D72BD556402B910190A87BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/004029547AAB1172AF2684D2CA89EA88BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/554024580088332FAF0EA9296BACE82EBD02851C2FB632864165FCA4920 46548.pygtex) [93] (./_minted-Tutorial/419ECEB266819C8DCC38EB3E1DC3E361BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/143B9D317680E51D3A6E5641208720CABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6CCC707502EDD92E9C355854215BF885BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0A4B1939051DE630E53C7151447C8DD4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/2B6197C314840AD3EC15C56F366120C5BD02851C2FB632864165FCA4920 46548.pygtex [94]) (./_minted-Tutorial/E5E00F47BD7A0C8BC5F8818526283868BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/52B42D5819C8EC5D57A21AE60D28F6CEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5F566D907B2F88621EC4175F1F17AE04BD02851C2FB632864165FCA4920 46548.pygtex) [95] (./_minted-Tutorial/0FE96E337A3BA73D52896D46E2E233DCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/434D41043E1630324FA64E8B55B90BD5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/48453D528762FF183499778647AF218BBD02851C2FB632864165FCA4920 46548.pygtex [96]) (./_minted-Tutorial/BD86EE3248811DE8FD9DE8ED02397A39BD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (76.42714pt too wide) in paragraph at lines 1707--1711 []\OT1/cmr/m/n/10 By de-fault, [][]\OT1/cmtt/m/n/10 aligner.substitution_matrix []\OT1/cmr/m/n/10 is [][]\OT1/cmtt/m/n/10 None[]\OT1/cmr/m/n/10 . The at-tribu tes [][]\OT1/cmtt/m/n/10 aligner.match_score []\OT1/cmr/m/n/10 and [][]\OT1/cmt t/m/n/10 aligner.mismatch_score Overfull \hbox (47.73264pt too wide) in paragraph at lines 1707--1711 []\OT1/cmr/m/n/10 are ig-nored if [][]\OT1/cmtt/m/n/10 aligner.substitution_mat rix []\OT1/cmr/m/n/10 is not [][]\OT1/cmtt/m/n/10 None[]\OT1/cmr/m/n/10 . Set-t ing [][]\OT1/cmtt/m/n/10 aligner.match_score []\OT1/cmr/m/n/10 or [][]\OT1/cmtt /m/n/10 aligner.mismatch_score LaTeX Warning: `h' float specifier changed to `ht'. Overfull \hbox (32.852pt too wide) in paragraph at lines 1776--1820 [][] (./_minted-Tutorial/DCCEE6D592009E7B8E7DE81563D8D4CEBD02851C2FB632864165FCA4920 46548.pygtex [97]) [98] [99] (./_minted-Tutorial/98D9A5E0CD47E306CA0DA2AFE878514ABD02851C2FB632864165FCA4920 46548.pygtex) [100] (./_minted-Tutorial/FBB2100548FA74FADE3EAE28A2DE1911BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5C9DFA2EBF75572BAC340EC89D69B3D4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B788F0FBC120E74A47922EA232EB8671BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/504D01562B8D0E8E16B44A19B5FCD5EFBD02851C2FB632864165FCA4920 46548.pygtex [101]) (./_minted-Tutorial/DE91DA6F7C30BDD779CED0A91AB75DAFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A59C6CF4854355E98CC312686998A38BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3D37B0AE7B982968C1F24FD3EAA535EBBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5214A9AAFC8A40430707E3A6B6DC0D01BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/32985CB8E0884A44019C3AD3006E3F9FBD02851C2FB632864165FCA4920 46548.pygtex [102]) (./_minted-Tutorial/0758643069FF669538B9540ECD26C94CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0BDC838410673E955B3534CCCB8AC77FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/385490B66B3AC742DD6257196C784FE2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/BF27E9BF2471340998870C4A34296592BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A072B421EFC519E90AA0A540338E8E4EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C5780017603AFBC3BB3E9F52ED6688C59543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/76E331C5187C259B69198E91FC4AD112BD02851C2FB632864165FCA4920 46548.pygtex [103]) (./_minted-Tutorial/BF7EA4D0E316F88B3A609CF62C6CD357BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A564D138D2F52B4E2858B9D14814966BBD02851C2FB632864165FCA4920 46548.pygtex [104]) (./_minted-Tutorial/68A0723415861BAD8A4809FC33D4A2EEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/66AABFA387595237A8CE2518915213F8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B15E737F9393063B641148640673D991BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/EB25FB90F1A09B5CEE3428AFC4487B46BD02851C2FB632864165FCA4920 46548.pygtex [105]) (./_minted-Tutorial/EACCEA5889A222FB9830265E6A8DACB9BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/874975627BAB24A36A35FD4C633D246DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/35E64D230C4D7DA7362D8F8BA278ABB5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B0937117DDA6BB67D133C99E550AD5BDBD02851C2FB632864165FCA4920 46548.pygtex [106]) (./_minted-Tutorial/9C81CE609C3C74FF6DDE53A3528FDA3ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/AF515AF157FE4840A244030AD4DCE3A7BD02851C2FB632864165FCA4920 46548.pygtex [107]) (./_minted-Tutorial/C8046F75BC00F97BFBB444E7FCFDE7BABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9249A0A01E1025FA8711414C0E36841FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D1BAA37DF09A601FA4C6F2BEF162C3E0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/52868B2F44504455E4969FEF2614B63BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/433C9892AE287F36B57A8A95FE75AB94BD02851C2FB632864165FCA4920 46548.pygtex) [108] (./_minted-Tutorial/E7E68A8851DEEE300947A0531513417DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/60C347B45B5A049CB5B00A20D29DEF65BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1498327D070D6F98AC2E3DB39EAA1733BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6502BA65433924876427DBB6013C1003BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DE6EBD36098288038E8FFA4A045EC8FDBD02851C2FB632864165FCA4920 46548.pygtex [109]) (./_minted-Tutorial/B66E52A450DAB10C11EF0A5303F7F66EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8791CE2DDF360A2EB13DED7B355F1012BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/ED55B2BAF04247D4F10E951590AA5077BD02851C2FB632864165FCA4920 46548.pygtex [110]) (./_minted-Tutorial/779C61444C54C1736794F4E11B0E326DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9FF41FE72E025C3EC8E41470B268E105BD02851C2FB632864165FCA4920 46548.pygtex [111]) (./_minted-Tutorial/779CE460F4F768A71E6F35DDB7FDFA77BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9EF49B98A62C70CD81126514DF796600BD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (19.80069pt too wide) in paragraph at lines 2612--2613 \OT1/cmr/m/n/10 In this ex-am-ple, the to-tal num-ber of op-ti-mal align-ments is huge (more than $4 \OMS/cmsy/m/n/10 ^^B \OT1/cmr/m/n/10 10[]$), and call-ing [][]\OT1/cmtt/m/n/10 len(alignments) (./_minted-Tutorial/F89522EF58FB067C6521C367C7134716BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/76A8D90A1791A7B42DD5E6329FCCBE20BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/399250FB2BC395588B8004ACD928BE9CBD02851C2FB632864165FCA4920 46548.pygtex [112]) (./_minted-Tutorial/882BD2544386DECA236BF25C7DD64857BD02851C2FB632864165FCA4920 46548.pygtex [113]) (./_minted-Tutorial/22FCA15B328DDB0383F97012E3C1FA70BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DA98355B1CF48169F9C82F2DD1F86A29BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/13D646E6B49807044DBDC43707A09846BD02851C2FB632864165FCA4920 46548.pygtex [114]) (./_minted-Tutorial/467CA50C36874E405E988587FEC07686BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E4398C5237FE7113BC5A8DE3B0E138A6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E827958137C7E69DAEDB0C4151298E62BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A94C18D2207C354646F831D57FD85B35BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/801A90831A5799E3FF1FC0A5E721F4F2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4329189CC201D756D0770BD7596DF0D8BD02851C2FB632864165FCA4920 46548.pygtex [115]) (./_minted-Tutorial/C7C0911CDDC1913791B1BD1EDA0EC55FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F13283947C7FDCA9456A70797E029A73BD02851C2FB632864165FCA4920 46548.pygtex [116]) (./_minted-Tutorial/AAF53200644F4F68779FB844730087D3BD02851C2FB632864165FCA4920 46548.pygtex [117]) (./_minted-Tutorial/FCBF8AC8128D86DFE3607A8465EC034BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/96A1DC106863D5F4D96B9200B7B5BE06BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7323803F0E90CDA6FB16D10E868318BBBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/FBFC10402209A281F117C1A7C3D2057DBD02851C2FB632864165FCA4920 46548.pygtex [118]) (./_minted-Tutorial/04CF4E50F88DE1F6947064E1188A1BABBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/88E3C6FE8CD1E52180656649B61F8CBBBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3352A1628AB7C0D638BB368952D0DEDCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/842D73F66680850822D006857AE71FE7BD02851C2FB632864165FCA4920 46548.pygtex) [119] (./_minted-Tutorial/FAF36BBB1FEE777074E1CB3B06F18C8ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6B4057929CCF1526CF34FF943CFE3135BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E0AB5DB602ED615A4FA228E22B0CC4F2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5E9D6563DE4DEF6BBF8840F7693212F4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7C466424D72F09AE5AACA884161416F9BD02851C2FB632864165FCA4920 46548.pygtex [120]) (./_minted-Tutorial/F3DBACE95BC0B45F9EEF5BC8C67DEB0ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CC9E9C07C5DC6BDB4071B2A0EA825278BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/55D34AF6272FC77B12E7D4DD16884A6BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A5A764AD6E5C1A70216D27249F680093BD02851C2FB632864165FCA4920 46548.pygtex [121]) (./_minted-Tutorial/54EF0A3F068FF357EC3C51C6E1172A57BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1E78F0FD7A0E228935EE2D650C9315ECBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CEB2F5A09DE2611D752331C16E5BE61FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/007A62C4B86AFB9385A7D86241664707BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E19493E35A1B212412F37B3A7079D5ADBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0B051755682044B54FDC8CE728FD23B5669566ECC2CFEDC7429F829576A D0DC6.pygtex [122]) (./_minted-Tutorial/659317FF2415828FBE0F4505ECB5B4E5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/60D893638743BD147116D13E00593D6CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/FC6687367D9EC6B1C018CE84CA30555D669566ECC2CFEDC7429F829576A D0DC6.pygtex [123]) (./_minted-Tutorial/9AD9216297281F0858F16EA5C03B98AFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CB8FA536E934FA2DC233E7FF52DEAED4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/14104DE21243051DA2E8D004C5D1A9EDBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3C42B04C08C3B07CABB6D2D7AE1F1B6DBD02851C2FB632864165FCA4920 46548.pygtex [124]) (./_minted-Tutorial/A6E4A89F3F3E07605D5B2BD57C7671CABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1795B10D0BABDD4E83A8B6EBE5DAF8CDBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/691C9A3D9A1EB52FAECF7E4C91F03BE9BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9A7868CC2484B4CFB34F94E7549F2519BD02851C2FB632864165FCA4920 46548.pygtex) (/usr/share/texlive/texmf-dist/tex/latex/base/omlcmr.fd) (./_minted-Tutorial/A7706714F4982C826867A73C2B665ED0BD02851C2FB632864165FCA4920 46548.pygtex) [125] (./_minted-Tutorial/44E2C06C8661B128385CD75A7E7608AABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F120EF3444F3192D48657B4E52407017BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9AC50DD22A56E4DC2B26465D89DE35EABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CFB7E0A19AF729834746B283E60F2091BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7DA73F8FE9E6D95C2255220886791B5DBD02851C2FB632864165FCA4920 46548.pygtex [126]) (./_minted-Tutorial/E9F207F5DA488246642864EBF9EA466DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/15FD2886E49804AE97038F2733592C71BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1D1D98CF394058EA9EB8F6FA3B0DB75ABD02851C2FB632864165FCA4920 46548.pygtex [127])) [128] (./Tutorial/chapter_blast.tex Chapter 7. Overfull \hbox (5.71313pt too wide) in paragraph at lines 45--46 []\OT1/cmr/m/n/10 NCBI guide-lines, from [][]$\OT1/cmtt/m/n/10 https : / / blas t . ncbi . nlm . nih . gov / Blast . cgi ? CMD = Web & PAGE _ TYPE = BlastDocs & [129] (./_minted-Tutorial/A6D333F851BCB09A0C02030C1BC37AB1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/69F91830197D9990EA9A0BD7D074EE21BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CF5D749C3878C5A1FD3C8C63CA51FD08BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/00F087159F0534545C0B7288838BEF0EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8A150C3E431DF572EF74B2B19AB15AF8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/2FDF7B3FB3DC9B4B3C157122F78C3F4EBD02851C2FB632864165FCA4920 46548.pygtex [130]) (./_minted-Tutorial/0E750E34F5C53FAE26988AF1CDC7FBC6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C9558BD802C8764E46CF73625C14C204BD02851C2FB632864165FCA4920 46548.pygtex) [131] (./_minted-Tutorial/21FCFA3232935EE0DF07988BE50D1AEF44BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/88BD5D9B190061FD4FD34D2573EE4792BD02851C2FB632864165FCA4920 46548.pygtex) [132] (./_minted-Tutorial/CF5D749C3878C5A1FD3C8C63CA51FD08BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C9558BD802C8764E46CF73625C14C204BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/16EEC09BFB431080BCE9C5E6ADA5DAA9BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E34865BFB20F9D165069B84AE5218004BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E0F63513A18DD0126288BC98B9F40394BD02851C2FB632864165FCA4920 46548.pygtex [133]) (./_minted-Tutorial/A614B982013DB6EC38FCADD82303A8BEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DD49CD888784736545A3066AC257FBFFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B7DE908D2BB5BA4FD1BB179810D8D238BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/16EEC09BFB431080BCE9C5E6ADA5DAA9BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/68259DF5B1930070C029D5A72D891A36BD02851C2FB632864165FCA4920 46548.pygtex [134]) (./_minted-Tutorial/0C1E2B9A587BB44A7E19E83A4E5B1924669566ECC2CFEDC7429F829576A D0DC6.pygtex) Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. LaTeX Warning: Float too large for page by 32.27644pt on input line 481. ) [135] [136 <./images/BlastRecord.png>] [137 <./images/PSIBlastRecord.png>] (./Tutorial/chapter_searchio.tex Chapter 8. (./_minted-Tutorial/6D0EADF658E662CBA394834EFAC7346E669566ECC2CFEDC7429F829576A D0DC6.pygtex) [138] Overfull \hbox (2.9019pt too wide) in paragraph at lines 85--93 [][][]\OT1/cmtt/m/n/10 HSPFragment[]\OT1/cmr/m/n/10 , to rep-re-sent a sin-gle con-tigu-ous align-ment be-tween query and hit se-quences. [][]\OT1/cmtt/m/n/10 HSPFragment Overfull \hbox (8.43927pt too wide) in paragraph at lines 105--107 [][][]\OT1/cmtt/m/n/10 parse []\OT1/cmr/m/n/10 is used for search out-put files with mul-ti-ple queries and re-turns a gen-er-a-tor that yields [][]\OT1/cmtt/ m/n/10 QueryResult (./_minted-Tutorial/0EF47CD31A1F702FF10BD5C95E6D18FCBD02851C2FB632864165FCA4920 46548.pygtex [139]) (./_minted-Tutorial/BCDD1F95C8585B3C70DE9C1280B51955BD02851C2FB632864165FCA4920 46548.pygtex [140]) (./_minted-Tutorial/7A12FEF8445FE62A62C651C8B4EC163FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/362861C831165FEA5413E0240053CD89BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/40227DD719AAD22E8DC2923BF43CE327BD02851C2FB632864165FCA4920 46548.pygtex [141]) (./_minted-Tutorial/FD9C81C098491598DBFB6208173BB575BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/87D36F7AE3CBC4EDC6FCCFDE0173412CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CA24D00985B075C56E7C71A246E439FFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DE8A481953AA0F7BD7A99C0E281AD1A0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E7AA701BE1D007CE77D402E8CBFC777ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/906546E8B6F7831A0E7C5FC93AA56A03BD02851C2FB632864165FCA4920 46548.pygtex) [142] (./_minted-Tutorial/0B914838010D3E86EC368E1702EB7253BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E4688DCAB619DBEB784ED0D836D1E619BD02851C2FB632864165FCA4920 46548.pygtex [143]) (./_minted-Tutorial/DDECA9EB99D9FA38003A52C176593072BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/578CBF904F35965EECFEC1FA694F0752BD02851C2FB632864165FCA4920 46548.pygtex [144]) (./_minted-Tutorial/C0EB7D270F64704BA5AF848A21AACD64BD02851C2FB632864165FCA4920 46548.pygtex) [145] (./_minted-Tutorial/84848AABE250EF05E85067B2CD3275B8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A2EA3A12F7596A64ECEE374A9C53499ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E7A6E47CCC64E8FADF02D1CDC6246863BD02851C2FB632864165FCA4920 46548.pygtex) [146] (./_minted-Tutorial/A3385B945E43CC076FFA693B27681F05BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DAAFD2AAF126ED8D7284764B561B5E2BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4B4824DE2ED3215F02082987EE573577BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/61406D58E5F7C40FD0A0280DCAA66B46BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/BF77764978D907008BC936FD2A5FCD95BD02851C2FB632864165FCA4920 46548.pygtex [147]) (./_minted-Tutorial/CE618F26D70602D511E57E53CD880444BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DE23F71CD74CF7717D38AD01C1E1C787BD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (27.24287pt too wide) in paragraph at lines 743--745 []\OT1/cmr/m/n/10 It should not sur-prise you now that the [][]\OT1/cmtt/m/n/10 HSP []\OT1/cmr/m/n/10 ob-ject has an [][]\OT1/cmtt/m/n/10 alignment []\OT1/cmr /m/n/10 prop-erty which is a [][]\OT1/cmtt/m/n/10 MultipleSeqAlignment (./_minted-Tutorial/338C616C7128C3DB7FFD516F5C2BDA12BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1195D6861E887568107FA7F463EA9BBABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/31F43A46088F6D2E63B39857A3536909BD02851C2FB632864165FCA4920 46548.pygtex [148]) (./_minted-Tutorial/16771935702D6A2A9762A80A621013D8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/046FE550C51B323D1E952A27E126FE19BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A55E467518B2E0F936A232F0970B1037BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6D69D310788199FBA6E8A5BF5CAB2021BD02851C2FB632864165FCA4920 46548.pygtex [149]) (./_minted-Tutorial/2C71B4AE1F4F9990447491C6C291ABC2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/FD7ECFDD9D017B829A54C995FEE42EEDBD02851C2FB632864165FCA4920 46548.pygtex [150]) (./_minted-Tutorial/3AD8335853E972C8E62AAF79CF0A3D33BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/758BAC7574A59544686354199D20892CBD02851C2FB632864165FCA4920 46548.pygtex) [151] (./_minted-Tutorial/7A63CB5E786CCE052981F7DD10653DA9BD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (14.20721pt too wide) in paragraph at lines 1055--1059 \OT1/cmr/m/n/10 func-tion re-turns a gen-er-a-tor ob-ject that yields a [][]\OT 1/cmtt/m/n/10 QueryResult []\OT1/cmr/m/n/10 ob-ject in each it-er-a-tion. Like [][]\OT1/cmtt/m/n/10 Bio.SearchIO.read[]\OT1/cmr/m/n/10 , (./_minted-Tutorial/DC4E434DA5B851CF1E22BD3608A311F4BD02851C2FB632864165FCA4920 46548.pygtex) [152] Overfull \hbox (20.13245pt too wide) in paragraph at lines 1087--1092 []\OT1/cmr/m/n/10 In this case, the ideal choice would be to in-dex the file us -ing [][]\OT1/cmtt/m/n/10 Bio.SearchIO.index []\OT1/cmr/m/n/10 or [][]\OT1/cmtt /m/n/10 Bio.SearchIO.index_db[]\OT1/cmr/m/n/10 . (./_minted-Tutorial/0AB25750C7D89E832295045C60D6B8C4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DFACFE04880AE0CA2E8E32ABDC9E9868BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/51F256FC56FFFAE1F1E84A4EFC5BAE55BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5BCEFFE3DBB7A0AE4FD5D950731D72DEBD02851C2FB632864165FCA4920 46548.pygtex) [153] Overfull \hbox (11.82602pt too wide) in paragraph at lines 1167--1170 []\OT1/cmr/m/n/10 Finally, [][]\OT1/cmtt/m/n/10 Bio.SearchIO []\OT1/cmr/m/n/10 also pro-vides a [][]\OT1/cmtt/m/n/10 convert []\OT1/cmr/m/n/10 func-tion, whic h is sim-ply a short-cut for [][]\OT1/cmtt/m/n/10 Bio.SearchIO.parse (./_minted-Tutorial/BDE985FA3ADA6B0D37013C3D5F37C176BD02851C2FB632864165FCA4920 46548.pygtex)) [154] (./Tutorial/chapter_entrez.tex Chapter 9. [155] (./_minted-Tutorial/95F72AA1E59C898262005610BC25A6BABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/320E9A38F759168BA03B078BD9CC013BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DAEC2235DDE454C09ECEB0DF4CD26FB5BD02851C2FB632864165FCA4920 46548.pygtex) [156] (./_minted-Tutorial/7692669934D8ED6DEE1B8B6684745421BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4E8E7490F3E1B9120A0B1B53C024FA36BD02851C2FB632864165FCA4920 46548.pygtex [157]) (./_minted-Tutorial/C21F612C84412948C9890ED976F536B0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7E05622F86D5C6456282864B1095B19CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/846A93AAA063B5CBA3EDEF3D5FC8C008BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/03DD15474BC34E37527B593FC22220FCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7B7AA3167A6472C6C33ACA91F8E88FACBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/82DFC9B19D35F2D9482DE6B365FC35F6BD02851C2FB632864165FCA4920 46548.pygtex [158]) (./_minted-Tutorial/01D9FCC3424FD0B497241E81D2FE83C6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F74B27B285F0D0CC7E69CABE07232C68BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/83C7791C8A9F82BA61AD4B1644D50277BD02851C2FB632864165FCA4920 46548.pygtex) [159] (./_minted-Tutorial/3B6409EA2F4B25B8F136CE97DC95E8C4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/53F668B0CE9069489F6D35B114D072B1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/49E5F2A1DFC2444E5A673AD6C6E3F19FBD02851C2FB632864165FCA4920 46548.pygtex) [160] (./_minted-Tutorial/96245EB54DC7A4475CD270566892BAE4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/AA26452EC447FD01D35D14B1CE4F3147BD02851C2FB632864165FCA4920 46548.pygtex [161] [162]) (./_minted-Tutorial/042DA7A7135DAEF797FB2EE6170C3B6DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/11417087354B0B78128E27B0162F48D59543DFECA235A69AE23006BA05B 4EB70.pygtex [163]) (./_minted-Tutorial/51CC2C09DB95235CA19612EAFF65F487BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/01919CABECEE21D3FA5A6B7A01CCCB5EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0DD80468D8C175A94BC63142BD16EF1DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/414E52C4377A1D0E6A428B032A7756FDBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6109D29005C5EC9FAE01CDFBE62EF008BD02851C2FB632864165FCA4920 46548.pygtex [164]) (./_minted-Tutorial/A0ED7F47BA117071BA21263E7AF6DB27BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3C5A1B892E98E1E6E8C179B5F465500ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/68622353B578A611D2F621023E3C4BD1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7455566FBE10CCFD5236DF65992A9F70BD02851C2FB632864165FCA4920 46548.pygtex [165]) (./_minted-Tutorial/6E7EC19AB4E894FD7BECB47DC082FC38BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E02371BEF7596435E8F90267E0362E0944BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/8A1D9304F979E03817FD393E44DC722ABD02851C2FB632864165FCA4920 46548.pygtex [166]) (./_minted-Tutorial/2B17732B358EE5D871A248019977CF38669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/2186E927D5A018F8950E8A7D0F734E71669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/DDE0AA7C839DD601590297B5D523D03BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1516062A6E16A043D5996183E67DEB86669566ECC2CFEDC7429F829576A D0DC6.pygtex) [167] (./_minted-Tutorial/08B5AC3C9DEAD2E377FE070B35391F0BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/898885F88FEAC697F30E8E063D95F24D669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/8BFD5A5D2A0A2DB21DA15E3F1719D3F6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B89E703729CE0DB5EB3456180292FA1B669566ECC2CFEDC7429F829576A D0DC6.pygtex [168]) (./_minted-Tutorial/06D29A54CBCE7E9BEC9B02AF3737953FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/115C0D8716DAB358EAFF936486F27AB9BD02851C2FB632864165FCA4920 46548.pygtex) [169] (./_minted-Tutorial/9BFD2F013E1A1D8756C2BFF5B3706AAD669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/9D66917D850D2EF232ECFE32D0F8D1CEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/474ACCF7269CF6DA8C1148E094B63C80BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/265BCBE09451F85D4BB86E81E6F3D4E1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/077B6C28FFFD9E8EB72387BF7F1D9BF1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/41118C19A2E462F9721E8AB1E52AAFC3BD02851C2FB632864165FCA4920 46548.pygtex [170]) (./_minted-Tutorial/8D1D071E3CA3DD9187A6F2C35836C58ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9E297F3C90950B761CCB974F597BCC12BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/30DFAED5DDA7DA75BB6A3BF0F0C12D75BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E07A958FADB74CD60F7086FF6319E277BD02851C2FB632864165FCA4920 46548.pygtex) [171] (./_minted-Tutorial/55E8C5FCC00AEE8A4E1D892ACA95C2BCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/473B4163A14D626D6B7A08A26A0A1266BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4802D221A3EBE7AAC3E07CB05144CA27BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F7C9857DB48F3111F31BB49EC39F2019669566ECC2CFEDC7429F829576A D0DC6.pygtex [172]) (./_minted-Tutorial/650077A39F2D52831A52D045B184B624BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/17E5085C64881C08DC82C2B5573291F2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/076325C16F7C56460228C73B3147DF7A9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/2018A02508D4B36EF0217BE478D18CE1BD02851C2FB632864165FCA4920 46548.pygtex) [173] (./_minted-Tutorial/67F7BC27D166185C4B7B9A9F270ACDA5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F01452391D049758B3588D8F37184AA19543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/04D54F815C5EFA53EF9010776D1AA07EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D46819E08D3CDD954897218A7EB7C8C0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/57648E2674FE9BB727770109CA65C71ABD02851C2FB632864165FCA4920 46548.pygtex [174]) (./_minted-Tutorial/676B968CE2CF2F3AEF6899757E020B1EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8778F0F3798A99FE0C3840234CAC2B5BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/FAD1D32BBD3E6FC5FE31DBBF8029928ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/85AA5F6E67E515A70F5F0A4D9A0548C0669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/24D6870F7CF00B7F93EF1F55424D4AD0BD02851C2FB632864165FCA4920 46548.pygtex) [175] (./_minted-Tutorial/964257041BEB9E732FF9A943209BD6EDBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/600193D5D5D44162E61A3CAB40448426BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E963D1B8D3330FC994CC39110B642038BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/574A29DDA761C1725F490FB0F1CD4EEFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6FD15C01D270A661A77854FF78F033B8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5845916CE276A61945EF5849B982E8A0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8905908F46BA67CB99A3360F253875C5BD02851C2FB632864165FCA4920 46548.pygtex [176]) (./_minted-Tutorial/4DA8ECCF1EA4588537B571B9F46E13A1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/714497BD693AE1BF76AD1C44D3A43F2FBD02851C2FB632864165FCA4920 46548.pygtex [177]) (./_minted-Tutorial/824F6600A92AA40841D5D9A4C2EDC5FDBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A3EC6E0F9D852E0B8DED607938A72797BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E8FC03C2B925F09D2849BD1DDCBB3848BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A137A30778671FFE0F193EED7A8819D7BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3D76169664531538D144C55FFC33571BBD02851C2FB632864165FCA4920 46548.pygtex [178]) (./_minted-Tutorial/D49E38D9D1357F6225DB42AC5AD5ED7EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CC6CFA7B6751FFF8C74660FCC40D3C45BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0D86B77B8C40BC4335F18EE35CB93649BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/37575ADC7CF832C14B5854633F9C88D8BD02851C2FB632864165FCA4920 46548.pygtex) [179] (./_minted-Tutorial/5E81FD2679BB8BC4F82244B31C22C477BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7212F8F4D805E6009D8612AB61498E24BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B038E9BC100BB2A231E2B4BF11B0330CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3256378680D2E01A0D283817FC4F9633BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1E93113A22D275DCF1ED22A91F77D5749543DFECA235A69AE23006BA05B 4EB70.pygtex [180]) (./_minted-Tutorial/4F9D9C998FB1DECE2FBF932B39921FFA9543DFECA235A69AE23006BA05B 4EB70.pygtex [181]) (./_minted-Tutorial/43EC7DBFBCAE4E8B197BA170F7FE7CB2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5F55F80E3D84EDCE0B63B5BCEC4E927ABD02851C2FB632864165FCA4920 46548.pygtex)) [182] (./Tutorial/chapter_uniprot.tex Chapter 10. (./_minted-Tutorial/DC3FD651AB93A0CE9D668FE4206D1A86BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DD1C7AE6EB54A3133F3D58EE95B3A668BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/BB844FCBFB442A424E4ED0D244DD6768BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/930B60BD569CAAF368B0E614553F3030BD02851C2FB632864165FCA4920 46548.pygtex) [183] (./_minted-Tutorial/ADCE00FC778B0EA886D44F1AA6519182BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3D3E040F0C8AAE9BF46C3D89DB934669BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C65ED72167AAF5D5730D19463FD69228BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CFBCB7DFF63857026EF72107C91C4D14BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D965DDAA766509A8449374C475416C06BD02851C2FB632864165FCA4920 46548.pygtex [184]) (./_minted-Tutorial/747E2FE5A2594F5385BB7437A4517918BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8837CDE38481CF679BB33997916F09ABBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9E15781AA166AC63C2DF3BCF25628224669566ECC2CFEDC7429F829576A D0DC6.pygtex [185]) (./_minted-Tutorial/956383F4066B9E093C9D2E3843CA0220BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/BA8B23CD43F97133B0CE8ECD0A9462AA669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/8B296BCFBFAA7137B45E8CB899424BE4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C2EF087C5641CFFF6A40A4396FE9307BBD02851C2FB632864165FCA4920 46548.pygtex [186]) (./_minted-Tutorial/9AB12EEC55BEE868B932EF7EF12109CEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6E2B75EC45BA35CA8C7799FFAFE69A4DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1DE080CE5283B4D334F81719880190E2BD02851C2FB632864165FCA4920 46548.pygtex) [187] (./_minted-Tutorial/6ED198EEC186F92A098C5692A874CF5B669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/F4AB180AFE85CC09CE3F73EE547FC783BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B1A88EF3A17DB1FA7EC5A60B27A37BF9BD02851C2FB632864165FCA4920 46548.pygtex [188]) (./_minted-Tutorial/454E46BC171F751C15F6A295F2284AB7BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8DCADA174B7DBC35827913027E1507B4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/20DD2D91201FBA08EE81FE73D557B622BD02851C2FB632864165FCA4920 46548.pygtex [189]) Overfull \hbox (24.29903pt too wide) in paragraph at lines 365--366 []\OT1/cmr/m/n/10 If the ac-ces-sion num-ber you pro-vided to [][]\OT1/cmtt/m/n /10 ExPASy.get_sprot_raw []\OT1/cmr/m/n/10 does not ex-ist, then [][]\OT1/cmtt/ m/n/10 SwissProt.read(handle) (./_minted-Tutorial/30A3D5D1EA4F73DD0984EDFDDAF9090CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/950511DA0658C1A2824DF92F06F34BE8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6A833CD3DDDD6A4CCF169D082C63D87DBD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (65.93893pt too wide) in paragraph at lines 409--410 []\OT1/cmr/m/n/10 The same func-tion can be used to re-trieve a Prosite doc-u-m en-ta-tion record and parse it into a [][]\OT1/cmtt/m/n/10 Bio.ExPASy.Prodoc.Re cord (./_minted-Tutorial/DF2DA17EFC0F6336210C74066809B753BD02851C2FB632864165FCA4920 46548.pygtex) [190] (./_minted-Tutorial/9457A436D281E066D350873A88476E59BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5C1399E579A6AA8D432E509AE441C2AEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7528F52197E46B376DB12FB34672D7A8669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/64ACD8E8EC2C5F323A9D84639080EBCBBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C8BC3187BF8F96BDF009A2CA8A95A3C3BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4323DBBD15E176599A70095217F377E7BD02851C2FB632864165FCA4920 46548.pygtex [191]) (./_minted-Tutorial/0B895A7CD7770AD5152A902E24E86169BD02851C2FB632864165FCA4920 46548.pygtex)) [192] (./Tutorial/chapter_pdb.tex Chapter 11. (./_minted-Tutorial/D779A8F555F6BCC207B905D5D6C22853BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/946CAECCFDBF1349958F40A0FC03463FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/2FDED7F9BEF9EA1F5CE28B11996ED43DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/05714E0F28AC6B36B176161D8A9FA84DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3D3953EF520FE9546FC19DB705E69085BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E37E6F74461E0075B61AF24790D37C71BD02851C2FB632864165FCA4920 46548.pygtex [193]) (./_minted-Tutorial/32D78458130807D5C8DD536942BA7388BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B49437C8CCF1C8D72B8DBA0CFE1DCB35BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A7F199DA98E2BD66B92177EFD14AA59ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/57A82B690A435E6AD7DAD62778DB8231BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3AABC2CB1B50E66D5DBACF20EF52245ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C79D210A6D0E5501910FFF311063879EBD02851C2FB632864165FCA4920 46548.pygtex) [194] (./_minted-Tutorial/41FC845107E552AB47AA881B90236E18BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B41B5BFD7D85ED4E7E70DA059AE1D176BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/36AD36AC9E663BF06BB871053927CDF0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1BBCC7F8F1756C270C4D99E9F943A024BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4AD3361A8DEC1848967C5C4904CBAA6BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D8411ECFB826F8858D5702457B0FB9A5BD02851C2FB632864165FCA4920 46548.pygtex) [195] (./_minted-Tutorial/684AC0ECE33D6BA84F0409CE669AB136BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C85B5FA2C9BF8127C2FEFF62553FECECBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/05AAA27695D5E74A2F0C892230E4EFA4BD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (13.022pt too wide) in paragraph at lines 262--264 \OT1/cmr/m/n/10 The over-all lay-out of a \OT1/cmtt/m/n/10 Structure \OT1/cmr/m /n/10 ob-ject fol-lows the so-called SM-CRA (Struc-ture/Model/Chain/Residue/Ato m) [196] Excluding 'htmlonly' comment. (./_minted-Tutorial/DCB043864D9F8E2B59DEBF1784B30CDCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B6B956752D54554859CB3FC041890BD7BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/958010CCD8250B2A6D359F037738B54EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/69627B7F3108FCBC466F45AE8D24D979BD02851C2FB632864165FCA4920 46548.pygtex) [197] [198 <./images/smcra.png (PNG copy)>] (./_minted-Tutorial/13774A78311C8B2B99285E3D509AD855BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/EC253507D414D1E9DDE9BC5CAF6BC78CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/69D3F9059506073A988980B78CEAB247BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5A42A68287048A843E1066F2E2727622BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/22421A9A4B194CFEBFABE1E2DDFC8A12BD02851C2FB632864165FCA4920 46548.pygtex) [199] (./_minted-Tutorial/8A579A2F82E38AFC725C7AD02B2F5D57BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C4346C691565244D87DFA5ED26B512E3BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/38F92E91F7EF83579513DC2A23D231DCBD02851C2FB632864165FCA4920 46548.pygtex) [200] (./_minted-Tutorial/35E34E333445AAAA4E33570211335BA5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A2470AECC1DA459F7A1ACC68FCD911B1BD02851C2FB632864165FCA4920 46548.pygtex [201]) (./_minted-Tutorial/874F41EC8F1C0D727A004EAEFDC88098BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/94A9BE470837AFDA4B8581B79BB12492BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/76657140082404C594EE786B642215C3BD02851C2FB632864165FCA4920 46548.pygtex [202]) (./_minted-Tutorial/17EB0A1D2812B68E199CC00449B9254CBD02851C2FB632864165FCA4920 46548.pygtex) [203] (./_minted-Tutorial/D94A742238FBA8E89BB46038CDBDEB90BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0BFD7EDA2178705DA7C24F4D3735823EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/73DA0F97AF01C85175F4AF2DFAE2C6B7BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7E80E6D2D75417229F3B2B705315B128BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/618AFB68C3893C2A344D3A532D9BD99ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/82DD3285068398C1A65910EDE1BE970CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0799FD26AFF50D33D257B86E8D3E40B3BD02851C2FB632864165FCA4920 46548.pygtex [204]) (./_minted-Tutorial/2857EE83D7FCEE22018F0C0AD63239E0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/365D7E5A27BEEE6ED9265079DF231899BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0B35B80BBDE5AE1373CAE9105C01A624BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/BDCD0910528B95EADEE1C7C6BD40AD3CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3A499902396CBA88B311EE3A93BC2663BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B2412D9441598FCD30172739CB3CCA39BD02851C2FB632864165FCA4920 46548.pygtex [205]) (./_minted-Tutorial/728242DAC9077785511462C5CD16E667BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/866FA21894DE0E73CE09F7F50E59FDC5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D6328A6D8E47F7B8E9530D396E8ED50DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/2CF9B1EBC15ECA1536AFA86FAF01899BBD02851C2FB632864165FCA4920 46548.pygtex [206]) (./_minted-Tutorial/F412BF266412BEC93BB127CA53AB4D0CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A73938953B2223965D08B528F27C56E8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B33389074760A02AC27316E67DAAB073BD02851C2FB632864165FCA4920 46548.pygtex [207]) Overfull \hbox (42.26714pt too wide) in paragraph at lines 956--960 \OT1/cmr/m/n/10 breaks and dis-or-dered residues and atoms as de-scribed above are han-dled cor-rectly. \OT1/cmtt/m/n/10 structure[]rebuild[]test(entity) Overfull \hbox (3.8904pt too wide) in paragraph at lines 976--996 [][] [208] (./_minted-Tutorial/10F60558792DABA08CE906FCD09A993CBD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Command \r invalid in math mode on input line 1049. (./_minted-Tutorial/10BEDFA26FE20B8B11FC832131C1705EBD02851C2FB632864165FCA4920 46548.pygtex) [209] (./_minted-Tutorial/12DBC9D94FB0B4B78A481C6C111C6709BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/895E3343902EFB0E5475667B01C4B691BD02851C2FB632864165FCA4920 46548.pygtex) [210] [211] (./_minted-Tutorial/7A6D5A10ECC42BAFEE724455549BCB15BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D5B0F5228C1E7FAD0C7AB40AEFF6B6A9BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/2810A7579DC6FE011D31E2F074471A74BD02851C2FB632864165FCA4920 46548.pygtex [212]) (./_minted-Tutorial/D9D0B8746EBF14CF4BE7DA480D9ECD5DBD02851C2FB632864165FCA4920 46548.pygtex) [213]) [214] (./Tutorial/chapter_popgen.tex Chapter 12. (./_minted-Tutorial/E5F1866C3CBB485B8C06B62764ACFBB29543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/331BEE386F268F55DE217F54E27EAB6B9543DFECA235A69AE23006BA05B 4EB70.pygtex) [215] (./_minted-Tutorial/6CD64A1F591B16F512F7EB6B68E5B3FC9543DFECA235A69AE23006BA05B 4EB70.pygtex)) [216] (./Tutorial/chapter_phylo.tex Chapter 13. (./_minted-Tutorial/8F8EFC1C83277AE6C5B5A259FAAC5671669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/4914B4679D1C933D9AD76E95F18CE15844BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/3D758844BE2A5D4414B741470EDE8C24BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/719B0C758B666CDEEB2B250C2143A4ADBD02851C2FB632864165FCA4920 46548.pygtex [217]) (./_minted-Tutorial/8698B66B622D8A91E7706D889D5F35DDBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6621A01BB423374C8FC608E267D0EA7DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/87517FEF82BFE1AB8D89A83F4DC5E8B9BD02851C2FB632864165FCA4920 46548.pygtex) Excluding 'htmlonly' comment. (./_minted-Tutorial/6C5156DAD460519324A5B7657B301B5DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1836031BC83AA94C8906762F613E6CBABD02851C2FB632864165FCA4920 46548.pygtex) [218] (./_minted-Tutorial/D0A75FB8C1C791E4AA80420B93F216A8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/FEC6C2CB5FA0AFCFE00D995BD3642FF2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/2B435DC3041611A5D6A663B437ADB1ADBD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (25.13162pt too wide) in paragraph at lines 182--185 []\OT1/cmr/m/n/10 Let's tar-get the most re-cent com-mon an-ces-tor (MRCA) of t he nodes named ``E'' and ``F''. The [][]\OT1/cmtt/m/n/10 common_ancestor (./_minted-Tutorial/29624A9666C9430AABADF395148BBF27BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D0F05D42BA0A9BC594EEDB16319A972DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/87517FEF82BFE1AB8D89A83F4DC5E8B9BD02851C2FB632864165FCA4920 46548.pygtex [219 <./images/phylo-simple-draw.png>]) Excluding 'htmlonly' comment. (./_minted-Tutorial/D713148814BA75DCDEB1C77B12674D9BBD02851C2FB632864165FCA4920 46548.pygtex [220 <./images/phylo-color-draw.png>]) (./_minted-Tutorial/69333D76AA5D97D8BF9E95DEECEEE2B1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/456F5679DCD4FF740E7A110889D86573BD02851C2FB632864165FCA4920 46548.pygtex [221]) (./_minted-Tutorial/2B3BFA62F3A778E4818959ED3E8AD3EEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/08F738B2988883F2B3BAD96FA439AD7CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8C7F4AB58CCB44E2FF66E36A26E59F55BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/00BD91C09868B2B26E32B5FB41A2583CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A1E441205EAE188E6F4319753E3982D3BD02851C2FB632864165FCA4920 46548.pygtex [222]) (./_minted-Tutorial/C3E382424C6F17EF8DB95D08D8AC9FEEBD02851C2FB632864165FCA4920 46548.pygtex) Excluding 'htmlonly' comment. [223 <./images/phylo-draw-example.p ng>] Overfull \hbox (19.85507pt too wide) in paragraph at lines 479--486 \OT1/cmr/m/n/10 For ex-am-ple, in a tree with clade names Foo1, Foo2 and Foo3, [][]\OT1/cmtt/m/n/10 tree.find_clades({"name": "Foo1"}) [224] Overfull \hbox (13.48741pt too wide) in paragraph at lines 534--537 []\OT1/cmr/m/n/10 Find each clade con-tain-ing a match-ing el-e-ment. That is, find each el-e-ment as with [][]\OT1/cmtt/m/n/10 find_elements[]\OT1/cmr/m/n/10 , [225] (./_minted-Tutorial/6AAB725DBD2E5B7C5FD79A9A16536BF69543DFECA235A69AE23006BA05B 4EB70.pygtex) [226] Overfull \hbox (15.04868pt too wide) in paragraph at lines 703--707 []\OT1/cmr/m/n/10 Below is an ex-am-ple on how to use a python script to in-ter -act with PhyML ([][]$\OT1/cmtt/m/n/10 http : / / www . atgc-[]montpellier . (./_minted-Tutorial/20AACD5E58630D4B64529F3A1ACD8119BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/EB4CA3626331FD00CE50FECC3590095BBD02851C2FB632864165FCA4920 46548.pygtex) [227] (./_minted-Tutorial/0702C9875263768417DD3ED2EF78755EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C395044A3DB827E8D2E36BA5259475D2BD02851C2FB632864165FCA4920 46548.pygtex) [228]) [229] (./Tutorial/chapter_motifs.tex Chapter 14. (./_minted-Tutorial/9344D5588F066D22473BF4F77E39E1F3BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/AB934E1AD357BE20BA1F223A29AE486ABD02851C2FB632864165FCA4920 46548.pygtex [230]) (./_minted-Tutorial/A7AAAF382950D3CAD77D17E6B6489D03BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CEBDE9089C5A4F125D8DD8D4E6ACD9C4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9293BA115F68336B4D0213D24C96AE75BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/BFC042DE8B1588B2D23A8510A608989CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5F3B74C4B4D1FF3D387E6F57F726D177BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0517D975CF92331B81AF837F9D257173BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C66E35936EA68A132264FDF63F70A42ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/86717C2BCE65F41FCDB8652763165857BD02851C2FB632864165FCA4920 46548.pygtex [231]) (./_minted-Tutorial/8572965E772BA3D97A5ACAB64A3CEA2BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0CFCBF886B5144440F79F61243192022BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/176227E746894D602FF7231BCB8E5F21BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/02A6CF1EA94D619AE2B9428BDA4531C5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/EDCE72CAE83814FFFF4AE6A97CBB2476BD02851C2FB632864165FCA4920 46548.pygtex) [232] (./_minted-Tutorial/C6095CA0913B3D01D81200EBA18DE7FA669566ECC2CFEDC7429F829576A D0DC6.pygtex [233]) (./_minted-Tutorial/2CAEA4D1EDEE84068D05546A212DB0C6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CD1D7AEBB145784C9665DAA472D55CE2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/30EDED7029501226C973943BBA0D1ECDBD02851C2FB632864165FCA4920 46548.pygtex [234]) (./_minted-Tutorial/5C8E141CD14F7220B986B96A3E564D14669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/95F985CC0D974FEE28E0B2667232BA3FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E778DA34B5EC9B33527CC22435275C76BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D11003572C5456D15CB1BF6CD74B860EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CD308858A86E4C77FD58BD7CFCB2EF92669566ECC2CFEDC7429F829576A D0DC6.pygtex [235]) (./_minted-Tutorial/4910FFD3FDCDF743F7F37BE10B04F706BD02851C2FB632864165FCA4920 46548.pygtex [236]) (./_minted-Tutorial/AF4CF0FDC0B4EBF46401E9953A293EF5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7D8B23E400A55050254232F7CA2CC9E1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0E771A916EB510C91DEEBFC8201442DCBD02851C2FB632864165FCA4920 46548.pygtex [237]) (./_minted-Tutorial/1C14559B3C7AC9C35B84F1518D8088FDBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/46FF514D13E6C4030C26EC4EFF8CFAFDBD02851C2FB632864165FCA4920 46548.pygtex [238]) (./_minted-Tutorial/8E9A5519710E4288CC6DA45EFD61B3AEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/47B231A79951117DFE8D7B369F5A0EDEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CF5314A9EF9BBFFA32CFF87ADC53C378BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/FD7EDF217AC860547FAAC456716F6D6BBD02851C2FB632864165FCA4920 46548.pygtex [239]) (./_minted-Tutorial/7EC0366BAB057E95DD30855AF8AD06F8669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/805B769BEA8271618919879EBC73D6AB669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/AD271A766709EB68A386A406C3E3DCB0669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/3C12150A1943B695BB045865F0A87E44669566ECC2CFEDC7429F829576A D0DC6.pygtex [240]) (./_minted-Tutorial/95318595464A829C3F1A431E3C76909FBD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (13.10551pt too wide) in paragraph at lines 603--606 \OT1/cmr/m/n/10 The [][]\OT1/cmtt/m/n/10 motifs.parse []\OT1/cmr/m/n/10 com-man d reads the com-plete file di-rectly, so you can close the file af-ter call-ing [][]\OT1/cmtt/m/n/10 motifs.parse[]\OT1/cmr/m/n/10 . (./_minted-Tutorial/147DE2DA7F37C2A5A1C1344033AB8B84BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/36E981BB5EF7EC3A1829EC830B0AF9C2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/22F78F0EFBBBF61FA3DB5795B5820CD7BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F87F681AD46E2F9ABF3B87ADA8B1EFB6BD02851C2FB632864165FCA4920 46548.pygtex [241]) (./_minted-Tutorial/CB1A766DCCC9D440884673396E012053BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/64B1E8E30714DF156170A704E0AF9B9E669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/744EE283B3B7A72BE718EF244D782CA7669566ECC2CFEDC7429F829576A D0DC6.pygtex [242]) (./_minted-Tutorial/BCCDFDD968CCC98039C6D6F4886917C1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/2F48F226FED2AEC7A54EAA6C769060B9BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9D8413811B6BC75226431D501B682BD9BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4293959D98D2DC2DC0CE6CA72DFD5D5CBD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: `h' float specifier changed to `ht'. [243] (./_minted-Tutorial/86BE687BF0F504548CFBA35246A755EFBD02851C2FB632864165FCA4920 46548.pygtex [244]) (./_minted-Tutorial/21510EFF9B5DA96F8CCEE8DFB8F26406BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7B5EBBADDB3E7B53C5C4AED82E42FFC4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0B25C484239457B0395121E60BF51495BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F8B39433E243DA74D8945D4CCEE70605BD02851C2FB632864165FCA4920 46548.pygtex [245]) (./_minted-Tutorial/46C8C36973CB3D67D276A48C8EA6FEE0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/99B6E6DD45FE4AED26044A4FD1A68C74BD02851C2FB632864165FCA4920 46548.pygtex [246]) (./_minted-Tutorial/001DF21D4EE824968A1A6CCAE41948EBBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5CBFAEFFA194A41048B5DAFCF4C98812BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E2EC88874CB26E442AD8A92E3073E225BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/176227E746894D602FF7231BCB8E5F21BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B9A36F2FAD2C11328984E7BBD1033E48BD02851C2FB632864165FCA4920 46548.pygtex [247]) (./_minted-Tutorial/31F98B5F648636905472A89ADB4396EABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6E38B20582EF8FBF09C0864F13C6172DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D36079E59E9C6C6FCEFB62B1C38D03DCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/949879BACF1AC9FDD5E01F1FDF5D0C7BBD02851C2FB632864165FCA4920 46548.pygtex [248]) (./_minted-Tutorial/CEF4EF7AD2559AA1A840E9E5F4F1E33EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8A4D3A313CCE21054A332F39A60F4F8DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8AC6389F07C07315B68A4843F8EC4A81BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CD7B5AA933F3E10D95D901D3BB5DA161BD02851C2FB632864165FCA4920 46548.pygtex) [249] (./_minted-Tutorial/21D3336F2855CBE535339D390FE18E25BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/33B5E369AD9661A05C861A5AE12A5092BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A80C26CD370CE20C0095D5E8948B4CA2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/34B3515117C70C6DAC332384F14FD0D0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6EC91D6C707FE27D0D4D730403C86073BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B3D49921528F0B11F6E5813C6062BEC5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3712C0CA690A1E7FF72D1693AABFE970BD02851C2FB632864165FCA4920 46548.pygtex [250]) (./_minted-Tutorial/4F50929124655BC08B3D6057B14984E5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DA79BC51C090F498913A417759345DF4BD02851C2FB632864165FCA4920 46548.pygtex [251]) (./_minted-Tutorial/4B2423E325126B67BF464F894752E322BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/25136DD7F6E2BE72E81866FB3F2A41C9BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/50111CA97C115B1826E19F91E69CE8BFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9E8A7295F5BEF290E7F4283BD7261603BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D5F089B3901176BD3F7658EA70DA2473BD02851C2FB632864165FCA4920 46548.pygtex [252]) (./_minted-Tutorial/753220AB94A0DA3FD9F8379D30465A7ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/35B38D8BFFB75E06C84D419CF8CBB21BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A6DBEC036FAC23CE4697722B836743C1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DF57AC6C176D67E4A7B147371D11BA16BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B593C755A27EDDCAF56E94C0930898D3BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/53BF343E6B63B739979E29182E1485D3BD02851C2FB632864165FCA4920 46548.pygtex) [253] (./_minted-Tutorial/868ABF9ABD2736A12F423306646D7706BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/912C817861E626118AB2FA06F12910B6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/62D830B5536F542C80973708E7B78A26BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4A6B49E72A96FB6AC93E0E280B4F4472669566ECC2CFEDC7429F829576A D0DC6.pygtex) [254] (./_minted-Tutorial/F99AB908B88D7B819F597C02D259A52BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CB4926B7151E97486270449C8F84AB41BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/852A3852541269829CE5DF380357F2CCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/AC8B7A8ADEC6FEB0B1260E665CF238B6BD02851C2FB632864165FCA4920 46548.pygtex) [255]) [256] (./Tutorial/chapter_cluster.tex Chapter 15. [257] [258] [259] [260] (./_minted-Tutorial/C7B59059E3AE6CDE790EFE6EB0ED4140BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C2B72A7408C7DF74DFCEBE0485997287BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/425EDAA643B5AA9589F3EEE601735827BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/50B5971EFCF22FCC4E1302DB2D0A25009543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/293084E63EA5C0E01F325A4DD59469C0BD02851C2FB632864165FCA4920 46548.pygtex [261]) Overfull \hbox (78.60634pt too wide) in paragraph at lines 245--246 \OT1/cmr/m/n/10 men-sions of these ar-rays are $[]$ if [][]\OT1/cmtt/m/n/10 tra nspose []\OT1/cmr/m/n/10 is [][]\OT1/cmtt/m/n/10 0[]\OT1/cmr/m/n/10 , or $[]$ (./_minted-Tutorial/05DC01C08B8EDF71F86E3C3A9C28EB34BD02851C2FB632864165FCA4920 46548.pygtex) [262] [263] (./_minted-Tutorial/A4A28B5A443208DEAB3B4D76AA3B762EBD02851C2FB632864165FCA4920 46548.pygtex) [264] (./_minted-Tutorial/C286E2777B917B774560CBDC7CF92626BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D04E097D8E8C4C039FEC20FA103CED189543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/36EF8931044EF448BC70F722AFADB43D9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/805B33438269C932AC54C0DAB5A3D7AC9543DFECA235A69AE23006BA05B 4EB70.pygtex) [265] [266] Overfull \hbox (16.73593pt too wide) in paragraph at lines 423--424 [][]\OT1/cmtt/m/n/10 distance []\OT1/cmr/m/n/10 is the dis-tance be-tween them. The items be-ing clus-tered are num-bered from 0 to $[]$, (./_minted-Tutorial/015798D317E9D8732518AFD186C997CABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A27E6BF4EEB8E8B1C239049267861739BD02851C2FB632864165FCA4920 46548.pygtex) [267] (./_minted-Tutorial/81E4060E427D22B8F0C63B69EEC10A2ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B8D2A546EC4941692F427A363193FBDEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A54EF6455421EFDFA1F63EB361CD74F6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8975A4CCBC4C6138C302117E04F203ADBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/636486BB1CF700F6391685224211BE22BD02851C2FB632864165FCA4920 46548.pygtex) [268] (./_minted-Tutorial/6EFE1AC811BF16FF597EBE3E25BD2F72BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F8E41E59FD44DADEB3740B0C0ED17D41BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1B924FC8FA13A8B73C1C9E6EF8895055BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/77B32E49165B4345FFCA9FACF597BEEBBD02851C2FB632864165FCA4920 46548.pygtex [269]) (./_minted-Tutorial/D04E097D8E8C4C039FEC20FA103CED189543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/36EF8931044EF448BC70F722AFADB43D9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/805B33438269C932AC54C0DAB5A3D7AC9543DFECA235A69AE23006BA05B 4EB70.pygtex) [270] (./_minted-Tutorial/E542C07D0131DF56A89D92F80416C175BD02851C2FB632864165FCA4920 46548.pygtex) [271] Overfull \hbox (106.77225pt too wide) in paragraph at lines 654--656 \OT1/cmr/m/n/10 An ar-ray with di-men-sions $[]$ if rows are be-ing clus-tered, or $[]$ (./_minted-Tutorial/7476A2D5F9D3A46EE00108837901FAEABD02851C2FB632864165FCA4920 46548.pygtex) [272] (./_minted-Tutorial/0420D397BA03971C0079F52E55FEABABBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8D3928D79091BFFA7AFB6D6F35A52C7CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4D59CC328F454A26A4BE9F91740D961CBD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (25.39864pt too wide) in paragraph at lines 739--750 [] [273] [274] (./_minted-Tutorial/EFB8602799AD543446B386107A8147F7BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/43B30B527C3A2D8148F25CA143719CAFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C77F1ABB31C6A53C1626E0E0B34BB0FCBD02851C2FB632864165FCA4920 46548.pygtex) [275] (./_minted-Tutorial/1F3E2EFB988F2639C701A920B547241DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3CAD921471DA4CA4441D02558CD1F2E0BD02851C2FB632864165FCA4920 46548.pygtex [276]) (./_minted-Tutorial/1A863BDE3A5754AA2C865F2A82DA8504BD02851C2FB632864165FCA4920 46548.pygtex) [277] Overfull \hbox (106.77225pt too wide) in paragraph at lines 929--931 \OT1/cmr/m/n/10 An ar-ray with di-men-sions $[]$ if rows are be-ing clus-tered, or $[]$ (./_minted-Tutorial/A39469F362670EDC6C7E8FD9FDF412C4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/12B5F20EFF78F0E8FE505D45A9786D70BD02851C2FB632864165FCA4920 46548.pygtex [278]) (./_minted-Tutorial/E6C8D570402CFDDB43A6AE5A198BCF58BD02851C2FB632864165FCA4920 46548.pygtex)) Overfull \hbox (26.21434pt too wide) in paragraph at lines 986--116 []\OT1/cmr/m/n/10 This will cre-ate the files [][]\OT1/cmtt/m/n/10 cyano_result _K_G2_A2.cdt[]\OT1/cmr/m/n/10 , [][]\OT1/cmtt/m/n/10 cyano_result_K_G2.kgg[]\OT 1/cmr/m/n/10 , and [][]\OT1/cmtt/m/n/10 cyano_result_K_A2.kag[]\OT1/cmr/m/n/10 . [279] (./Tutorial/chapter_learning.tex Chapter 16. [280] (./_minted-Tutorial/A66CDD6792A98054D498A97A3A920D4DBD02851C2FB632864165FCA4920 46548.pygtex [281]) (./_minted-Tutorial/390D9013E6AF7385E3C5A71EC44014AABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9153ABDB5D850EC42F344B9B42C10E4FBD02851C2FB632864165FCA4920 46548.pygtex [282]) (./_minted-Tutorial/183EBB0903E699FF7289E5FDA71CB096BD02851C2FB632864165FCA4920 46548.pygtex [283]) (./_minted-Tutorial/7E494FD25838EE4C9E476EBA48BDF0CEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B53BAB1CC7569CE8ADFECF2CFC02D402BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0201F5A7D34B6F74CAF2C8723DA28C0ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/906DB90E50544D69A8A7FA2703E3A012BD02851C2FB632864165FCA4920 46548.pygtex [284]) Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 267. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 267. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 275. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 275. (./_minted-Tutorial/AE2B91C0366D79644B870EB1EB9436E6BD02851C2FB632864165FCA4920 46548.pygtex) [285] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 287. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 287. (./_minted-Tutorial/B35CDBE12860937BD1F854583E7BA595BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B38BF6A3D910590D450B331A075B723CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E59729DAB9242AE915A0943E44B8DF9BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/AEF267C3082CB68394DCEE656CEB2FC1BD02851C2FB632864165FCA4920 46548.pygtex [286]) (./_minted-Tutorial/A38355D92EE3DC8D96655428C0CEDC15BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A586FFDD9483C890754DBE5DFC420710BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8F9899A476407D923F0AEB91D4FF3D35BD02851C2FB632864165FCA4920 46548.pygtex [287])) [288] (./Tutorial/chapter_graphics.tex Chapter 17. [289] (./_minted-Tutorial/775A7C8BD2C1E8942CA7A717928F51A09543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/997BE59EDA00B2D427337713C8A7E3D99543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/684A3C9C1713469B78289C6B9952D8169543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/F1FF3DF6D6F3CDAA260F74B59EE3502F9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/864F43F6883D29AB2276A3D7B4C4B0359543DFECA235A69AE23006BA05B 4EB70.pygtex) Excluding 'htmlonly' comment. (./_minted-Tutorial/F52EB727435E5F7D4D3C22DD13755CA79543DFECA235A69AE23006BA05B 4EB70.pygtex [290]) Excluding 'htmlonly' comment. (./_minted-Tutorial/68BE5A2D2503535D27E3B265B36AB36E9543DFECA235A69AE23006BA05B 4EB70.pygtex [291 <./images/plasmid_linear.png (PNG copy)>]) [292 <./images/pla smid_circular.png (PNG copy)>] (./_minted-Tutorial/ECF4549C3ED9BED5D89616D96689FF279543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/F6FC21242AEF7E7CBB38249DA932A7359543DFECA235A69AE23006BA05B 4EB70.pygtex) Excluding 'htmlonly' comment. (./_minted-Tutorial/E9061B00D3D1F94D19518B622458CA8B9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/869D4007B198B35A03870134DB69E5F29543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/83AFE18710C133D7AFEBCF65D9D3D8509543DFECA235A69AE23006BA05B 4EB70.pygtex [293]) Excluding 'htmlonly' comment. (./_minted-Tutorial/7767B7CE8DD842D17DB77A8BF9691B949543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/B7F9EB41E9BA682D9273C414D13CA80C9543DFECA235A69AE23006BA05B 4EB70.pygtex [294] [295 <./images/GD_sigil_labels.png (PNG copy)>]) Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. (./_minted-Tutorial/6EE3865BBB66BBD15ABFD7BAE73F8FEB9543DFECA235A69AE23006BA05B 4EB70.pygtex) Excluding 'htmlonly' comment. (./_minted-Tutorial/74C150D1D11511477A4CD9DC0CD7863A9543DFECA235A69AE23006BA05B 4EB70.pygtex) Excluding 'htmlonly' comment. (./_minted-Tutorial/2216BF82E557F1E99146777612D2BA8F9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/67B3F646AA5F8690151428081229D39B9543DFECA235A69AE23006BA05B 4EB70.pygtex [296] [297 <./images/GD_sigils.png>] [298 <./images/GD_sigil_arrow _shafts.png>] [299 <./images/GD_sigil_arrow_heads.png>] [300]) Excluding 'htmlonly' comment. [301 <./images/plasmid_linear_nice.png (PNG copy) >] [302 <./images/plasmid_circular_nice.png>] (./_minted-Tutorial/7CAF22FEDE98A6B9B7990010CA8709DC9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/FA676816242752C9FE9F5EB12D4DAA899543DFECA235A69AE23006BA05B 4EB70.pygtex [303]) (./_minted-Tutorial/7926619D7609A591C404A01B2A99177A9543DFECA235A69AE23006BA05B 4EB70.pygtex [304]) Excluding 'htmlonly' comment. [305 <./images/three_track_si mple.png>] (./_minted-Tutorial/A2465D4E8908256A31684D5DDE7DA1119543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/347EB36A3001532221DDF6C29AA04AFB9543DFECA235A69AE23006BA05B 4EB70.pygtex [306]) (./_minted-Tutorial/F46F39DD7A8EC7B20CD42ACF6EFD18409543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/2CF2D2FC7E96B3F426F22452724A4C289543DFECA235A69AE23006BA05B 4EB70.pygtex) Overfull \hbox (2.65141pt too wide) in paragraph at lines 873--879 []\OT1/cmr/m/n/10 There are sev-eral im-por-tant pieces to this code. First the [][]\OT1/cmtt/m/n/10 GenomeDiagram []\OT1/cmr/m/n/10 ob-ject has a [][]\OT1/cm tt/m/n/10 cross_track_links Excluding 'htmlonly' comment. [307] Excluding 'htmlonly' comment. [308 <./image s/three_track_cl.png>] [309 <./images/three_track_cl2a.png>] (./_minted-Tutorial/F9FFB9659EC22BC166AEB6F7284149779543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/A9695DE54C455E13B400269BF9F424FE9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/F545B5C3D394029AA34E76D27DC2DBAF9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/3BACFFDF9009929D690C44BF09EFB67F9543DFECA235A69AE23006BA05B 4EB70.pygtex) [310] (./_minted-Tutorial/0AC11BF466D4AA0B0536F05378BEC9CC9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/F5380F7F462C2A51219D9EF8994C192C9543DFECA235A69AE23006BA05B 4EB70.pygtex [311] [312 <./images/simple_chrom.pdf> <./images/tRNA_chrom.pdf>]) Excluding 'htmlonly' comment. (./_minted-Tutorial/7B75AD289117B9F25E36C48BBFCB0A759543DFECA235A69AE23006BA05B 4EB70.pygtex [313]) Excluding 'htmlonly' comment.) [314] (./Tutorial/chapter_kegg.tex Chapter 18. (./_minted-Tutorial/27731B46F813E809C1F5AB60C050CD4ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4FAF7CA55B5CBF29D4D0569020062C71BD02851C2FB632864165FCA4920 46548.pygtex) [315] (./_minted-Tutorial/39B217C0E81B95398ED4BBC9D1B0F5CCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D9724C7E513E9BF6FDCCF6A64359AD4B9543DFECA235A69AE23006BA05B 4EB70.pygtex [316]) (./_minted-Tutorial/64868CEDE925B08BA4840E27792F9C95669566ECC2CFEDC7429F829576A D0DC6.pygtex)) [317] (./Tutorial/chapter_phenotype.tex Chapter 19. (./_minted-Tutorial/252224E77AA1520CEA1F05EB2C082F8DBD02851C2FB632864165FCA4920 46548.pygtex) [318] (./_minted-Tutorial/1742F69ECDDF3F5D15E6B5DBFEFA9721BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4835A2D15014EC539B36FCA111ABBB44BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/FD6100DF6B4884776EB70DBE176DB081BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/943877B8F1F5B9C773FB1AA7B24E159EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0BDF372B652AEF5EA570E28DA8244BF8BD02851C2FB632864165FCA4920 46548.pygtex [319]) (./_minted-Tutorial/BE8D8FA0E8D3D6C871BF41D7B5DEB51DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/290D0631491AEE7E10A3CE09C85D7206BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/EA2967473FD2864501AEB5123E3D579DBD02851C2FB632864165FCA4920 46548.pygtex [320]) (./_minted-Tutorial/AEDB3BBBBA5C2503EDA86617E0872188BD02851C2FB632864165FCA4920 46548.pygtex [321]) (./_minted-Tutorial/43A346E75A27D33FDB3F346C240E06E6BD02851C2FB632864165FCA4920 46548.pygtex)) [322] (./Tutorial/chapter_cookbook.tex Chapter 20. (./_minted-Tutorial/D080533227BF139CB7F7C56D06E7D6EB9543DFECA235A69AE23006BA05B 4EB70.pygtex [323]) (./_minted-Tutorial/CA0835D76EF6887731674D8AB555091B9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/1F5CA35662EA2CAC7BDBA9D33CDB13A0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A3BD1DBCF883DB2E1DD394B912E57164BD02851C2FB632864165FCA4920 46548.pygtex) [324] (./_minted-Tutorial/C6B2C783E94EA95E84DF3F108F727AD4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/EC0DF654B46A2F2CE5F2C795E0321ED29543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/19A3D00CDA3CDDA100F55F41BCAAF54F9543DFECA235A69AE23006BA05B 4EB70.pygtex [325]) (./_minted-Tutorial/FF8E30AFA718C8DC6288D5C9AD354F649543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/019E169CFF67EC7D891D6A02396470619543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/9CFE18F499906D88CC2737F15500C03B9543DFECA235A69AE23006BA05B 4EB70.pygtex [326]) (./_minted-Tutorial/C2311B95BFB64D51B766D16ACEF028DD9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/D6A48411D1CBD21E55ABF85BFBC655419543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/7448CA91BF0AA6E19C1517B6DE4087939543DFECA235A69AE23006BA05B 4EB70.pygtex) [327] (./_minted-Tutorial/C3FBD2FC664129F7A578076AD05E79D99543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/38576C78990D3D95691E2AC6EB80ABA29543DFECA235A69AE23006BA05B 4EB70.pygtex) [328] (./_minted-Tutorial/D08928CA73DF435476A35E8ADF6418319543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/D51441AC892832CAA5031DFFA5F354509543DFECA235A69AE23006BA05B 4EB70.pygtex) Overfull \hbox (5.83499pt too wide) in paragraph at lines 454--458 \OT1/cmr/m/n/10 mat (e.g. FASTA files). How-ever, for large FASTQ files it woul d be faster the low-level [][]\OT1/cmtt/m/n/10 FastqGeneralIterator (./_minted-Tutorial/AB16E58608A2F17CC79E6929557208879543DFECA235A69AE23006BA05B 4EB70.pygtex [329]) Overfull \hbox (4.57849pt too wide) in paragraph at lines 475--477 \OT1/cmr/m/n/10 That should find $13819$ reads from \OT1/cmtt/m/n/10 SRR014849. fastq \OT1/cmr/m/n/10 and save them to a new FASTQ file, \OT1/cmtt/m/n/10 with[ ]primer.fastq\OT1/cmr/m/n/10 . (./_minted-Tutorial/6D336A88208F39729D1A90FF60CB5EBD9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/2C62FFE33ECD45881AC7A8296BCCA5569543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/7E077104A49653CA66AAC778C604E64A9543DFECA235A69AE23006BA05B 4EB70.pygtex [330]) (./_minted-Tutorial/ECD311074B098CDA38E7451A88AC0F9C9543DFECA235A69AE23006BA05B 4EB70.pygtex) [331] (./_minted-Tutorial/CC6E723850600015A2C6BAC6C88F89159543DFECA235A69AE23006BA05B 4EB70.pygtex) [332] (./_minted-Tutorial/1E88A30624397E1FA5202CD67F078C319543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/55F15E0B4613AC1B2AC177DC407373679543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/C6B1FCFF3C4616196F6CE060D97D2587BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7B877C459BB3438E40CD76B614F605B69543DFECA235A69AE23006BA05B 4EB70.pygtex [333]) (./_minted-Tutorial/C47681A25A04F989A9657602F996D5B59543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/20E6EE0734FD2ED211933BE632478CAB9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/BF6F632251CC051592D2BE57B36A38A09543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/C8587EE0D03D0937B88179912FC3582EBD02851C2FB632864165FCA4920 46548.pygtex [334]) (./_minted-Tutorial/7F8C2BBB4F26A8E6A0FD7BCC41E2BB80BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/FCE533CC3550AB6D1B3C6F6ED53E0CEBBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/37A86DCC1F181ADAA1855D9EBC303BAC44BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/474B445E26A3CD55A1BA5820E4D03C7DBD02851C2FB632864165FCA4920 46548.pygtex [335]) (./_minted-Tutorial/DDBEEE137CB936CA422E560A63FB97B8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B802763B27D7694A759DB2EBF16EF098BD02851C2FB632864165FCA4920 46548.pygtex) [336] (./_minted-Tutorial/EE9671DEE2B114F544A5881F074C33B29543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/5A7FB5AC8923F9582CAE20A770A63052669566ECC2CFEDC7429F829576A D0DC6.pygtex [337]) (./_minted-Tutorial/8F229FE70B397EEE7D48ECD1D5BAD1CCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/71434DB3B51372DFED40CEB6F06647B79543DFECA235A69AE23006BA05B 4EB70.pygtex [338]) Excluding 'htmlonly' comment. Overfull \hbox (4.00363pt too wide) in paragraph at lines 1117--1120 []\OT1/cmr/m/it/10 Tip: \OT1/cmr/m/n/10 Rather than us-ing [][]\OT1/cmtt/m/n/10 pylab.show() []\OT1/cmr/m/n/10 to show the plot in a win-dow, you can also use [][]\OT1/cmtt/m/n/10 pylab.savefig(...) (./_minted-Tutorial/798776F436EA559BACD9C305C09973919543DFECA235A69AE23006BA05B 4EB70.pygtex [339 <./images/hist_plot.png>]) (./_minted-Tutorial/CB78AD94DFE82ADBAF348C0EC1D261CD9543DFECA235A69AE23006BA05B 4EB70.pygtex) Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. [340 <./images/gc_plot.png>] (./_minted-Tutorial/6E0DA723E11A7B9CA8E2353A984B5DF79543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/80A47C8780CE3021D53829563E8166569543DFECA235A69AE23006BA05B 4EB70.pygtex [341 <./images/dot_plot.png>]) (./_minted-Tutorial/9574E55C4A182E2A0201DF18689F52F49543DFECA235A69AE23006BA05B 4EB70.pygtex) Excluding 'htmlonly' comment. (./_minted-Tutorial/24C65C38DAD936B7AA15C7ED02EA36B39543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/6655B5CD97C33186A22E6897501301FF9543DFECA235A69AE23006BA05B 4EB70.pygtex [342]) (./_minted-Tutorial/7727E7020AA1BDC4C2A426B7590C20AD9543DFECA235A69AE23006BA05B 4EB70.pygtex) Excluding 'htmlonly' comment. [343 <./images/dot_plot_scatter.png >] (./_minted-Tutorial/601CCA4B782F1DA528DB81B0248031959543DFECA235A69AE23006BA05B 4EB70.pygtex) Excluding 'htmlonly' comment. (./_minted-Tutorial/9D2779E6D02C00C016A7A73A452EBC739543DFECA235A69AE23006BA05B 4EB70.pygtex) [344] (./_minted-Tutorial/06CAA397021B5D0CD904B7CF0209DCA39543DFECA235A69AE23006BA05B 4EB70.pygtex) [345 <./images/SRR001666.png>] (./_minted-Tutorial/16711B0A63F93BBACAF3C86CFFB7BEFA669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/96EC77291C119EF69670ACDB1C35CE21669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/6C14F4F0692168BA7165351C706B643D9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/E686FC2D122CF1560FAF4512CD53777F9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/E09A8EBF1B7CB9F831FC2D9DA48145359543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/E598995EF885D7803642E8685DCB8F90669566ECC2CFEDC7429F829576A D0DC6.pygtex) Overfull \hbox (49.0755pt too wide) in paragraph at lines 1528--1529 []\OT1/cmr/m/n/10 You can ac-cess any el-e-ment of the PSSM by sub-script-ing l ike [][]\OT1/cmtt/m/n/10 your_pssm[sequence_number][residue_count_name][]\OT1/c mr/m/n/10 . (./_minted-Tutorial/7F027F6FD8E839F99A1077399D9B8EFFBD02851C2FB632864165FCA4920 46548.pygtex [346]) (./_minted-Tutorial/25AF2FA7C23EEF982CD3578DCB5300659543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/7662755469082A25B2A4B53656D96A409543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/EA8748814B0C57E7E4D7F8619D00D0439543DFECA235A69AE23006BA05B 4EB70.pygtex [347]) (./_minted-Tutorial/99476F758194110AC0ED8AAAFD8ECB7C9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/504DC4F75F719CFF95C5294B2961C973BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/486C8450148EF1EADB63A41AB9A896FABD02851C2FB632864165FCA4920 46548.pygtex [348]) (./_minted-Tutorial/DD48495FAB2341AA078121E9286C0717BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DE31628D815724B7B422A1012BAA0C37BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5740381D1C5E453AC66BA80B49407915BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/19B054992CCA481AA19D78F9C6DD93BFBD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (13.15053pt too wide) in paragraph at lines 1703--1704 \OT1/cmr/m/n/10 two [][]\OT1/cmtt/m/n/10 residue_frequencies []\OT1/cmr/m/n/10 val-ues mul-ti-plied with each other. For ex-am-ple, [][]\OT1/cmtt/m/n/10 expec ted_frequencies[^^MD^^M, ^^ME^^M] (./_minted-Tutorial/40ECF2E139F38209730D3B02B624EF74BD02851C2FB632864165FCA4920 46548.pygtex [349]) (./_minted-Tutorial/8965C8E87A0A43ECCE216C12F7DE7A4FBD02851C2FB632864165FCA4920 46548.pygtex)) [350] (./Tutorial/chapter_testing.tex Chapter 21. (./_minted-Tutorial/867AD481B37AFD4F1A17FC0F2F42FCAE44BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/E8078015A2C53794A733DDC875BD062144BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/754EBE4BCCE307413E74F18728530D0444BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/E40D6903CCE8EA230C75C80B7C2D907344BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/7A0DBB9735CDAA1699A6FA164701062F44BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/BC243371043473AEE20C23FF0FABFF0D44BBF456F55B5DC060035246D76 9EADB.pygtex) Overfull \hbox (39.35472pt too wide) in paragraph at lines 73--77 []\OT1/cmr/m/n/10 Tests based on Python's stan-dard [][]\OT1/cmtt/m/n/10 unitte st []\OT1/cmr/m/n/10 frame-work will [][]\OT1/cmtt/m/n/10 import unittest []\OT 1/cmr/m/n/10 and then de-fine [][]\OT1/cmtt/m/n/10 unittest.TestCase [351] (./_minted-Tutorial/9373056942403CCACDB96B0F438E4B64669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/2A1F0B8D037B993D748BF652420448ED44BBF456F55B5DC060035246D76 9EADB.pygtex [352]) (./_minted-Tutorial/61465735FDB5BC7ADF12D7A4628FC9A79543DFECA235A69AE23006BA05B 4EB70.pygtex) [353] (./_minted-Tutorial/826F7B9143F73D7CFCAB00906377DAB99543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/B1E279D3993E4775FBE4555B6DD342AD44BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/313C740A73E814DA220EB71149FE706E9543DFECA235A69AE23006BA05B 4EB70.pygtex [354]) (./_minted-Tutorial/99DA0A53F2BD41D9D1BCE2B0332444F444BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/4916E014295B56C6CDDB3C287542DA299543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/1B0AB11BDA71CF4763A5A4A8B82977119543DFECA235A69AE23006BA05B 4EB70.pygtex [355]) (./_minted-Tutorial/7A0DBB9735CDAA1699A6FA164701062F44BBF456F55B5DC060035246D76 9EADB.pygtex) [356] (./_minted-Tutorial/3E57444149EF1ACC12DA2995F5B0345644BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/DD3A1A642CB850F292FC934F9336EC4344BBF456F55B5DC060035246D76 9EADB.pygtex)) [357] (./Tutorial/chapter_contributing.tex Chapter 22. [358] (./_minted-Tutorial/7713FA97EA16E9508BA3E6B94494492544BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/61D19A91BF1A1F95030292E40EF87A3644BBF456F55B5DC060035246D76 9EADB.pygtex) [359]) [360] (./Tutorial/chapter_appendix.tex Chapter 23. (./_minted-Tutorial/109DA6882E9B770A79B0E47E5D014D32BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D8DF7F2BE4A1010E81F7C5AD3A4628599543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/268983882DD871BC94F164D025D08B429543DFECA235A69AE23006BA05B 4EB70.pygtex [361]) (./_minted-Tutorial/940D9D0165FD2273E52C2D203CE26C429543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/4B521F4803AD1FD3B86D09A2ECD5A203BD02851C2FB632864165FCA4920 46548.pygtex)) [362] [363] [364] [365] (./Tutorial.aux (./Tutorial/chapter_introduction.aux) (./Tutorial/chapter_quick_start.aux) (./Tutorial/chapter_seq_objects.aux) (./Tutorial/chapter_seq_annot.aux) (./Tutorial/chapter_seqio.aux) (./Tutorial/chapter_align.aux) (./Tutorial/chapter_blast.aux) (./Tutorial/chapter_searchio.aux) (./Tutorial/chapter_entrez.aux) (./Tutorial/chapter_uniprot.aux) (./Tutorial/chapter_pdb.aux) (./Tutorial/chapter_popgen.aux) (./Tutorial/chapter_phylo.aux) (./Tutorial/chapter_motifs.aux) (./Tutorial/chapter_cluster.aux) (./Tutorial/chapter_learning.aux) (./Tutorial/chapter_graphics.aux) (./Tutorial/chapter_kegg.aux) (./Tutorial/chapter_phenotype.aux) (./Tutorial/chapter_cookbook.aux) (./Tutorial/chapter_testing.aux) (./Tutorial/chapter_contributing.aux) (./Tutorial/chapter_appendix.aux)) LaTeX Warning: There were undefined references. LaTeX Warning: There were multiply-defined labels. ) (see the transcript file for additional information) < /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb> Output written on Tutorial.pdf (366 pages, 2520425 bytes). Transcript written on Tutorial.log. pdflatex --shell-escape "\def\bpversion{1.80}\input{Tutorial}" This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdflatex) \write18 enabled. entering extended mode LaTeX2e <2022-11-01> patch level 1 L3 programming layer <2023-01-16> (./Tutorial.tex (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2022/07/02 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/preprint/fullpage.sty) (/usr/share/texmf/tex/latex/misc/hevea.sty (/usr/share/texlive/texmf-dist/tex/latex/comment/comment.sty Excluding comment 'comment') Excluding comment 'rawhtml' Excluding comment 'htmlonly') (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/minted/minted.sty (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty)) (/usr/share/texlive/texmf-dist/tex/latex/fvextra/fvextra.sty (/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty) (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty) (/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty) (/usr/share/texlive/texmf-dist/tex/latex/lineno/lineno.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/calc.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/shellesc.sty) (/usr/share/texlive/texmf-dist/tex/latex/ifplatform/ifplatform.sty (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty)) (/usr/share/texlive/texmf-dist/tex/generic/catchfile/catchfile.sty (/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty)) (/usr/share/texlive/texmf-dist/tex/generic/iftex/ifluatex.sty) (./Tutorial.w18) ) (/usr/share/texlive/texmf-dist/tex/generic/xstring/xstring.sty (/usr/share/texlive/texmf-dist/tex/generic/xstring/xstring.tex)) (/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 70. (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx))/usr/bin/pygmentize (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./Tutorial.aux (./Tutorial/chapter_introduction.aux) (./Tutorial/chapter_quick_start.aux) (./Tutorial/chapter_seq_objects.aux) (./Tutorial/chapter_seq_annot.aux) (./Tutorial/chapter_seqio.aux) (./Tutorial/chapter_align.aux LaTeX Warning: Label `sec:pairwise-general-gapscores' multiply defined. ) (./Tutorial/chapter_blast.aux) (./Tutorial/chapter_searchio.aux) (./Tutorial/chapter_entrez.aux) (./Tutorial/chapter_uniprot.aux) (./Tutorial/chapter_pdb.aux) (./Tutorial/chapter_popgen.aux) (./Tutorial/chapter_phylo.aux) (./Tutorial/chapter_motifs.aux) (./Tutorial/chapter_cluster.aux) (./Tutorial/chapter_learning.aux) (./Tutorial/chapter_graphics.aux) (./Tutorial/chapter_kegg.aux) (./Tutorial/chapter_phenotype.aux) (./Tutorial/chapter_cookbook.aux) (./Tutorial/chapter_testing.aux) (./Tutorial/chapter_contributing.aux) (./Tutorial/chapter_appendix.aux)) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (./Tutorial.out) (./Tutorial.out) Excluding 'htmlonly' comment. Excluding 'rawhtml' comment. [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.m ap} <./images/biopython_logo.pdf>] (./Tutorial.toc pdfTeX warning (ext4): destination with the same identifier (name{page.1}) has been already used, duplicate ignored \relax l.39 ...tions and locations}{37}{subsection.4.3.2} % [1] [2] [3] [4] [5] [6] [7]) [8] (./Tutorial/chapter_introduction.tex Chapter 1. [9] [10] Excluding 'rawhtml' comment. Underfull \hbox (badness 10000) in paragraph at lines 122--128 Underfull \hbox (badness 10000) in paragraph at lines 134--136 (./_minted-Tutorial/default.pygstyle) (./_minted-Tutorial/C3217FD04973F24516F5530BB525A22CBD02851C2FB632864165FCA4920 46548.pygtex) [11 <./images/biopython_logo_old.jpg>] Overfull \hbox (2.99303pt too wide) in paragraph at lines 187--189 \OT1/cmr/m/n/10 Check the built in doc-strings (\OT1/cmtt/m/n/10 from Bio impor t SeqIO\OT1/cmr/m/n/10 , then \OT1/cmtt/m/n/10 help(SeqIO)\OT1/cmr/m/n/10 ), or see [][]$\OT1/cmtt/m/n/10 http : / / biopython . [12]) [13] (./Tutorial/chapter_quick_start.tex Chapter 2. LaTeX Warning: Reference `chapter:advanced' on page 14 undefined on input line 14. (./_minted-Tutorial/C083BA757ADC0A392BD8802D1351612CBD02851C2FB632864165FCA4920 46548.pygtex [14]) (./_minted-Tutorial/BCD1E3D53103B8919C8BBE66D33535ABBD02851C2FB632864165FCA4920 46548.pygtex) [15] (./_minted-Tutorial/AD9EF2BC42CEF4E413923F9BFFE1BE07669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/33F85FAC7266F854F2B0213346781855BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/57D5D2D450B93D59CC2D6708C6BA430BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9951EE2B2EB57108F1B91BF42B5EF26DBD02851C2FB632864165FCA4920 46548.pygtex [16]) (./_minted-Tutorial/D0C141F7F69A52FF8D2723831BF439F2BD02851C2FB632864165FCA4920 46548.pygtex) [17]) [18] (./Tutorial/chapter_seq_objects.tex Chapter 3. (./_minted-Tutorial/048D805D0CE39D0271B0A9A9F6FA0B90BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CCFAD09A7C678CC6F23FB63113DD1EDCBD02851C2FB632864165FCA4920 46548.pygtex) [19] (./_minted-Tutorial/FD65D36A7B14289ADEAB241851842BCABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C0F44B540F3531194878FC29AF017902BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/739024CAA2FC886FEC674E3B4C3FD3A4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/EB307D8D2C6B186F102975D2F777C5C8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/504E820336D4D852A5104D8E97622504BD02851C2FB632864165FCA4920 46548.pygtex [20]) (./_minted-Tutorial/21058E2884DE0E2797798658CEC2E54FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6C027F180664948287C5ED0C06A70E36BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8900FA9A050CA74204F5DCB8D9386420BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5A43D1A8AC729BFB659D75BFD070C79ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/732D927996C79742AC990312B3D6EEB0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/36BB9CB69ABA7149C7050E321F74C270BD02851C2FB632864165FCA4920 46548.pygtex [21]) (./_minted-Tutorial/14DC45CA9BEAFF3B8A49C8E43A9FF33CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4FC9049D1029A23D48B33F9D862ACC47BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E62329AC6ED4D8F7B1EF4988F8DBA19FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/008EC869056581873654FF9A8E92D394BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/457BF67E0722BB5B93A17BD27C0B6D8DBD02851C2FB632864165FCA4920 46548.pygtex [22]) (./_minted-Tutorial/21058E2884DE0E2797798658CEC2E54FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/34FD0122B81370E5F3563284D60CFF17BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A54827F8BB70B416D99923FF5088CCC0BD02851C2FB632864165FCA4920 46548.pygtex [23]) (./_minted-Tutorial/427B060556C1BB93F326E658CF6C8753BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/692203B43955DEEBA597180E090EBEBDBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0A4AF1735B84470B955325263082B386BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F7FFCC027B254744B7B47314F48923FEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/186028EBD7A9B4B4276808BC5B218A70BD02851C2FB632864165FCA4920 46548.pygtex [24]) (./_minted-Tutorial/2F42D08D321C7BC408E4704103B70F2EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/544C1E23D35FAC62FBE120AA24D6EF82BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A487EC21D16913E80A948528AA61CD64BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7BC83BB268F7BA2D207FDE001034CF98BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/59D2BC7361BC3147180163BF1D4DDE79BD02851C2FB632864165FCA4920 46548.pygtex [25]) (./_minted-Tutorial/087889BE640F25A1E1D26EB819B55990BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C387354CBEC6317F42CD9F596E775BE0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A3542F02D57EFCE9A6BD62C8FAB75CE3BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F712265A78CB2524ABF9371BE2F3874DBD02851C2FB632864165FCA4920 46548.pygtex [26]) (./_minted-Tutorial/3A75E7306D7D2D81DE0C37038600A10ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/06DBC59F2EAD33E7A951888537876615BD02851C2FB632864165FCA4920 46548.pygtex) [27] (./_minted-Tutorial/4393B8540CDD633A481E29B1CF252CE6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7F9F7641B195E2CACA3F77158DBE190CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/04626286E6AB345CB89BE7B7A049C338BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F2723D89FDBA794E82A8285BABB369CB669566ECC2CFEDC7429F829576A D0DC6.pygtex [28]) (./_minted-Tutorial/64147FAF6F5C5028B073B3C809EE3E84BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DFDB859800920408E228736AD921B5DFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D95D20C3283ADEDD76DAB3382BB1B040BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/AA99EB190DCB9061B7FD403ECDCEE451BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F5B125A1E250BEBA411CA3B2BBF3EDDDBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/39AA48793A64869F7458C1A2A0D69D2EBD02851C2FB632864165FCA4920 46548.pygtex [29]) (./_minted-Tutorial/29E9F3CE64EB99D132246C3633BA375CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/394CF49B3AAB621203EE87F2BD334CC4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3F2DB933A33BDAA3DB2299F2701B61CBBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4307A980AB242F22FB1B0952E3FD37C0BD02851C2FB632864165FCA4920 46548.pygtex)) [30] [31] (./Tutorial/chapter_seq_annot.tex Chapter 4. (./_minted-Tutorial/032C91EF2474FD3535629DC0CDABC809BD02851C2FB632864165FCA4920 46548.pygtex) [32] (./_minted-Tutorial/28ED5ED993E569AC59FDA480CD731BBCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/AD6AF21FB49ADADD3E9DF52EA341F92CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6A9404FB47549766BD16858F97A6D407BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B9321587EBA597104E435182128B200FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/22FC566F5A2B47EFD3D63327C15F7FC2BD02851C2FB632864165FCA4920 46548.pygtex [33]) (./_minted-Tutorial/510764EE0BB38AD6C688E71989677507669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/885E3C393ABBD6448EFA8A6D8D849822BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D582F58715BB8D12B0A5A9CF9631A27CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C60AA1EB70D11A096523A07FC1BD2085BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7D4386614F3407AC9AFEDB894B0987D9669566ECC2CFEDC7429F829576A D0DC6.pygtex [34]) (./_minted-Tutorial/B659A3B495F4BF5A9945B83B9A29DC2BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/20D2783513E8123B155B9FE0B3FE7B4A669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/86FA506E88E30EB82E7186A57112C98CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D582F58715BB8D12B0A5A9CF9631A27CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C9D6C80CD8B460806CB6E7C2935EA601BD02851C2FB632864165FCA4920 46548.pygtex [35]) (./_minted-Tutorial/332D9C95CC14B124A8528A76F4917ECEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/925BCB3D0BD30380832BA5F2C6367AD9BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D20F0AF7810B74883E42451F5810F926BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/47F0F8DD59EC4A71D5CA336E217F0C0DBD02851C2FB632864165FCA4920 46548.pygtex) [36] [37] (./_minted-Tutorial/AD47AD29D6F7927F9406BE5609676388BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A89E686BA7930FBF8AE5CCC27E1AC5BFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CD11055284C1F524585846BFB03F6EE8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1C597DC49857D56C7E140B1D795218F3BD02851C2FB632864165FCA4920 46548.pygtex [38]) (./_minted-Tutorial/EF871449F651FE5E7DFD84165065B14ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9ABE11BA111CDBEACB55DC5424AC66A1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D86C559003980DC8749AF92530435DFDBD02851C2FB632864165FCA4920 46548.pygtex) [39] (./_minted-Tutorial/1C0A562378DEEE8E210765437B3E1700BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C7BB516F80A4A8F5C291ABDF3B6E0B49BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C737C9C2EF139AD4F965B3AC1FF72C75BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/411A7DB0F7208D21C6099C86249233F3BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0C3ED75879971F09D72A92585654A32CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A4ED33BCBC94515EF1D3FF0CB0F2ACE9BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1432CF672342B0A065BD2202A12E3920BD02851C2FB632864165FCA4920 46548.pygtex [40]) (./_minted-Tutorial/3B61DDBFCC5B04C6BD9F6ED183CD312DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5039524AFDCC2184E0FA37B45448443DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/93B3AF8F7193FF3944CC29E4FE0F9689BD02851C2FB632864165FCA4920 46548.pygtex [41]) (./_minted-Tutorial/B952BEC5DDC5176F8F8F8984196831F3BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D16AA28F327A9B07E6AE64737A6B2340BD02851C2FB632864165FCA4920 46548.pygtex [42]) (./_minted-Tutorial/C08741A8063662E3CF1313052B7EA7A4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/83934A12FA213409ADDBED937D121BEBBD02851C2FB632864165FCA4920 46548.pygtex [43]) (./_minted-Tutorial/7693A79AF1B5C3B342CEF51858B48A85BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C59A3BD3577D6DA7BB95528A68C9B311BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7FC68DDC3F22A92C79064A5F631D2457BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E4EE1174D845FF0CABBFC735D0B5DF82BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/890A92414EE9EE5FB3B2F7B834307EDFBD02851C2FB632864165FCA4920 46548.pygtex [44]) (./_minted-Tutorial/CC2666A1113601FF5DADD7ED2118A3FEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E29BCA3E51B6B75E0E5EFF1718501669BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D20811F7EAA2FB2ED0A37B2C0F1B24D4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E92A933EB86A743F11CDB887CD2A9C1BBD02851C2FB632864165FCA4920 46548.pygtex [45]) (./_minted-Tutorial/675833B93A69F5DE13F680548E25EA3EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A8312A90F6B97A21EE1619F9A898ED36BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/68AB1E9E397375F82B6F3361E55900E7BD02851C2FB632864165FCA4920 46548.pygtex) [46] (./_minted-Tutorial/023FBCDB71B9572D8D436D0AA1193B63BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1B29C13B779A89B3DE705BA0061B8793BD02851C2FB632864165FCA4920 46548.pygtex)) [47] (./Tutorial/chapter_seqio.tex Chapter 5. (./_minted-Tutorial/3F38D5012926DD7C810DA2383F53D498BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CE17C15EEBC1BDC9846A29B8188EB6789543DFECA235A69AE23006BA05B 4EB70.pygtex [48]) (./_minted-Tutorial/357B0F655AFAF3808FD8EE23EE5009549543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/480025795249845BAA7F48D4A45ADB21BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F164035E9D5F8C01F84F5F95E2B166F19543DFECA235A69AE23006BA05B 4EB70.pygtex [49]) (./_minted-Tutorial/C82398A4A04383A063D2E648811230529543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/1A4F5B10F895EA1A0898B313C8FE3AED9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/665A7700DAC7A651C288CFBC04910736669566ECC2CFEDC7429F829576A D0DC6.pygtex) [50] (./_minted-Tutorial/3FC3FD6D12B3257730F3B4F11F7F82E99543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/8C2F2A27559FC0864F47BBE543950C26669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/C1B7B447DBB266302BC82D7DBD1622219543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/3453EFD7B001ACCBD0126A13C98BAA4F9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/23C65980427B41C7D9E32947CD41FD829543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/36073AAEBADCD344208056C9868E001CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/32EC540B3F53C56F8F39A2A185A32CE6BD02851C2FB632864165FCA4920 46548.pygtex [51]) (./_minted-Tutorial/3B09F0463D35461C42D2272763E734519543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/16EB556A216CBBE3D3F735350EA21A2A9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/F1A3FE258B41FCC45D4A8272B13EC395669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/AD9EF2BC42CEF4E413923F9BFFE1BE07669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/58A82383AA9DEBBEEEC6694BA2DE777ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9562C263804C6DD613F075A435553A9FBD02851C2FB632864165FCA4920 46548.pygtex [52]) (./_minted-Tutorial/5654C63CA8B2C75821B4DD795E1D9C91BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1525A6F338DC70B7A056F15305A9579DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DCDC3EB1E5C136F423AC65A1907BE6B1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/23394A4616015FFE4619934E98424178BD02851C2FB632864165FCA4920 46548.pygtex [53]) (./_minted-Tutorial/48D36449ADA742065AC871DB512A14FFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7160C98DFF3E9F14B8FDC3EDEA5AAADEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1E26B09583F35CC794E34E0D3C822C09BD02851C2FB632864165FCA4920 46548.pygtex) [54] (./_minted-Tutorial/A06B859656EACE1EB197B276B0CAD4769543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/5B68AB5634E46F0A59E5C238174AC4F0669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/AAC02B6C28E92C88B051BB2DE451DBD89543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/FECB9DCFA3C63121DB586752E4215990669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/CC27A8BEB077BCA7346A8D13F39867D79543DFECA235A69AE23006BA05B 4EB70.pygtex [55]) (./_minted-Tutorial/AE8667CEAACFF0F40839EE86774DD05D669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/6467B5574DF68CEA13D016BEEC8841A49543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/3D2A207C38AC647D99F5A8861A9D1AA6669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/DDD2E1D663317F4FFB7F8B7F03E4989FBD02851C2FB632864165FCA4920 46548.pygtex [56]) (./_minted-Tutorial/2EE890D1737C8A159C79BA4FCA81BB03BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/77FD1FB1550DD72BE3E8CFAC5C21C7DFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/022009B5C6117EE88C29BE7A45D87CF6BD02851C2FB632864165FCA4920 46548.pygtex [57]) (./_minted-Tutorial/FE4CF732C73126A3874795838D95FAB5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E7420F7622CCC097E8ADA484A405A3C6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/07A24756D2FDD5E9B66DEB7412FC4D6E9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/7F04F15A8B73F26152ED44DB3C48528F669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/55430EAFE498E385842834603E0B8C869543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/47CA5358E0862EF3920CC2BF888DBDB89543DFECA235A69AE23006BA05B 4EB70.pygtex [58]) (./_minted-Tutorial/A50FCDC5880666D012F0A802072B4AC5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D27A33312B4E81447304AAB2BAF2F6DC9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/11D55B86CA819707A4B89E7FDA2E6E83669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/74E272C92C546FD61FA6D3DA5C178893BD02851C2FB632864165FCA4920 46548.pygtex) [59] (./_minted-Tutorial/415024C641C8DA7A09117B3DFE240C78BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/487DCC9F44A2539C9B32C0122AEF4065BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5098CD053449CEC3C9C30C90A007A364BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/EEEF4ABAD66CE989F67C9E27EEDE95CCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F6AFF5A59B0706E4973BC1656FBD2D669543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/C4099CB0613585FCCD5EA7D8198704CEBD02851C2FB632864165FCA4920 46548.pygtex [60]) Overfull \hbox (9.93459pt too wide) in paragraph at lines 848--853 \OT1/cmr/m/n/10 FTP site ([][]$\OT1/cmtt/m/n/10 ftp : / / ftp . uniprot . org / pub / databases / uniprot / current _ release / knowledgebase / complete / (./_minted-Tutorial/D52DA4EEEEE2BF0FBE89EE253714929DBD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (4.48064pt too wide) in paragraph at lines 891--894 []\OT1/cmr/m/n/10 As of Gen-Bank re-lease $210$, there are $38$ files mak-ing u p the vi-ral se-quences, \OT1/cmtt/m/n/10 gbvrl1.seq\OT1/cmr/m/n/10 , ..., \OT1 /cmtt/m/n/10 gbvrl38.seq\OT1/cmr/m/n/10 , (./_minted-Tutorial/D41A88D88AB398F0C3B719A5C7D017C144BBF456F55B5DC060035246D76 9EADB.pygtex [61]) (./_minted-Tutorial/B4D970E8C81930851D8639D77EC3E41044BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/7C4E0944FB13EC4E75DD6FC64900395ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C68CC3C9B3A505FB972706356D7F336FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/61AD507889ED86CFCEFC880BAF2A2777BD02851C2FB632864165FCA4920 46548.pygtex) [62] (./_minted-Tutorial/DC5117490176932EFB8A7F0E0DA450F6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/657D43328835FC01F9133F8BC964475D44BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/82CBCD9B9F23373D67D9D0D7D2CA363FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/36F8D0FD2B4ADF57AC4203A0C80C6471BD02851C2FB632864165FCA4920 46548.pygtex) [63] (./_minted-Tutorial/9CEF7BF9B2634ACBC930BA5EB6DD73429543DFECA235A69AE23006BA05B 4EB70.pygtex [64]) (./_minted-Tutorial/AC02E3950380715FC960C04EF317D69F9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/1C65F538FA7F22F7BB5183FC1553A0C6669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/935F773BF84C3BF326F4BA093FEC79D4669566ECC2CFEDC7429F829576A D0DC6.pygtex [65]) (./_minted-Tutorial/C194E2231D844AE7D0223173D2A899919543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/10CB116B7358444BA68AFA046B5B84D59543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/29D12D495374A5A8C37AEB7083851DEABD02851C2FB632864165FCA4920 46548.pygtex) [66] (./_minted-Tutorial/920133226A22EEB682D854077D7FB78FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4EBA0A67E686E73FAA1A0EB27C260028BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C06224D76A18C126B27DFE55444AA3FDBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E381FF526AC999B71717F178C997F6B2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5F05AD4A17978E60C531612707D8F26ABD02851C2FB632864165FCA4920 46548.pygtex) [67] (./_minted-Tutorial/D19467E367634413AE9EE17A62E5D9EA9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/EDF3737891061C33EDE0FBFD16CCC63B9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/D1EAD55A1F8AD3DEAB82383A4F020F539543DFECA235A69AE23006BA05B 4EB70.pygtex) Overfull \hbox (19.46596pt too wide) in paragraph at lines 1349--1351 \OT1/cmr/m/n/10 Making a sin-gle call to [][]\OT1/cmtt/m/n/10 SeqIO.write(...) []\OT1/cmr/m/n/10 is also much quicker than mul-ti-ple calls to the [][]\OT1/cm tt/m/n/10 SeqRecord.format(...) [68] (./_minted-Tutorial/2F337ECD1F936D416FF9C5C6F41A02D7BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3337CD054623BAC21B6021E996EE0DFD9543DFECA235A69AE23006BA05B 4EB70.pygtex) Overfull \hbox (21.32593pt too wide) in paragraph at lines 1393--1397 []\OT1/cmr/m/n/10 Likewise, when pars-ing FASTQ files, in-ter-nally [][]\OT1/cm tt/m/n/10 Bio.SeqIO.parse() []\OT1/cmr/m/n/10 calls the low-level [][]\OT1/cmtt /m/n/10 FastqGeneralIterator (./_minted-Tutorial/D3AF6542680CA390CDA8C8DF87C693D3BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D749A84299CF58E876E9A899069830DB9543DFECA235A69AE23006BA05B 4EB70.pygtex)) [69] (./Tutorial/chapter_align.tex Chapter 6. (./_minted-Tutorial/9CC7A6864E21FFDDB3F4D02F2870DF42669566ECC2CFEDC7429F829576A D0DC6.pygtex [70]) (./_minted-Tutorial/81FAFBAECB3A03B11080ECF19D4CCC80BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/31E7567531B3A1035700A1E555A47FC0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D2523B56ECD3F392CD3E37EEBE302AECBD02851C2FB632864165FCA4920 46548.pygtex [71]) (./_minted-Tutorial/AC12821BA0AEE8F48238EAC359A31077BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A6D29782988E1FB75F30F2D60AB93C4EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E48647CD11476AB33349258EA43C50F2669566ECC2CFEDC7429F829576A D0DC6.pygtex) [72] (./_minted-Tutorial/16CCFD1DA7A71D5F6D9A86870C560407BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C0B89B536EECC0E9CC886A8B4CC9713EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/EE5558D4A829B63692DC55F8215FD331669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/FA669D1E3279749AAAA27A72F3B44533669566ECC2CFEDC7429F829576A D0DC6.pygtex [73]) (./_minted-Tutorial/9119ACDDD7EFFD39008E7F98AB7BF756BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5C54BE5D00F2871BB58E36C383B3B4DE669566ECC2CFEDC7429F829576A D0DC6.pygtex) [74] (./_minted-Tutorial/CE4E385956165A535376F6D73447D3F7BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F55715342346472744E837C465922E6E669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/1B5E788850B45798FCA06125D5880A14669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/B913EFE8AC0AC995AF3DCCAC856FF020669566ECC2CFEDC7429F829576A D0DC6.pygtex [75]) (./_minted-Tutorial/5F9DFDCFBF42A04D6BD31E8E9638DA57BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/BDB62F4C6418AA14588B7DBEA69D61C5669566ECC2CFEDC7429F829576A D0DC6.pygtex) [76] (./_minted-Tutorial/A8D0C008D3D8E2CB96D91B2A5FF2D318BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9458BC75C22971F0F7F09C79C7D6AFE0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/FEF99AFE39529F3F1A5EFC7A23714477669566ECC2CFEDC7429F829576A D0DC6.pygtex [77]) Overfull \hbox (5.54102pt too wide) in paragraph at lines 434--435 \OT1/cmr/m/n/10 ever you can't do that when your records come from a gen-er-a-t or/iterator. There-fore the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write() Overfull \hbox (39.68698pt too wide) in paragraph at lines 442--447 [][]\OT1/cmtt/m/n/10 Bio.AlignIO.parse() []\OT1/cmr/m/n/10 and then save them u s-ing the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write() []\OT1/cmr/m/n/10 -- or just use the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.convert() (./_minted-Tutorial/9776F24C4F96F850E549BEF997E4D18CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D8256B42DA32121F3B83617DD03F4024BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DA108466F70572EEAE2D54AEA4C156A1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8FD10ACD641F4427B35E96F33B44479F669566ECC2CFEDC7429F829576A D0DC6.pygtex [78]) (./_minted-Tutorial/ACC9FF1F2F025F77815D96DC3115B7DFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7E530BB128C8AE6BCF7BCE91DD4AF189669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/C17F8CD5F33DB6EB328532E02ADD1FE6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C02EB78C9555A4FEE4954D77162ACF99669566ECC2CFEDC7429F829576A D0DC6.pygtex [79]) (./_minted-Tutorial/74D8F602592BD3646F12A04951B2C44CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CB14E2060AF38515C129AB5808537F169543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/E78F5A80C222A5B2777910FED4F43F56669566ECC2CFEDC7429F829576A D0DC6.pygtex [80]) (./_minted-Tutorial/4D0AF4A40C449D27FF181EC477C63CE6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/2590B11C695B984E246A0A91734F786CBD02851C2FB632864165FCA4920 46548.pygtex) [81] (./_minted-Tutorial/508710FC1759BFFED598544DEC99BC0DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/886094CE2C1CAC714387144709D5A47ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6DC12DBE1D4FD44E7395C66258B5EAC9BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CAC16111FAD8C2E739F6D7C04A986BF0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A4149E9BEF55B5853014A59A3CBBFBE5BD02851C2FB632864165FCA4920 46548.pygtex [82]) (./_minted-Tutorial/8327145320A3BCB412D977F6683B71A2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1E096B06E33D157FFE18E045579F838CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C7331D522D75BB7830A1364BC3B71692BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C45FE25766D82D1C4A245CBB9A77DB00BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C0937EED558D842CEA8E3DB9514C6E59BD02851C2FB632864165FCA4920 46548.pygtex [83]) (./_minted-Tutorial/8EC03E9C8500D05C6439AC85123A9253BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/AE857C14E4731CC6F6EBA53051460097BD02851C2FB632864165FCA4920 46548.pygtex) [84] (./_minted-Tutorial/F88E003F9A4A95A929AA549FA710239CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/523928538FA511A925EC995B1803BD16BD02851C2FB632864165FCA4920 46548.pygtex) [85] (./_minted-Tutorial/CD47D1913C82182C164BD47DA4715282BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E7AA94166BAA5F4CBB44EF4336F3E893BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B49F47BF4F2EB4093BDE51E631C63064BD02851C2FB632864165FCA4920 46548.pygtex) [86] (./_minted-Tutorial/230B4706E315BD2F2A44F2EBCB37A442BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C11A66992B6C74B61F5A0BE7757AF3BCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/EAE190D91CC491562308EE568F986368BD02851C2FB632864165FCA4920 46548.pygtex [87]) (./_minted-Tutorial/6256254C5A7DFD21185291C77133BFDFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/FC96AF22EDD72BC4AC2EE47EBAA6B045BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E941CFC951CAE25312D9A5CAC9B27425BD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (8.40039pt too wide) in paragraph at lines 1126--1130 []\OT1/cmr/m/n/10 By de-fault MUS-CLE will out-put the align-ment as a FASTA fi le (us-ing gapped se-quences). The [][]\OT1/cmtt/m/n/10 Bio.AlignIO (./_minted-Tutorial/EA6A02999040945446E72AC6A00E56D8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/106ED62B0CFC10E7D5BC6CFC9CE003BDBD02851C2FB632864165FCA4920 46548.pygtex [88]) (./_minted-Tutorial/4D75AC9EDD74C466535F1EC4944833F7BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/14F1F3BAF80772F5999B0773C02432E7BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A261B9E9E2D4EB3C1DF5131C6F739998BD02851C2FB632864165FCA4920 46548.pygtex [89]) (./_minted-Tutorial/E2B86D066966C8BA13EEEF614D3E7454BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E87BDA1F176DA567A757DBA0231BC5BABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6BF1884F2D94AF8D067A2A20A9A41E2CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F551ABCEBB0043257A807C76B9D81B5CBD02851C2FB632864165FCA4920 46548.pygtex [90]) (./_minted-Tutorial/37B6E52C66902FA821D4B0E80172CE74BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0BA045AD7DFE0F0F3DD972F3E2C40BA1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/482576AF06E80D82290535FF7857A240BD02851C2FB632864165FCA4920 46548.pygtex) [91] (./_minted-Tutorial/5D3CCD84BC2EC46BF5FD98E7A3FC7266669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/D9565472E525C9F2B734FC37A70D258E669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/39152F199CEBB3375366F2E947824519BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/256B036DA9C3EDBC9EE41E2E52FDE1ADBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DC6CF8B5CDDD2C32E2052C03AF385674BD02851C2FB632864165FCA4920 46548.pygtex [92]) (./_minted-Tutorial/CEE035FF629B69F7D6B6351C1DCE2493BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DF151703751D72BD556402B910190A87BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/004029547AAB1172AF2684D2CA89EA88BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/554024580088332FAF0EA9296BACE82EBD02851C2FB632864165FCA4920 46548.pygtex) [93] (./_minted-Tutorial/419ECEB266819C8DCC38EB3E1DC3E361BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/143B9D317680E51D3A6E5641208720CABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6CCC707502EDD92E9C355854215BF885BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0A4B1939051DE630E53C7151447C8DD4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/2B6197C314840AD3EC15C56F366120C5BD02851C2FB632864165FCA4920 46548.pygtex [94]) (./_minted-Tutorial/E5E00F47BD7A0C8BC5F8818526283868BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/52B42D5819C8EC5D57A21AE60D28F6CEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5F566D907B2F88621EC4175F1F17AE04BD02851C2FB632864165FCA4920 46548.pygtex) [95] (./_minted-Tutorial/0FE96E337A3BA73D52896D46E2E233DCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/434D41043E1630324FA64E8B55B90BD5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/48453D528762FF183499778647AF218BBD02851C2FB632864165FCA4920 46548.pygtex [96]) (./_minted-Tutorial/BD86EE3248811DE8FD9DE8ED02397A39BD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (76.42714pt too wide) in paragraph at lines 1707--1711 []\OT1/cmr/m/n/10 By de-fault, [][]\OT1/cmtt/m/n/10 aligner.substitution_matrix []\OT1/cmr/m/n/10 is [][]\OT1/cmtt/m/n/10 None[]\OT1/cmr/m/n/10 . The at-tribu tes [][]\OT1/cmtt/m/n/10 aligner.match_score []\OT1/cmr/m/n/10 and [][]\OT1/cmt t/m/n/10 aligner.mismatch_score Overfull \hbox (47.73264pt too wide) in paragraph at lines 1707--1711 []\OT1/cmr/m/n/10 are ig-nored if [][]\OT1/cmtt/m/n/10 aligner.substitution_mat rix []\OT1/cmr/m/n/10 is not [][]\OT1/cmtt/m/n/10 None[]\OT1/cmr/m/n/10 . Set-t ing [][]\OT1/cmtt/m/n/10 aligner.match_score []\OT1/cmr/m/n/10 or [][]\OT1/cmtt /m/n/10 aligner.mismatch_score LaTeX Warning: `h' float specifier changed to `ht'. Overfull \hbox (32.852pt too wide) in paragraph at lines 1776--1820 [][] (./_minted-Tutorial/DCCEE6D592009E7B8E7DE81563D8D4CEBD02851C2FB632864165FCA4920 46548.pygtex [97]) [98] [99] (./_minted-Tutorial/98D9A5E0CD47E306CA0DA2AFE878514ABD02851C2FB632864165FCA4920 46548.pygtex) [100] (./_minted-Tutorial/FBB2100548FA74FADE3EAE28A2DE1911BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5C9DFA2EBF75572BAC340EC89D69B3D4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B788F0FBC120E74A47922EA232EB8671BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/504D01562B8D0E8E16B44A19B5FCD5EFBD02851C2FB632864165FCA4920 46548.pygtex [101]) (./_minted-Tutorial/DE91DA6F7C30BDD779CED0A91AB75DAFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A59C6CF4854355E98CC312686998A38BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3D37B0AE7B982968C1F24FD3EAA535EBBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5214A9AAFC8A40430707E3A6B6DC0D01BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/32985CB8E0884A44019C3AD3006E3F9FBD02851C2FB632864165FCA4920 46548.pygtex [102]) (./_minted-Tutorial/0758643069FF669538B9540ECD26C94CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0BDC838410673E955B3534CCCB8AC77FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/385490B66B3AC742DD6257196C784FE2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/BF27E9BF2471340998870C4A34296592BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A072B421EFC519E90AA0A540338E8E4EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C5780017603AFBC3BB3E9F52ED6688C59543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/76E331C5187C259B69198E91FC4AD112BD02851C2FB632864165FCA4920 46548.pygtex [103]) (./_minted-Tutorial/BF7EA4D0E316F88B3A609CF62C6CD357BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A564D138D2F52B4E2858B9D14814966BBD02851C2FB632864165FCA4920 46548.pygtex [104]) (./_minted-Tutorial/68A0723415861BAD8A4809FC33D4A2EEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/66AABFA387595237A8CE2518915213F8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B15E737F9393063B641148640673D991BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/EB25FB90F1A09B5CEE3428AFC4487B46BD02851C2FB632864165FCA4920 46548.pygtex [105]) (./_minted-Tutorial/EACCEA5889A222FB9830265E6A8DACB9BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/874975627BAB24A36A35FD4C633D246DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/35E64D230C4D7DA7362D8F8BA278ABB5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B0937117DDA6BB67D133C99E550AD5BDBD02851C2FB632864165FCA4920 46548.pygtex [106]) (./_minted-Tutorial/9C81CE609C3C74FF6DDE53A3528FDA3ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/AF515AF157FE4840A244030AD4DCE3A7BD02851C2FB632864165FCA4920 46548.pygtex [107]) (./_minted-Tutorial/C8046F75BC00F97BFBB444E7FCFDE7BABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9249A0A01E1025FA8711414C0E36841FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D1BAA37DF09A601FA4C6F2BEF162C3E0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/52868B2F44504455E4969FEF2614B63BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/433C9892AE287F36B57A8A95FE75AB94BD02851C2FB632864165FCA4920 46548.pygtex) [108] (./_minted-Tutorial/E7E68A8851DEEE300947A0531513417DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/60C347B45B5A049CB5B00A20D29DEF65BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1498327D070D6F98AC2E3DB39EAA1733BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6502BA65433924876427DBB6013C1003BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DE6EBD36098288038E8FFA4A045EC8FDBD02851C2FB632864165FCA4920 46548.pygtex [109]) (./_minted-Tutorial/B66E52A450DAB10C11EF0A5303F7F66EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8791CE2DDF360A2EB13DED7B355F1012BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/ED55B2BAF04247D4F10E951590AA5077BD02851C2FB632864165FCA4920 46548.pygtex [110]) (./_minted-Tutorial/779C61444C54C1736794F4E11B0E326DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9FF41FE72E025C3EC8E41470B268E105BD02851C2FB632864165FCA4920 46548.pygtex [111]) (./_minted-Tutorial/779CE460F4F768A71E6F35DDB7FDFA77BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9EF49B98A62C70CD81126514DF796600BD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (19.80069pt too wide) in paragraph at lines 2612--2613 \OT1/cmr/m/n/10 In this ex-am-ple, the to-tal num-ber of op-ti-mal align-ments is huge (more than $4 \OMS/cmsy/m/n/10 ^^B \OT1/cmr/m/n/10 10[]$), and call-ing [][]\OT1/cmtt/m/n/10 len(alignments) (./_minted-Tutorial/F89522EF58FB067C6521C367C7134716BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/76A8D90A1791A7B42DD5E6329FCCBE20BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/399250FB2BC395588B8004ACD928BE9CBD02851C2FB632864165FCA4920 46548.pygtex [112]) (./_minted-Tutorial/882BD2544386DECA236BF25C7DD64857BD02851C2FB632864165FCA4920 46548.pygtex [113]) (./_minted-Tutorial/22FCA15B328DDB0383F97012E3C1FA70BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DA98355B1CF48169F9C82F2DD1F86A29BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/13D646E6B49807044DBDC43707A09846BD02851C2FB632864165FCA4920 46548.pygtex [114]) (./_minted-Tutorial/467CA50C36874E405E988587FEC07686BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E4398C5237FE7113BC5A8DE3B0E138A6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E827958137C7E69DAEDB0C4151298E62BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A94C18D2207C354646F831D57FD85B35BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/801A90831A5799E3FF1FC0A5E721F4F2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4329189CC201D756D0770BD7596DF0D8BD02851C2FB632864165FCA4920 46548.pygtex [115]) (./_minted-Tutorial/C7C0911CDDC1913791B1BD1EDA0EC55FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F13283947C7FDCA9456A70797E029A73BD02851C2FB632864165FCA4920 46548.pygtex [116]) (./_minted-Tutorial/AAF53200644F4F68779FB844730087D3BD02851C2FB632864165FCA4920 46548.pygtex [117]) (./_minted-Tutorial/FCBF8AC8128D86DFE3607A8465EC034BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/96A1DC106863D5F4D96B9200B7B5BE06BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7323803F0E90CDA6FB16D10E868318BBBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/FBFC10402209A281F117C1A7C3D2057DBD02851C2FB632864165FCA4920 46548.pygtex [118]) (./_minted-Tutorial/04CF4E50F88DE1F6947064E1188A1BABBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/88E3C6FE8CD1E52180656649B61F8CBBBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3352A1628AB7C0D638BB368952D0DEDCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/842D73F66680850822D006857AE71FE7BD02851C2FB632864165FCA4920 46548.pygtex) [119] (./_minted-Tutorial/FAF36BBB1FEE777074E1CB3B06F18C8ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6B4057929CCF1526CF34FF943CFE3135BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E0AB5DB602ED615A4FA228E22B0CC4F2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5E9D6563DE4DEF6BBF8840F7693212F4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7C466424D72F09AE5AACA884161416F9BD02851C2FB632864165FCA4920 46548.pygtex [120]) (./_minted-Tutorial/F3DBACE95BC0B45F9EEF5BC8C67DEB0ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CC9E9C07C5DC6BDB4071B2A0EA825278BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/55D34AF6272FC77B12E7D4DD16884A6BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A5A764AD6E5C1A70216D27249F680093BD02851C2FB632864165FCA4920 46548.pygtex [121]) (./_minted-Tutorial/54EF0A3F068FF357EC3C51C6E1172A57BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1E78F0FD7A0E228935EE2D650C9315ECBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CEB2F5A09DE2611D752331C16E5BE61FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/007A62C4B86AFB9385A7D86241664707BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E19493E35A1B212412F37B3A7079D5ADBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0B051755682044B54FDC8CE728FD23B5669566ECC2CFEDC7429F829576A D0DC6.pygtex [122]) (./_minted-Tutorial/659317FF2415828FBE0F4505ECB5B4E5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/60D893638743BD147116D13E00593D6CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/FC6687367D9EC6B1C018CE84CA30555D669566ECC2CFEDC7429F829576A D0DC6.pygtex [123]) (./_minted-Tutorial/9AD9216297281F0858F16EA5C03B98AFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CB8FA536E934FA2DC233E7FF52DEAED4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/14104DE21243051DA2E8D004C5D1A9EDBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3C42B04C08C3B07CABB6D2D7AE1F1B6DBD02851C2FB632864165FCA4920 46548.pygtex [124]) (./_minted-Tutorial/A6E4A89F3F3E07605D5B2BD57C7671CABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1795B10D0BABDD4E83A8B6EBE5DAF8CDBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/691C9A3D9A1EB52FAECF7E4C91F03BE9BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9A7868CC2484B4CFB34F94E7549F2519BD02851C2FB632864165FCA4920 46548.pygtex) (/usr/share/texlive/texmf-dist/tex/latex/base/omlcmr.fd) (./_minted-Tutorial/A7706714F4982C826867A73C2B665ED0BD02851C2FB632864165FCA4920 46548.pygtex) [125] (./_minted-Tutorial/44E2C06C8661B128385CD75A7E7608AABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F120EF3444F3192D48657B4E52407017BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9AC50DD22A56E4DC2B26465D89DE35EABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CFB7E0A19AF729834746B283E60F2091BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7DA73F8FE9E6D95C2255220886791B5DBD02851C2FB632864165FCA4920 46548.pygtex [126]) (./_minted-Tutorial/E9F207F5DA488246642864EBF9EA466DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/15FD2886E49804AE97038F2733592C71BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1D1D98CF394058EA9EB8F6FA3B0DB75ABD02851C2FB632864165FCA4920 46548.pygtex [127])) [128] (./Tutorial/chapter_blast.tex Chapter 7. Overfull \hbox (5.71313pt too wide) in paragraph at lines 45--46 []\OT1/cmr/m/n/10 NCBI guide-lines, from [][]$\OT1/cmtt/m/n/10 https : / / blas t . ncbi . nlm . nih . gov / Blast . cgi ? CMD = Web & PAGE _ TYPE = BlastDocs & [129] (./_minted-Tutorial/A6D333F851BCB09A0C02030C1BC37AB1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/69F91830197D9990EA9A0BD7D074EE21BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CF5D749C3878C5A1FD3C8C63CA51FD08BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/00F087159F0534545C0B7288838BEF0EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8A150C3E431DF572EF74B2B19AB15AF8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/2FDF7B3FB3DC9B4B3C157122F78C3F4EBD02851C2FB632864165FCA4920 46548.pygtex [130]) (./_minted-Tutorial/0E750E34F5C53FAE26988AF1CDC7FBC6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C9558BD802C8764E46CF73625C14C204BD02851C2FB632864165FCA4920 46548.pygtex) [131] (./_minted-Tutorial/21FCFA3232935EE0DF07988BE50D1AEF44BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/88BD5D9B190061FD4FD34D2573EE4792BD02851C2FB632864165FCA4920 46548.pygtex) [132] (./_minted-Tutorial/CF5D749C3878C5A1FD3C8C63CA51FD08BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C9558BD802C8764E46CF73625C14C204BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/16EEC09BFB431080BCE9C5E6ADA5DAA9BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E34865BFB20F9D165069B84AE5218004BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E0F63513A18DD0126288BC98B9F40394BD02851C2FB632864165FCA4920 46548.pygtex [133]) (./_minted-Tutorial/A614B982013DB6EC38FCADD82303A8BEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DD49CD888784736545A3066AC257FBFFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B7DE908D2BB5BA4FD1BB179810D8D238BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/16EEC09BFB431080BCE9C5E6ADA5DAA9BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/68259DF5B1930070C029D5A72D891A36BD02851C2FB632864165FCA4920 46548.pygtex [134]) (./_minted-Tutorial/0C1E2B9A587BB44A7E19E83A4E5B1924669566ECC2CFEDC7429F829576A D0DC6.pygtex) Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. LaTeX Warning: Float too large for page by 32.27644pt on input line 481. ) [135] [136 <./images/BlastRecord.png>] [137 <./images/PSIBlastRecord.png>] (./Tutorial/chapter_searchio.tex Chapter 8. (./_minted-Tutorial/6D0EADF658E662CBA394834EFAC7346E669566ECC2CFEDC7429F829576A D0DC6.pygtex) [138] Overfull \hbox (2.9019pt too wide) in paragraph at lines 85--93 [][][]\OT1/cmtt/m/n/10 HSPFragment[]\OT1/cmr/m/n/10 , to rep-re-sent a sin-gle con-tigu-ous align-ment be-tween query and hit se-quences. [][]\OT1/cmtt/m/n/10 HSPFragment Overfull \hbox (8.43927pt too wide) in paragraph at lines 105--107 [][][]\OT1/cmtt/m/n/10 parse []\OT1/cmr/m/n/10 is used for search out-put files with mul-ti-ple queries and re-turns a gen-er-a-tor that yields [][]\OT1/cmtt/ m/n/10 QueryResult (./_minted-Tutorial/0EF47CD31A1F702FF10BD5C95E6D18FCBD02851C2FB632864165FCA4920 46548.pygtex [139]) (./_minted-Tutorial/BCDD1F95C8585B3C70DE9C1280B51955BD02851C2FB632864165FCA4920 46548.pygtex [140]) (./_minted-Tutorial/7A12FEF8445FE62A62C651C8B4EC163FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/362861C831165FEA5413E0240053CD89BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/40227DD719AAD22E8DC2923BF43CE327BD02851C2FB632864165FCA4920 46548.pygtex [141]) (./_minted-Tutorial/FD9C81C098491598DBFB6208173BB575BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/87D36F7AE3CBC4EDC6FCCFDE0173412CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CA24D00985B075C56E7C71A246E439FFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DE8A481953AA0F7BD7A99C0E281AD1A0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E7AA701BE1D007CE77D402E8CBFC777ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/906546E8B6F7831A0E7C5FC93AA56A03BD02851C2FB632864165FCA4920 46548.pygtex) [142] (./_minted-Tutorial/0B914838010D3E86EC368E1702EB7253BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E4688DCAB619DBEB784ED0D836D1E619BD02851C2FB632864165FCA4920 46548.pygtex [143]) (./_minted-Tutorial/DDECA9EB99D9FA38003A52C176593072BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/578CBF904F35965EECFEC1FA694F0752BD02851C2FB632864165FCA4920 46548.pygtex [144]) (./_minted-Tutorial/C0EB7D270F64704BA5AF848A21AACD64BD02851C2FB632864165FCA4920 46548.pygtex) [145] (./_minted-Tutorial/84848AABE250EF05E85067B2CD3275B8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A2EA3A12F7596A64ECEE374A9C53499ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E7A6E47CCC64E8FADF02D1CDC6246863BD02851C2FB632864165FCA4920 46548.pygtex) [146] (./_minted-Tutorial/A3385B945E43CC076FFA693B27681F05BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DAAFD2AAF126ED8D7284764B561B5E2BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4B4824DE2ED3215F02082987EE573577BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/61406D58E5F7C40FD0A0280DCAA66B46BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/BF77764978D907008BC936FD2A5FCD95BD02851C2FB632864165FCA4920 46548.pygtex [147]) (./_minted-Tutorial/CE618F26D70602D511E57E53CD880444BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DE23F71CD74CF7717D38AD01C1E1C787BD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (27.24287pt too wide) in paragraph at lines 743--745 []\OT1/cmr/m/n/10 It should not sur-prise you now that the [][]\OT1/cmtt/m/n/10 HSP []\OT1/cmr/m/n/10 ob-ject has an [][]\OT1/cmtt/m/n/10 alignment []\OT1/cmr /m/n/10 prop-erty which is a [][]\OT1/cmtt/m/n/10 MultipleSeqAlignment (./_minted-Tutorial/338C616C7128C3DB7FFD516F5C2BDA12BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1195D6861E887568107FA7F463EA9BBABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/31F43A46088F6D2E63B39857A3536909BD02851C2FB632864165FCA4920 46548.pygtex [148]) (./_minted-Tutorial/16771935702D6A2A9762A80A621013D8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/046FE550C51B323D1E952A27E126FE19BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A55E467518B2E0F936A232F0970B1037BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6D69D310788199FBA6E8A5BF5CAB2021BD02851C2FB632864165FCA4920 46548.pygtex [149]) (./_minted-Tutorial/2C71B4AE1F4F9990447491C6C291ABC2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/FD7ECFDD9D017B829A54C995FEE42EEDBD02851C2FB632864165FCA4920 46548.pygtex [150]) (./_minted-Tutorial/3AD8335853E972C8E62AAF79CF0A3D33BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/758BAC7574A59544686354199D20892CBD02851C2FB632864165FCA4920 46548.pygtex) [151] (./_minted-Tutorial/7A63CB5E786CCE052981F7DD10653DA9BD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (14.20721pt too wide) in paragraph at lines 1055--1059 \OT1/cmr/m/n/10 func-tion re-turns a gen-er-a-tor ob-ject that yields a [][]\OT 1/cmtt/m/n/10 QueryResult []\OT1/cmr/m/n/10 ob-ject in each it-er-a-tion. Like [][]\OT1/cmtt/m/n/10 Bio.SearchIO.read[]\OT1/cmr/m/n/10 , (./_minted-Tutorial/DC4E434DA5B851CF1E22BD3608A311F4BD02851C2FB632864165FCA4920 46548.pygtex) [152] Overfull \hbox (20.13245pt too wide) in paragraph at lines 1087--1092 []\OT1/cmr/m/n/10 In this case, the ideal choice would be to in-dex the file us -ing [][]\OT1/cmtt/m/n/10 Bio.SearchIO.index []\OT1/cmr/m/n/10 or [][]\OT1/cmtt /m/n/10 Bio.SearchIO.index_db[]\OT1/cmr/m/n/10 . (./_minted-Tutorial/0AB25750C7D89E832295045C60D6B8C4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DFACFE04880AE0CA2E8E32ABDC9E9868BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/51F256FC56FFFAE1F1E84A4EFC5BAE55BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5BCEFFE3DBB7A0AE4FD5D950731D72DEBD02851C2FB632864165FCA4920 46548.pygtex) [153] Overfull \hbox (11.82602pt too wide) in paragraph at lines 1167--1170 []\OT1/cmr/m/n/10 Finally, [][]\OT1/cmtt/m/n/10 Bio.SearchIO []\OT1/cmr/m/n/10 also pro-vides a [][]\OT1/cmtt/m/n/10 convert []\OT1/cmr/m/n/10 func-tion, whic h is sim-ply a short-cut for [][]\OT1/cmtt/m/n/10 Bio.SearchIO.parse (./_minted-Tutorial/BDE985FA3ADA6B0D37013C3D5F37C176BD02851C2FB632864165FCA4920 46548.pygtex)) [154] (./Tutorial/chapter_entrez.tex Chapter 9. [155] (./_minted-Tutorial/95F72AA1E59C898262005610BC25A6BABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/320E9A38F759168BA03B078BD9CC013BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DAEC2235DDE454C09ECEB0DF4CD26FB5BD02851C2FB632864165FCA4920 46548.pygtex) [156] (./_minted-Tutorial/7692669934D8ED6DEE1B8B6684745421BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4E8E7490F3E1B9120A0B1B53C024FA36BD02851C2FB632864165FCA4920 46548.pygtex [157]) (./_minted-Tutorial/C21F612C84412948C9890ED976F536B0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7E05622F86D5C6456282864B1095B19CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/846A93AAA063B5CBA3EDEF3D5FC8C008BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/03DD15474BC34E37527B593FC22220FCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7B7AA3167A6472C6C33ACA91F8E88FACBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/82DFC9B19D35F2D9482DE6B365FC35F6BD02851C2FB632864165FCA4920 46548.pygtex [158]) (./_minted-Tutorial/01D9FCC3424FD0B497241E81D2FE83C6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F74B27B285F0D0CC7E69CABE07232C68BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/83C7791C8A9F82BA61AD4B1644D50277BD02851C2FB632864165FCA4920 46548.pygtex) [159] (./_minted-Tutorial/3B6409EA2F4B25B8F136CE97DC95E8C4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/53F668B0CE9069489F6D35B114D072B1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/49E5F2A1DFC2444E5A673AD6C6E3F19FBD02851C2FB632864165FCA4920 46548.pygtex) [160] (./_minted-Tutorial/96245EB54DC7A4475CD270566892BAE4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/AA26452EC447FD01D35D14B1CE4F3147BD02851C2FB632864165FCA4920 46548.pygtex [161] [162]) (./_minted-Tutorial/042DA7A7135DAEF797FB2EE6170C3B6DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/11417087354B0B78128E27B0162F48D59543DFECA235A69AE23006BA05B 4EB70.pygtex [163]) (./_minted-Tutorial/51CC2C09DB95235CA19612EAFF65F487BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/01919CABECEE21D3FA5A6B7A01CCCB5EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0DD80468D8C175A94BC63142BD16EF1DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/414E52C4377A1D0E6A428B032A7756FDBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6109D29005C5EC9FAE01CDFBE62EF008BD02851C2FB632864165FCA4920 46548.pygtex [164]) (./_minted-Tutorial/A0ED7F47BA117071BA21263E7AF6DB27BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3C5A1B892E98E1E6E8C179B5F465500ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/68622353B578A611D2F621023E3C4BD1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7455566FBE10CCFD5236DF65992A9F70BD02851C2FB632864165FCA4920 46548.pygtex [165]) (./_minted-Tutorial/6E7EC19AB4E894FD7BECB47DC082FC38BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E02371BEF7596435E8F90267E0362E0944BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/8A1D9304F979E03817FD393E44DC722ABD02851C2FB632864165FCA4920 46548.pygtex [166]) (./_minted-Tutorial/2B17732B358EE5D871A248019977CF38669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/2186E927D5A018F8950E8A7D0F734E71669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/DDE0AA7C839DD601590297B5D523D03BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1516062A6E16A043D5996183E67DEB86669566ECC2CFEDC7429F829576A D0DC6.pygtex) [167] (./_minted-Tutorial/08B5AC3C9DEAD2E377FE070B35391F0BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/898885F88FEAC697F30E8E063D95F24D669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/8BFD5A5D2A0A2DB21DA15E3F1719D3F6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B89E703729CE0DB5EB3456180292FA1B669566ECC2CFEDC7429F829576A D0DC6.pygtex [168]) (./_minted-Tutorial/06D29A54CBCE7E9BEC9B02AF3737953FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/115C0D8716DAB358EAFF936486F27AB9BD02851C2FB632864165FCA4920 46548.pygtex) [169] (./_minted-Tutorial/9BFD2F013E1A1D8756C2BFF5B3706AAD669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/9D66917D850D2EF232ECFE32D0F8D1CEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/474ACCF7269CF6DA8C1148E094B63C80BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/265BCBE09451F85D4BB86E81E6F3D4E1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/077B6C28FFFD9E8EB72387BF7F1D9BF1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/41118C19A2E462F9721E8AB1E52AAFC3BD02851C2FB632864165FCA4920 46548.pygtex [170]) (./_minted-Tutorial/8D1D071E3CA3DD9187A6F2C35836C58ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9E297F3C90950B761CCB974F597BCC12BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/30DFAED5DDA7DA75BB6A3BF0F0C12D75BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E07A958FADB74CD60F7086FF6319E277BD02851C2FB632864165FCA4920 46548.pygtex) [171] (./_minted-Tutorial/55E8C5FCC00AEE8A4E1D892ACA95C2BCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/473B4163A14D626D6B7A08A26A0A1266BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4802D221A3EBE7AAC3E07CB05144CA27BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F7C9857DB48F3111F31BB49EC39F2019669566ECC2CFEDC7429F829576A D0DC6.pygtex [172]) (./_minted-Tutorial/650077A39F2D52831A52D045B184B624BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/17E5085C64881C08DC82C2B5573291F2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/076325C16F7C56460228C73B3147DF7A9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/2018A02508D4B36EF0217BE478D18CE1BD02851C2FB632864165FCA4920 46548.pygtex) [173] (./_minted-Tutorial/67F7BC27D166185C4B7B9A9F270ACDA5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F01452391D049758B3588D8F37184AA19543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/04D54F815C5EFA53EF9010776D1AA07EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D46819E08D3CDD954897218A7EB7C8C0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/57648E2674FE9BB727770109CA65C71ABD02851C2FB632864165FCA4920 46548.pygtex [174]) (./_minted-Tutorial/676B968CE2CF2F3AEF6899757E020B1EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8778F0F3798A99FE0C3840234CAC2B5BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/FAD1D32BBD3E6FC5FE31DBBF8029928ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/85AA5F6E67E515A70F5F0A4D9A0548C0669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/24D6870F7CF00B7F93EF1F55424D4AD0BD02851C2FB632864165FCA4920 46548.pygtex) [175] (./_minted-Tutorial/964257041BEB9E732FF9A943209BD6EDBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/600193D5D5D44162E61A3CAB40448426BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E963D1B8D3330FC994CC39110B642038BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/574A29DDA761C1725F490FB0F1CD4EEFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6FD15C01D270A661A77854FF78F033B8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5845916CE276A61945EF5849B982E8A0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8905908F46BA67CB99A3360F253875C5BD02851C2FB632864165FCA4920 46548.pygtex [176]) (./_minted-Tutorial/4DA8ECCF1EA4588537B571B9F46E13A1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/714497BD693AE1BF76AD1C44D3A43F2FBD02851C2FB632864165FCA4920 46548.pygtex [177]) (./_minted-Tutorial/824F6600A92AA40841D5D9A4C2EDC5FDBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A3EC6E0F9D852E0B8DED607938A72797BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E8FC03C2B925F09D2849BD1DDCBB3848BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A137A30778671FFE0F193EED7A8819D7BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3D76169664531538D144C55FFC33571BBD02851C2FB632864165FCA4920 46548.pygtex [178]) (./_minted-Tutorial/D49E38D9D1357F6225DB42AC5AD5ED7EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CC6CFA7B6751FFF8C74660FCC40D3C45BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0D86B77B8C40BC4335F18EE35CB93649BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/37575ADC7CF832C14B5854633F9C88D8BD02851C2FB632864165FCA4920 46548.pygtex) [179] (./_minted-Tutorial/5E81FD2679BB8BC4F82244B31C22C477BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7212F8F4D805E6009D8612AB61498E24BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B038E9BC100BB2A231E2B4BF11B0330CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3256378680D2E01A0D283817FC4F9633BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1E93113A22D275DCF1ED22A91F77D5749543DFECA235A69AE23006BA05B 4EB70.pygtex [180]) (./_minted-Tutorial/4F9D9C998FB1DECE2FBF932B39921FFA9543DFECA235A69AE23006BA05B 4EB70.pygtex [181]) (./_minted-Tutorial/43EC7DBFBCAE4E8B197BA170F7FE7CB2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5F55F80E3D84EDCE0B63B5BCEC4E927ABD02851C2FB632864165FCA4920 46548.pygtex)) [182] (./Tutorial/chapter_uniprot.tex Chapter 10. (./_minted-Tutorial/DC3FD651AB93A0CE9D668FE4206D1A86BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DD1C7AE6EB54A3133F3D58EE95B3A668BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/BB844FCBFB442A424E4ED0D244DD6768BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/930B60BD569CAAF368B0E614553F3030BD02851C2FB632864165FCA4920 46548.pygtex) [183] (./_minted-Tutorial/ADCE00FC778B0EA886D44F1AA6519182BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3D3E040F0C8AAE9BF46C3D89DB934669BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C65ED72167AAF5D5730D19463FD69228BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CFBCB7DFF63857026EF72107C91C4D14BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D965DDAA766509A8449374C475416C06BD02851C2FB632864165FCA4920 46548.pygtex [184]) (./_minted-Tutorial/747E2FE5A2594F5385BB7437A4517918BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8837CDE38481CF679BB33997916F09ABBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9E15781AA166AC63C2DF3BCF25628224669566ECC2CFEDC7429F829576A D0DC6.pygtex [185]) (./_minted-Tutorial/956383F4066B9E093C9D2E3843CA0220BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/BA8B23CD43F97133B0CE8ECD0A9462AA669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/8B296BCFBFAA7137B45E8CB899424BE4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C2EF087C5641CFFF6A40A4396FE9307BBD02851C2FB632864165FCA4920 46548.pygtex [186]) (./_minted-Tutorial/9AB12EEC55BEE868B932EF7EF12109CEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6E2B75EC45BA35CA8C7799FFAFE69A4DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1DE080CE5283B4D334F81719880190E2BD02851C2FB632864165FCA4920 46548.pygtex) [187] (./_minted-Tutorial/6ED198EEC186F92A098C5692A874CF5B669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/F4AB180AFE85CC09CE3F73EE547FC783BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B1A88EF3A17DB1FA7EC5A60B27A37BF9BD02851C2FB632864165FCA4920 46548.pygtex [188]) (./_minted-Tutorial/454E46BC171F751C15F6A295F2284AB7BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8DCADA174B7DBC35827913027E1507B4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/20DD2D91201FBA08EE81FE73D557B622BD02851C2FB632864165FCA4920 46548.pygtex [189]) Overfull \hbox (24.29903pt too wide) in paragraph at lines 365--366 []\OT1/cmr/m/n/10 If the ac-ces-sion num-ber you pro-vided to [][]\OT1/cmtt/m/n /10 ExPASy.get_sprot_raw []\OT1/cmr/m/n/10 does not ex-ist, then [][]\OT1/cmtt/ m/n/10 SwissProt.read(handle) (./_minted-Tutorial/30A3D5D1EA4F73DD0984EDFDDAF9090CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/950511DA0658C1A2824DF92F06F34BE8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6A833CD3DDDD6A4CCF169D082C63D87DBD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (65.93893pt too wide) in paragraph at lines 409--410 []\OT1/cmr/m/n/10 The same func-tion can be used to re-trieve a Prosite doc-u-m en-ta-tion record and parse it into a [][]\OT1/cmtt/m/n/10 Bio.ExPASy.Prodoc.Re cord (./_minted-Tutorial/DF2DA17EFC0F6336210C74066809B753BD02851C2FB632864165FCA4920 46548.pygtex) [190] (./_minted-Tutorial/9457A436D281E066D350873A88476E59BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5C1399E579A6AA8D432E509AE441C2AEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7528F52197E46B376DB12FB34672D7A8669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/64ACD8E8EC2C5F323A9D84639080EBCBBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C8BC3187BF8F96BDF009A2CA8A95A3C3BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4323DBBD15E176599A70095217F377E7BD02851C2FB632864165FCA4920 46548.pygtex [191]) (./_minted-Tutorial/0B895A7CD7770AD5152A902E24E86169BD02851C2FB632864165FCA4920 46548.pygtex)) [192] (./Tutorial/chapter_pdb.tex Chapter 11. (./_minted-Tutorial/D779A8F555F6BCC207B905D5D6C22853BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/946CAECCFDBF1349958F40A0FC03463FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/2FDED7F9BEF9EA1F5CE28B11996ED43DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/05714E0F28AC6B36B176161D8A9FA84DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3D3953EF520FE9546FC19DB705E69085BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E37E6F74461E0075B61AF24790D37C71BD02851C2FB632864165FCA4920 46548.pygtex [193]) (./_minted-Tutorial/32D78458130807D5C8DD536942BA7388BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B49437C8CCF1C8D72B8DBA0CFE1DCB35BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A7F199DA98E2BD66B92177EFD14AA59ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/57A82B690A435E6AD7DAD62778DB8231BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3AABC2CB1B50E66D5DBACF20EF52245ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C79D210A6D0E5501910FFF311063879EBD02851C2FB632864165FCA4920 46548.pygtex) [194] (./_minted-Tutorial/41FC845107E552AB47AA881B90236E18BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B41B5BFD7D85ED4E7E70DA059AE1D176BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/36AD36AC9E663BF06BB871053927CDF0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1BBCC7F8F1756C270C4D99E9F943A024BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4AD3361A8DEC1848967C5C4904CBAA6BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D8411ECFB826F8858D5702457B0FB9A5BD02851C2FB632864165FCA4920 46548.pygtex) [195] (./_minted-Tutorial/684AC0ECE33D6BA84F0409CE669AB136BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C85B5FA2C9BF8127C2FEFF62553FECECBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/05AAA27695D5E74A2F0C892230E4EFA4BD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (13.022pt too wide) in paragraph at lines 262--264 \OT1/cmr/m/n/10 The over-all lay-out of a \OT1/cmtt/m/n/10 Structure \OT1/cmr/m /n/10 ob-ject fol-lows the so-called SM-CRA (Struc-ture/Model/Chain/Residue/Ato m) [196] Excluding 'htmlonly' comment. (./_minted-Tutorial/DCB043864D9F8E2B59DEBF1784B30CDCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B6B956752D54554859CB3FC041890BD7BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/958010CCD8250B2A6D359F037738B54EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/69627B7F3108FCBC466F45AE8D24D979BD02851C2FB632864165FCA4920 46548.pygtex) [197] [198 <./images/smcra.png (PNG copy)>] (./_minted-Tutorial/13774A78311C8B2B99285E3D509AD855BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/EC253507D414D1E9DDE9BC5CAF6BC78CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/69D3F9059506073A988980B78CEAB247BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5A42A68287048A843E1066F2E2727622BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/22421A9A4B194CFEBFABE1E2DDFC8A12BD02851C2FB632864165FCA4920 46548.pygtex) [199] (./_minted-Tutorial/8A579A2F82E38AFC725C7AD02B2F5D57BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C4346C691565244D87DFA5ED26B512E3BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/38F92E91F7EF83579513DC2A23D231DCBD02851C2FB632864165FCA4920 46548.pygtex) [200] (./_minted-Tutorial/35E34E333445AAAA4E33570211335BA5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A2470AECC1DA459F7A1ACC68FCD911B1BD02851C2FB632864165FCA4920 46548.pygtex [201]) (./_minted-Tutorial/874F41EC8F1C0D727A004EAEFDC88098BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/94A9BE470837AFDA4B8581B79BB12492BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/76657140082404C594EE786B642215C3BD02851C2FB632864165FCA4920 46548.pygtex [202]) (./_minted-Tutorial/17EB0A1D2812B68E199CC00449B9254CBD02851C2FB632864165FCA4920 46548.pygtex) [203] (./_minted-Tutorial/D94A742238FBA8E89BB46038CDBDEB90BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0BFD7EDA2178705DA7C24F4D3735823EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/73DA0F97AF01C85175F4AF2DFAE2C6B7BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7E80E6D2D75417229F3B2B705315B128BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/618AFB68C3893C2A344D3A532D9BD99ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/82DD3285068398C1A65910EDE1BE970CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0799FD26AFF50D33D257B86E8D3E40B3BD02851C2FB632864165FCA4920 46548.pygtex [204]) (./_minted-Tutorial/2857EE83D7FCEE22018F0C0AD63239E0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/365D7E5A27BEEE6ED9265079DF231899BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0B35B80BBDE5AE1373CAE9105C01A624BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/BDCD0910528B95EADEE1C7C6BD40AD3CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3A499902396CBA88B311EE3A93BC2663BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B2412D9441598FCD30172739CB3CCA39BD02851C2FB632864165FCA4920 46548.pygtex [205]) (./_minted-Tutorial/728242DAC9077785511462C5CD16E667BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/866FA21894DE0E73CE09F7F50E59FDC5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D6328A6D8E47F7B8E9530D396E8ED50DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/2CF9B1EBC15ECA1536AFA86FAF01899BBD02851C2FB632864165FCA4920 46548.pygtex [206]) (./_minted-Tutorial/F412BF266412BEC93BB127CA53AB4D0CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A73938953B2223965D08B528F27C56E8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B33389074760A02AC27316E67DAAB073BD02851C2FB632864165FCA4920 46548.pygtex [207]) Overfull \hbox (42.26714pt too wide) in paragraph at lines 956--960 \OT1/cmr/m/n/10 breaks and dis-or-dered residues and atoms as de-scribed above are han-dled cor-rectly. \OT1/cmtt/m/n/10 structure[]rebuild[]test(entity) Overfull \hbox (3.8904pt too wide) in paragraph at lines 976--996 [][] [208] (./_minted-Tutorial/10F60558792DABA08CE906FCD09A993CBD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Command \r invalid in math mode on input line 1049. (./_minted-Tutorial/10BEDFA26FE20B8B11FC832131C1705EBD02851C2FB632864165FCA4920 46548.pygtex) [209] (./_minted-Tutorial/12DBC9D94FB0B4B78A481C6C111C6709BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/895E3343902EFB0E5475667B01C4B691BD02851C2FB632864165FCA4920 46548.pygtex) [210] [211] (./_minted-Tutorial/7A6D5A10ECC42BAFEE724455549BCB15BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D5B0F5228C1E7FAD0C7AB40AEFF6B6A9BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/2810A7579DC6FE011D31E2F074471A74BD02851C2FB632864165FCA4920 46548.pygtex [212]) (./_minted-Tutorial/D9D0B8746EBF14CF4BE7DA480D9ECD5DBD02851C2FB632864165FCA4920 46548.pygtex) [213]) [214] (./Tutorial/chapter_popgen.tex Chapter 12. (./_minted-Tutorial/E5F1866C3CBB485B8C06B62764ACFBB29543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/331BEE386F268F55DE217F54E27EAB6B9543DFECA235A69AE23006BA05B 4EB70.pygtex) [215] (./_minted-Tutorial/6CD64A1F591B16F512F7EB6B68E5B3FC9543DFECA235A69AE23006BA05B 4EB70.pygtex)) [216] (./Tutorial/chapter_phylo.tex Chapter 13. (./_minted-Tutorial/8F8EFC1C83277AE6C5B5A259FAAC5671669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/4914B4679D1C933D9AD76E95F18CE15844BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/3D758844BE2A5D4414B741470EDE8C24BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/719B0C758B666CDEEB2B250C2143A4ADBD02851C2FB632864165FCA4920 46548.pygtex [217]) (./_minted-Tutorial/8698B66B622D8A91E7706D889D5F35DDBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6621A01BB423374C8FC608E267D0EA7DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/87517FEF82BFE1AB8D89A83F4DC5E8B9BD02851C2FB632864165FCA4920 46548.pygtex) Excluding 'htmlonly' comment. (./_minted-Tutorial/6C5156DAD460519324A5B7657B301B5DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1836031BC83AA94C8906762F613E6CBABD02851C2FB632864165FCA4920 46548.pygtex) [218] (./_minted-Tutorial/D0A75FB8C1C791E4AA80420B93F216A8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/FEC6C2CB5FA0AFCFE00D995BD3642FF2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/2B435DC3041611A5D6A663B437ADB1ADBD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (25.13162pt too wide) in paragraph at lines 182--185 []\OT1/cmr/m/n/10 Let's tar-get the most re-cent com-mon an-ces-tor (MRCA) of t he nodes named ``E'' and ``F''. The [][]\OT1/cmtt/m/n/10 common_ancestor (./_minted-Tutorial/29624A9666C9430AABADF395148BBF27BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D0F05D42BA0A9BC594EEDB16319A972DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/87517FEF82BFE1AB8D89A83F4DC5E8B9BD02851C2FB632864165FCA4920 46548.pygtex [219 <./images/phylo-simple-draw.png>]) Excluding 'htmlonly' comment. (./_minted-Tutorial/D713148814BA75DCDEB1C77B12674D9BBD02851C2FB632864165FCA4920 46548.pygtex [220 <./images/phylo-color-draw.png>]) (./_minted-Tutorial/69333D76AA5D97D8BF9E95DEECEEE2B1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/456F5679DCD4FF740E7A110889D86573BD02851C2FB632864165FCA4920 46548.pygtex [221]) (./_minted-Tutorial/2B3BFA62F3A778E4818959ED3E8AD3EEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/08F738B2988883F2B3BAD96FA439AD7CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8C7F4AB58CCB44E2FF66E36A26E59F55BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/00BD91C09868B2B26E32B5FB41A2583CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A1E441205EAE188E6F4319753E3982D3BD02851C2FB632864165FCA4920 46548.pygtex [222]) (./_minted-Tutorial/C3E382424C6F17EF8DB95D08D8AC9FEEBD02851C2FB632864165FCA4920 46548.pygtex) Excluding 'htmlonly' comment. [223 <./images/phylo-draw-example.p ng>] Overfull \hbox (19.85507pt too wide) in paragraph at lines 479--486 \OT1/cmr/m/n/10 For ex-am-ple, in a tree with clade names Foo1, Foo2 and Foo3, [][]\OT1/cmtt/m/n/10 tree.find_clades({"name": "Foo1"}) [224] Overfull \hbox (13.48741pt too wide) in paragraph at lines 534--537 []\OT1/cmr/m/n/10 Find each clade con-tain-ing a match-ing el-e-ment. That is, find each el-e-ment as with [][]\OT1/cmtt/m/n/10 find_elements[]\OT1/cmr/m/n/10 , [225] (./_minted-Tutorial/6AAB725DBD2E5B7C5FD79A9A16536BF69543DFECA235A69AE23006BA05B 4EB70.pygtex) [226] Overfull \hbox (15.04868pt too wide) in paragraph at lines 703--707 []\OT1/cmr/m/n/10 Below is an ex-am-ple on how to use a python script to in-ter -act with PhyML ([][]$\OT1/cmtt/m/n/10 http : / / www . atgc-[]montpellier . (./_minted-Tutorial/20AACD5E58630D4B64529F3A1ACD8119BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/EB4CA3626331FD00CE50FECC3590095BBD02851C2FB632864165FCA4920 46548.pygtex) [227] (./_minted-Tutorial/0702C9875263768417DD3ED2EF78755EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C395044A3DB827E8D2E36BA5259475D2BD02851C2FB632864165FCA4920 46548.pygtex) [228]) [229] (./Tutorial/chapter_motifs.tex Chapter 14. (./_minted-Tutorial/9344D5588F066D22473BF4F77E39E1F3BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/AB934E1AD357BE20BA1F223A29AE486ABD02851C2FB632864165FCA4920 46548.pygtex [230]) (./_minted-Tutorial/A7AAAF382950D3CAD77D17E6B6489D03BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CEBDE9089C5A4F125D8DD8D4E6ACD9C4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9293BA115F68336B4D0213D24C96AE75BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/BFC042DE8B1588B2D23A8510A608989CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5F3B74C4B4D1FF3D387E6F57F726D177BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0517D975CF92331B81AF837F9D257173BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C66E35936EA68A132264FDF63F70A42ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/86717C2BCE65F41FCDB8652763165857BD02851C2FB632864165FCA4920 46548.pygtex [231]) (./_minted-Tutorial/8572965E772BA3D97A5ACAB64A3CEA2BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0CFCBF886B5144440F79F61243192022BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/176227E746894D602FF7231BCB8E5F21BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/02A6CF1EA94D619AE2B9428BDA4531C5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/EDCE72CAE83814FFFF4AE6A97CBB2476BD02851C2FB632864165FCA4920 46548.pygtex) [232] (./_minted-Tutorial/C6095CA0913B3D01D81200EBA18DE7FA669566ECC2CFEDC7429F829576A D0DC6.pygtex [233]) (./_minted-Tutorial/2CAEA4D1EDEE84068D05546A212DB0C6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CD1D7AEBB145784C9665DAA472D55CE2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/30EDED7029501226C973943BBA0D1ECDBD02851C2FB632864165FCA4920 46548.pygtex [234]) (./_minted-Tutorial/5C8E141CD14F7220B986B96A3E564D14669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/95F985CC0D974FEE28E0B2667232BA3FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E778DA34B5EC9B33527CC22435275C76BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D11003572C5456D15CB1BF6CD74B860EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CD308858A86E4C77FD58BD7CFCB2EF92669566ECC2CFEDC7429F829576A D0DC6.pygtex [235]) (./_minted-Tutorial/4910FFD3FDCDF743F7F37BE10B04F706BD02851C2FB632864165FCA4920 46548.pygtex [236]) (./_minted-Tutorial/AF4CF0FDC0B4EBF46401E9953A293EF5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7D8B23E400A55050254232F7CA2CC9E1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0E771A916EB510C91DEEBFC8201442DCBD02851C2FB632864165FCA4920 46548.pygtex [237]) (./_minted-Tutorial/1C14559B3C7AC9C35B84F1518D8088FDBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/46FF514D13E6C4030C26EC4EFF8CFAFDBD02851C2FB632864165FCA4920 46548.pygtex [238]) (./_minted-Tutorial/8E9A5519710E4288CC6DA45EFD61B3AEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/47B231A79951117DFE8D7B369F5A0EDEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CF5314A9EF9BBFFA32CFF87ADC53C378BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/FD7EDF217AC860547FAAC456716F6D6BBD02851C2FB632864165FCA4920 46548.pygtex [239]) (./_minted-Tutorial/7EC0366BAB057E95DD30855AF8AD06F8669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/805B769BEA8271618919879EBC73D6AB669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/AD271A766709EB68A386A406C3E3DCB0669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/3C12150A1943B695BB045865F0A87E44669566ECC2CFEDC7429F829576A D0DC6.pygtex [240]) (./_minted-Tutorial/95318595464A829C3F1A431E3C76909FBD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (13.10551pt too wide) in paragraph at lines 603--606 \OT1/cmr/m/n/10 The [][]\OT1/cmtt/m/n/10 motifs.parse []\OT1/cmr/m/n/10 com-man d reads the com-plete file di-rectly, so you can close the file af-ter call-ing [][]\OT1/cmtt/m/n/10 motifs.parse[]\OT1/cmr/m/n/10 . (./_minted-Tutorial/147DE2DA7F37C2A5A1C1344033AB8B84BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/36E981BB5EF7EC3A1829EC830B0AF9C2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/22F78F0EFBBBF61FA3DB5795B5820CD7BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F87F681AD46E2F9ABF3B87ADA8B1EFB6BD02851C2FB632864165FCA4920 46548.pygtex [241]) (./_minted-Tutorial/CB1A766DCCC9D440884673396E012053BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/64B1E8E30714DF156170A704E0AF9B9E669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/744EE283B3B7A72BE718EF244D782CA7669566ECC2CFEDC7429F829576A D0DC6.pygtex [242]) (./_minted-Tutorial/BCCDFDD968CCC98039C6D6F4886917C1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/2F48F226FED2AEC7A54EAA6C769060B9BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9D8413811B6BC75226431D501B682BD9BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4293959D98D2DC2DC0CE6CA72DFD5D5CBD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: `h' float specifier changed to `ht'. [243] (./_minted-Tutorial/86BE687BF0F504548CFBA35246A755EFBD02851C2FB632864165FCA4920 46548.pygtex [244]) (./_minted-Tutorial/21510EFF9B5DA96F8CCEE8DFB8F26406BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7B5EBBADDB3E7B53C5C4AED82E42FFC4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0B25C484239457B0395121E60BF51495BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F8B39433E243DA74D8945D4CCEE70605BD02851C2FB632864165FCA4920 46548.pygtex [245]) (./_minted-Tutorial/46C8C36973CB3D67D276A48C8EA6FEE0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/99B6E6DD45FE4AED26044A4FD1A68C74BD02851C2FB632864165FCA4920 46548.pygtex [246]) (./_minted-Tutorial/001DF21D4EE824968A1A6CCAE41948EBBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5CBFAEFFA194A41048B5DAFCF4C98812BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E2EC88874CB26E442AD8A92E3073E225BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/176227E746894D602FF7231BCB8E5F21BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B9A36F2FAD2C11328984E7BBD1033E48BD02851C2FB632864165FCA4920 46548.pygtex [247]) (./_minted-Tutorial/31F98B5F648636905472A89ADB4396EABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6E38B20582EF8FBF09C0864F13C6172DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D36079E59E9C6C6FCEFB62B1C38D03DCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/949879BACF1AC9FDD5E01F1FDF5D0C7BBD02851C2FB632864165FCA4920 46548.pygtex [248]) (./_minted-Tutorial/CEF4EF7AD2559AA1A840E9E5F4F1E33EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8A4D3A313CCE21054A332F39A60F4F8DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8AC6389F07C07315B68A4843F8EC4A81BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CD7B5AA933F3E10D95D901D3BB5DA161BD02851C2FB632864165FCA4920 46548.pygtex) [249] (./_minted-Tutorial/21D3336F2855CBE535339D390FE18E25BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/33B5E369AD9661A05C861A5AE12A5092BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A80C26CD370CE20C0095D5E8948B4CA2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/34B3515117C70C6DAC332384F14FD0D0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6EC91D6C707FE27D0D4D730403C86073BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B3D49921528F0B11F6E5813C6062BEC5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3712C0CA690A1E7FF72D1693AABFE970BD02851C2FB632864165FCA4920 46548.pygtex [250]) (./_minted-Tutorial/4F50929124655BC08B3D6057B14984E5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DA79BC51C090F498913A417759345DF4BD02851C2FB632864165FCA4920 46548.pygtex [251]) (./_minted-Tutorial/4B2423E325126B67BF464F894752E322BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/25136DD7F6E2BE72E81866FB3F2A41C9BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/50111CA97C115B1826E19F91E69CE8BFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9E8A7295F5BEF290E7F4283BD7261603BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D5F089B3901176BD3F7658EA70DA2473BD02851C2FB632864165FCA4920 46548.pygtex [252]) (./_minted-Tutorial/753220AB94A0DA3FD9F8379D30465A7ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/35B38D8BFFB75E06C84D419CF8CBB21BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A6DBEC036FAC23CE4697722B836743C1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DF57AC6C176D67E4A7B147371D11BA16BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B593C755A27EDDCAF56E94C0930898D3BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/53BF343E6B63B739979E29182E1485D3BD02851C2FB632864165FCA4920 46548.pygtex) [253] (./_minted-Tutorial/868ABF9ABD2736A12F423306646D7706BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/912C817861E626118AB2FA06F12910B6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/62D830B5536F542C80973708E7B78A26BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4A6B49E72A96FB6AC93E0E280B4F4472669566ECC2CFEDC7429F829576A D0DC6.pygtex) [254] (./_minted-Tutorial/F99AB908B88D7B819F597C02D259A52BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CB4926B7151E97486270449C8F84AB41BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/852A3852541269829CE5DF380357F2CCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/AC8B7A8ADEC6FEB0B1260E665CF238B6BD02851C2FB632864165FCA4920 46548.pygtex) [255]) [256] (./Tutorial/chapter_cluster.tex Chapter 15. [257] [258] [259] [260] (./_minted-Tutorial/C7B59059E3AE6CDE790EFE6EB0ED4140BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C2B72A7408C7DF74DFCEBE0485997287BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/425EDAA643B5AA9589F3EEE601735827BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/50B5971EFCF22FCC4E1302DB2D0A25009543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/293084E63EA5C0E01F325A4DD59469C0BD02851C2FB632864165FCA4920 46548.pygtex [261]) Overfull \hbox (78.60634pt too wide) in paragraph at lines 245--246 \OT1/cmr/m/n/10 men-sions of these ar-rays are $[]$ if [][]\OT1/cmtt/m/n/10 tra nspose []\OT1/cmr/m/n/10 is [][]\OT1/cmtt/m/n/10 0[]\OT1/cmr/m/n/10 , or $[]$ (./_minted-Tutorial/05DC01C08B8EDF71F86E3C3A9C28EB34BD02851C2FB632864165FCA4920 46548.pygtex) [262] [263] (./_minted-Tutorial/A4A28B5A443208DEAB3B4D76AA3B762EBD02851C2FB632864165FCA4920 46548.pygtex) [264] (./_minted-Tutorial/C286E2777B917B774560CBDC7CF92626BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D04E097D8E8C4C039FEC20FA103CED189543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/36EF8931044EF448BC70F722AFADB43D9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/805B33438269C932AC54C0DAB5A3D7AC9543DFECA235A69AE23006BA05B 4EB70.pygtex) [265] [266] Overfull \hbox (16.73593pt too wide) in paragraph at lines 423--424 [][]\OT1/cmtt/m/n/10 distance []\OT1/cmr/m/n/10 is the dis-tance be-tween them. The items be-ing clus-tered are num-bered from 0 to $[]$, (./_minted-Tutorial/015798D317E9D8732518AFD186C997CABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A27E6BF4EEB8E8B1C239049267861739BD02851C2FB632864165FCA4920 46548.pygtex) [267] (./_minted-Tutorial/81E4060E427D22B8F0C63B69EEC10A2ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B8D2A546EC4941692F427A363193FBDEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A54EF6455421EFDFA1F63EB361CD74F6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8975A4CCBC4C6138C302117E04F203ADBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/636486BB1CF700F6391685224211BE22BD02851C2FB632864165FCA4920 46548.pygtex) [268] (./_minted-Tutorial/6EFE1AC811BF16FF597EBE3E25BD2F72BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F8E41E59FD44DADEB3740B0C0ED17D41BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1B924FC8FA13A8B73C1C9E6EF8895055BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/77B32E49165B4345FFCA9FACF597BEEBBD02851C2FB632864165FCA4920 46548.pygtex [269]) (./_minted-Tutorial/D04E097D8E8C4C039FEC20FA103CED189543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/36EF8931044EF448BC70F722AFADB43D9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/805B33438269C932AC54C0DAB5A3D7AC9543DFECA235A69AE23006BA05B 4EB70.pygtex) [270] (./_minted-Tutorial/E542C07D0131DF56A89D92F80416C175BD02851C2FB632864165FCA4920 46548.pygtex) [271] Overfull \hbox (106.77225pt too wide) in paragraph at lines 654--656 \OT1/cmr/m/n/10 An ar-ray with di-men-sions $[]$ if rows are be-ing clus-tered, or $[]$ (./_minted-Tutorial/7476A2D5F9D3A46EE00108837901FAEABD02851C2FB632864165FCA4920 46548.pygtex) [272] (./_minted-Tutorial/0420D397BA03971C0079F52E55FEABABBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8D3928D79091BFFA7AFB6D6F35A52C7CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4D59CC328F454A26A4BE9F91740D961CBD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (25.39864pt too wide) in paragraph at lines 739--750 [] [273] [274] (./_minted-Tutorial/EFB8602799AD543446B386107A8147F7BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/43B30B527C3A2D8148F25CA143719CAFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C77F1ABB31C6A53C1626E0E0B34BB0FCBD02851C2FB632864165FCA4920 46548.pygtex) [275] (./_minted-Tutorial/1F3E2EFB988F2639C701A920B547241DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3CAD921471DA4CA4441D02558CD1F2E0BD02851C2FB632864165FCA4920 46548.pygtex [276]) (./_minted-Tutorial/1A863BDE3A5754AA2C865F2A82DA8504BD02851C2FB632864165FCA4920 46548.pygtex) [277] Overfull \hbox (106.77225pt too wide) in paragraph at lines 929--931 \OT1/cmr/m/n/10 An ar-ray with di-men-sions $[]$ if rows are be-ing clus-tered, or $[]$ (./_minted-Tutorial/A39469F362670EDC6C7E8FD9FDF412C4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/12B5F20EFF78F0E8FE505D45A9786D70BD02851C2FB632864165FCA4920 46548.pygtex [278]) (./_minted-Tutorial/E6C8D570402CFDDB43A6AE5A198BCF58BD02851C2FB632864165FCA4920 46548.pygtex)) Overfull \hbox (26.21434pt too wide) in paragraph at lines 986--116 []\OT1/cmr/m/n/10 This will cre-ate the files [][]\OT1/cmtt/m/n/10 cyano_result _K_G2_A2.cdt[]\OT1/cmr/m/n/10 , [][]\OT1/cmtt/m/n/10 cyano_result_K_G2.kgg[]\OT 1/cmr/m/n/10 , and [][]\OT1/cmtt/m/n/10 cyano_result_K_A2.kag[]\OT1/cmr/m/n/10 . [279] (./Tutorial/chapter_learning.tex Chapter 16. [280] (./_minted-Tutorial/A66CDD6792A98054D498A97A3A920D4DBD02851C2FB632864165FCA4920 46548.pygtex [281]) (./_minted-Tutorial/390D9013E6AF7385E3C5A71EC44014AABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/9153ABDB5D850EC42F344B9B42C10E4FBD02851C2FB632864165FCA4920 46548.pygtex [282]) (./_minted-Tutorial/183EBB0903E699FF7289E5FDA71CB096BD02851C2FB632864165FCA4920 46548.pygtex [283]) (./_minted-Tutorial/7E494FD25838EE4C9E476EBA48BDF0CEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B53BAB1CC7569CE8ADFECF2CFC02D402BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0201F5A7D34B6F74CAF2C8723DA28C0ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/906DB90E50544D69A8A7FA2703E3A012BD02851C2FB632864165FCA4920 46548.pygtex [284]) Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 267. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 267. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 275. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 275. (./_minted-Tutorial/AE2B91C0366D79644B870EB1EB9436E6BD02851C2FB632864165FCA4920 46548.pygtex) [285] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 287. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 287. (./_minted-Tutorial/B35CDBE12860937BD1F854583E7BA595BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B38BF6A3D910590D450B331A075B723CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E59729DAB9242AE915A0943E44B8DF9BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/AEF267C3082CB68394DCEE656CEB2FC1BD02851C2FB632864165FCA4920 46548.pygtex [286]) (./_minted-Tutorial/A38355D92EE3DC8D96655428C0CEDC15BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A586FFDD9483C890754DBE5DFC420710BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8F9899A476407D923F0AEB91D4FF3D35BD02851C2FB632864165FCA4920 46548.pygtex [287])) [288] (./Tutorial/chapter_graphics.tex Chapter 17. [289] (./_minted-Tutorial/775A7C8BD2C1E8942CA7A717928F51A09543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/997BE59EDA00B2D427337713C8A7E3D99543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/684A3C9C1713469B78289C6B9952D8169543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/F1FF3DF6D6F3CDAA260F74B59EE3502F9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/864F43F6883D29AB2276A3D7B4C4B0359543DFECA235A69AE23006BA05B 4EB70.pygtex) Excluding 'htmlonly' comment. (./_minted-Tutorial/F52EB727435E5F7D4D3C22DD13755CA79543DFECA235A69AE23006BA05B 4EB70.pygtex [290]) Excluding 'htmlonly' comment. (./_minted-Tutorial/68BE5A2D2503535D27E3B265B36AB36E9543DFECA235A69AE23006BA05B 4EB70.pygtex [291 <./images/plasmid_linear.png (PNG copy)>]) [292 <./images/pla smid_circular.png (PNG copy)>] (./_minted-Tutorial/ECF4549C3ED9BED5D89616D96689FF279543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/F6FC21242AEF7E7CBB38249DA932A7359543DFECA235A69AE23006BA05B 4EB70.pygtex) Excluding 'htmlonly' comment. (./_minted-Tutorial/E9061B00D3D1F94D19518B622458CA8B9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/869D4007B198B35A03870134DB69E5F29543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/83AFE18710C133D7AFEBCF65D9D3D8509543DFECA235A69AE23006BA05B 4EB70.pygtex [293]) Excluding 'htmlonly' comment. (./_minted-Tutorial/7767B7CE8DD842D17DB77A8BF9691B949543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/B7F9EB41E9BA682D9273C414D13CA80C9543DFECA235A69AE23006BA05B 4EB70.pygtex [294] [295 <./images/GD_sigil_labels.png (PNG copy)>]) Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. (./_minted-Tutorial/6EE3865BBB66BBD15ABFD7BAE73F8FEB9543DFECA235A69AE23006BA05B 4EB70.pygtex) Excluding 'htmlonly' comment. (./_minted-Tutorial/74C150D1D11511477A4CD9DC0CD7863A9543DFECA235A69AE23006BA05B 4EB70.pygtex) Excluding 'htmlonly' comment. (./_minted-Tutorial/2216BF82E557F1E99146777612D2BA8F9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/67B3F646AA5F8690151428081229D39B9543DFECA235A69AE23006BA05B 4EB70.pygtex [296] [297 <./images/GD_sigils.png>] [298 <./images/GD_sigil_arrow _shafts.png>] [299 <./images/GD_sigil_arrow_heads.png>] [300]) Excluding 'htmlonly' comment. [301 <./images/plasmid_linear_nice.png (PNG copy) >] [302 <./images/plasmid_circular_nice.png>] (./_minted-Tutorial/7CAF22FEDE98A6B9B7990010CA8709DC9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/FA676816242752C9FE9F5EB12D4DAA899543DFECA235A69AE23006BA05B 4EB70.pygtex [303]) (./_minted-Tutorial/7926619D7609A591C404A01B2A99177A9543DFECA235A69AE23006BA05B 4EB70.pygtex [304]) Excluding 'htmlonly' comment. [305 <./images/three_track_si mple.png>] (./_minted-Tutorial/A2465D4E8908256A31684D5DDE7DA1119543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/347EB36A3001532221DDF6C29AA04AFB9543DFECA235A69AE23006BA05B 4EB70.pygtex [306]) (./_minted-Tutorial/F46F39DD7A8EC7B20CD42ACF6EFD18409543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/2CF2D2FC7E96B3F426F22452724A4C289543DFECA235A69AE23006BA05B 4EB70.pygtex) Overfull \hbox (2.65141pt too wide) in paragraph at lines 873--879 []\OT1/cmr/m/n/10 There are sev-eral im-por-tant pieces to this code. First the [][]\OT1/cmtt/m/n/10 GenomeDiagram []\OT1/cmr/m/n/10 ob-ject has a [][]\OT1/cm tt/m/n/10 cross_track_links Excluding 'htmlonly' comment. [307] Excluding 'htmlonly' comment. [308 <./image s/three_track_cl.png>] [309 <./images/three_track_cl2a.png>] (./_minted-Tutorial/F9FFB9659EC22BC166AEB6F7284149779543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/A9695DE54C455E13B400269BF9F424FE9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/F545B5C3D394029AA34E76D27DC2DBAF9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/3BACFFDF9009929D690C44BF09EFB67F9543DFECA235A69AE23006BA05B 4EB70.pygtex) [310] (./_minted-Tutorial/0AC11BF466D4AA0B0536F05378BEC9CC9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/F5380F7F462C2A51219D9EF8994C192C9543DFECA235A69AE23006BA05B 4EB70.pygtex [311] [312 <./images/simple_chrom.pdf> <./images/tRNA_chrom.pdf>]) Excluding 'htmlonly' comment. (./_minted-Tutorial/7B75AD289117B9F25E36C48BBFCB0A759543DFECA235A69AE23006BA05B 4EB70.pygtex [313]) Excluding 'htmlonly' comment.) [314] (./Tutorial/chapter_kegg.tex Chapter 18. (./_minted-Tutorial/27731B46F813E809C1F5AB60C050CD4ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4FAF7CA55B5CBF29D4D0569020062C71BD02851C2FB632864165FCA4920 46548.pygtex) [315] (./_minted-Tutorial/39B217C0E81B95398ED4BBC9D1B0F5CCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D9724C7E513E9BF6FDCCF6A64359AD4B9543DFECA235A69AE23006BA05B 4EB70.pygtex [316]) (./_minted-Tutorial/64868CEDE925B08BA4840E27792F9C95669566ECC2CFEDC7429F829576A D0DC6.pygtex)) [317] (./Tutorial/chapter_phenotype.tex Chapter 19. (./_minted-Tutorial/252224E77AA1520CEA1F05EB2C082F8DBD02851C2FB632864165FCA4920 46548.pygtex) [318] (./_minted-Tutorial/1742F69ECDDF3F5D15E6B5DBFEFA9721BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4835A2D15014EC539B36FCA111ABBB44BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/FD6100DF6B4884776EB70DBE176DB081BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/943877B8F1F5B9C773FB1AA7B24E159EBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0BDF372B652AEF5EA570E28DA8244BF8BD02851C2FB632864165FCA4920 46548.pygtex [319]) (./_minted-Tutorial/BE8D8FA0E8D3D6C871BF41D7B5DEB51DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/290D0631491AEE7E10A3CE09C85D7206BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/EA2967473FD2864501AEB5123E3D579DBD02851C2FB632864165FCA4920 46548.pygtex [320]) (./_minted-Tutorial/AEDB3BBBBA5C2503EDA86617E0872188BD02851C2FB632864165FCA4920 46548.pygtex [321]) (./_minted-Tutorial/43A346E75A27D33FDB3F346C240E06E6BD02851C2FB632864165FCA4920 46548.pygtex)) [322] (./Tutorial/chapter_cookbook.tex Chapter 20. (./_minted-Tutorial/D080533227BF139CB7F7C56D06E7D6EB9543DFECA235A69AE23006BA05B 4EB70.pygtex [323]) (./_minted-Tutorial/CA0835D76EF6887731674D8AB555091B9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/1F5CA35662EA2CAC7BDBA9D33CDB13A0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A3BD1DBCF883DB2E1DD394B912E57164BD02851C2FB632864165FCA4920 46548.pygtex) [324] (./_minted-Tutorial/C6B2C783E94EA95E84DF3F108F727AD4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/EC0DF654B46A2F2CE5F2C795E0321ED29543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/19A3D00CDA3CDDA100F55F41BCAAF54F9543DFECA235A69AE23006BA05B 4EB70.pygtex [325]) (./_minted-Tutorial/FF8E30AFA718C8DC6288D5C9AD354F649543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/019E169CFF67EC7D891D6A02396470619543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/9CFE18F499906D88CC2737F15500C03B9543DFECA235A69AE23006BA05B 4EB70.pygtex [326]) (./_minted-Tutorial/C2311B95BFB64D51B766D16ACEF028DD9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/D6A48411D1CBD21E55ABF85BFBC655419543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/7448CA91BF0AA6E19C1517B6DE4087939543DFECA235A69AE23006BA05B 4EB70.pygtex) [327] (./_minted-Tutorial/C3FBD2FC664129F7A578076AD05E79D99543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/38576C78990D3D95691E2AC6EB80ABA29543DFECA235A69AE23006BA05B 4EB70.pygtex) [328] (./_minted-Tutorial/D08928CA73DF435476A35E8ADF6418319543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/D51441AC892832CAA5031DFFA5F354509543DFECA235A69AE23006BA05B 4EB70.pygtex) Overfull \hbox (5.83499pt too wide) in paragraph at lines 454--458 \OT1/cmr/m/n/10 mat (e.g. FASTA files). How-ever, for large FASTQ files it woul d be faster the low-level [][]\OT1/cmtt/m/n/10 FastqGeneralIterator (./_minted-Tutorial/AB16E58608A2F17CC79E6929557208879543DFECA235A69AE23006BA05B 4EB70.pygtex [329]) Overfull \hbox (4.57849pt too wide) in paragraph at lines 475--477 \OT1/cmr/m/n/10 That should find $13819$ reads from \OT1/cmtt/m/n/10 SRR014849. fastq \OT1/cmr/m/n/10 and save them to a new FASTQ file, \OT1/cmtt/m/n/10 with[ ]primer.fastq\OT1/cmr/m/n/10 . (./_minted-Tutorial/6D336A88208F39729D1A90FF60CB5EBD9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/2C62FFE33ECD45881AC7A8296BCCA5569543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/7E077104A49653CA66AAC778C604E64A9543DFECA235A69AE23006BA05B 4EB70.pygtex [330]) (./_minted-Tutorial/ECD311074B098CDA38E7451A88AC0F9C9543DFECA235A69AE23006BA05B 4EB70.pygtex) [331] (./_minted-Tutorial/CC6E723850600015A2C6BAC6C88F89159543DFECA235A69AE23006BA05B 4EB70.pygtex) [332] (./_minted-Tutorial/1E88A30624397E1FA5202CD67F078C319543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/55F15E0B4613AC1B2AC177DC407373679543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/C6B1FCFF3C4616196F6CE060D97D2587BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7B877C459BB3438E40CD76B614F605B69543DFECA235A69AE23006BA05B 4EB70.pygtex [333]) (./_minted-Tutorial/C47681A25A04F989A9657602F996D5B59543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/20E6EE0734FD2ED211933BE632478CAB9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/BF6F632251CC051592D2BE57B36A38A09543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/C8587EE0D03D0937B88179912FC3582EBD02851C2FB632864165FCA4920 46548.pygtex [334]) (./_minted-Tutorial/7F8C2BBB4F26A8E6A0FD7BCC41E2BB80BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/FCE533CC3550AB6D1B3C6F6ED53E0CEBBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/37A86DCC1F181ADAA1855D9EBC303BAC44BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/474B445E26A3CD55A1BA5820E4D03C7DBD02851C2FB632864165FCA4920 46548.pygtex [335]) (./_minted-Tutorial/DDBEEE137CB936CA422E560A63FB97B8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B802763B27D7694A759DB2EBF16EF098BD02851C2FB632864165FCA4920 46548.pygtex) [336] (./_minted-Tutorial/EE9671DEE2B114F544A5881F074C33B29543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/5A7FB5AC8923F9582CAE20A770A63052669566ECC2CFEDC7429F829576A D0DC6.pygtex [337]) (./_minted-Tutorial/8F229FE70B397EEE7D48ECD1D5BAD1CCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/71434DB3B51372DFED40CEB6F06647B79543DFECA235A69AE23006BA05B 4EB70.pygtex [338]) Excluding 'htmlonly' comment. Overfull \hbox (4.00363pt too wide) in paragraph at lines 1117--1120 []\OT1/cmr/m/it/10 Tip: \OT1/cmr/m/n/10 Rather than us-ing [][]\OT1/cmtt/m/n/10 pylab.show() []\OT1/cmr/m/n/10 to show the plot in a win-dow, you can also use [][]\OT1/cmtt/m/n/10 pylab.savefig(...) (./_minted-Tutorial/798776F436EA559BACD9C305C09973919543DFECA235A69AE23006BA05B 4EB70.pygtex [339 <./images/hist_plot.png>]) (./_minted-Tutorial/CB78AD94DFE82ADBAF348C0EC1D261CD9543DFECA235A69AE23006BA05B 4EB70.pygtex) Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. [340 <./images/gc_plot.png>] (./_minted-Tutorial/6E0DA723E11A7B9CA8E2353A984B5DF79543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/80A47C8780CE3021D53829563E8166569543DFECA235A69AE23006BA05B 4EB70.pygtex [341 <./images/dot_plot.png>]) (./_minted-Tutorial/9574E55C4A182E2A0201DF18689F52F49543DFECA235A69AE23006BA05B 4EB70.pygtex) Excluding 'htmlonly' comment. (./_minted-Tutorial/24C65C38DAD936B7AA15C7ED02EA36B39543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/6655B5CD97C33186A22E6897501301FF9543DFECA235A69AE23006BA05B 4EB70.pygtex [342]) (./_minted-Tutorial/7727E7020AA1BDC4C2A426B7590C20AD9543DFECA235A69AE23006BA05B 4EB70.pygtex) Excluding 'htmlonly' comment. [343 <./images/dot_plot_scatter.png >] (./_minted-Tutorial/601CCA4B782F1DA528DB81B0248031959543DFECA235A69AE23006BA05B 4EB70.pygtex) Excluding 'htmlonly' comment. (./_minted-Tutorial/9D2779E6D02C00C016A7A73A452EBC739543DFECA235A69AE23006BA05B 4EB70.pygtex) [344] (./_minted-Tutorial/06CAA397021B5D0CD904B7CF0209DCA39543DFECA235A69AE23006BA05B 4EB70.pygtex) [345 <./images/SRR001666.png>] (./_minted-Tutorial/16711B0A63F93BBACAF3C86CFFB7BEFA669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/96EC77291C119EF69670ACDB1C35CE21669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/6C14F4F0692168BA7165351C706B643D9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/E686FC2D122CF1560FAF4512CD53777F9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/E09A8EBF1B7CB9F831FC2D9DA48145359543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/E598995EF885D7803642E8685DCB8F90669566ECC2CFEDC7429F829576A D0DC6.pygtex) Overfull \hbox (49.0755pt too wide) in paragraph at lines 1528--1529 []\OT1/cmr/m/n/10 You can ac-cess any el-e-ment of the PSSM by sub-script-ing l ike [][]\OT1/cmtt/m/n/10 your_pssm[sequence_number][residue_count_name][]\OT1/c mr/m/n/10 . (./_minted-Tutorial/7F027F6FD8E839F99A1077399D9B8EFFBD02851C2FB632864165FCA4920 46548.pygtex [346]) (./_minted-Tutorial/25AF2FA7C23EEF982CD3578DCB5300659543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/7662755469082A25B2A4B53656D96A409543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/EA8748814B0C57E7E4D7F8619D00D0439543DFECA235A69AE23006BA05B 4EB70.pygtex [347]) (./_minted-Tutorial/99476F758194110AC0ED8AAAFD8ECB7C9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/504DC4F75F719CFF95C5294B2961C973BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/486C8450148EF1EADB63A41AB9A896FABD02851C2FB632864165FCA4920 46548.pygtex [348]) (./_minted-Tutorial/DD48495FAB2341AA078121E9286C0717BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DE31628D815724B7B422A1012BAA0C37BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5740381D1C5E453AC66BA80B49407915BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/19B054992CCA481AA19D78F9C6DD93BFBD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (13.15053pt too wide) in paragraph at lines 1703--1704 \OT1/cmr/m/n/10 two [][]\OT1/cmtt/m/n/10 residue_frequencies []\OT1/cmr/m/n/10 val-ues mul-ti-plied with each other. For ex-am-ple, [][]\OT1/cmtt/m/n/10 expec ted_frequencies[^^MD^^M, ^^ME^^M] (./_minted-Tutorial/40ECF2E139F38209730D3B02B624EF74BD02851C2FB632864165FCA4920 46548.pygtex [349]) (./_minted-Tutorial/8965C8E87A0A43ECCE216C12F7DE7A4FBD02851C2FB632864165FCA4920 46548.pygtex)) [350] (./Tutorial/chapter_testing.tex Chapter 21. (./_minted-Tutorial/867AD481B37AFD4F1A17FC0F2F42FCAE44BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/E8078015A2C53794A733DDC875BD062144BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/754EBE4BCCE307413E74F18728530D0444BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/E40D6903CCE8EA230C75C80B7C2D907344BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/7A0DBB9735CDAA1699A6FA164701062F44BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/BC243371043473AEE20C23FF0FABFF0D44BBF456F55B5DC060035246D76 9EADB.pygtex) Overfull \hbox (39.35472pt too wide) in paragraph at lines 73--77 []\OT1/cmr/m/n/10 Tests based on Python's stan-dard [][]\OT1/cmtt/m/n/10 unitte st []\OT1/cmr/m/n/10 frame-work will [][]\OT1/cmtt/m/n/10 import unittest []\OT 1/cmr/m/n/10 and then de-fine [][]\OT1/cmtt/m/n/10 unittest.TestCase [351] (./_minted-Tutorial/9373056942403CCACDB96B0F438E4B64669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/2A1F0B8D037B993D748BF652420448ED44BBF456F55B5DC060035246D76 9EADB.pygtex [352]) (./_minted-Tutorial/61465735FDB5BC7ADF12D7A4628FC9A79543DFECA235A69AE23006BA05B 4EB70.pygtex) [353] (./_minted-Tutorial/826F7B9143F73D7CFCAB00906377DAB99543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/B1E279D3993E4775FBE4555B6DD342AD44BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/313C740A73E814DA220EB71149FE706E9543DFECA235A69AE23006BA05B 4EB70.pygtex [354]) (./_minted-Tutorial/99DA0A53F2BD41D9D1BCE2B0332444F444BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/4916E014295B56C6CDDB3C287542DA299543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/1B0AB11BDA71CF4763A5A4A8B82977119543DFECA235A69AE23006BA05B 4EB70.pygtex [355]) (./_minted-Tutorial/7A0DBB9735CDAA1699A6FA164701062F44BBF456F55B5DC060035246D76 9EADB.pygtex) [356] (./_minted-Tutorial/3E57444149EF1ACC12DA2995F5B0345644BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/DD3A1A642CB850F292FC934F9336EC4344BBF456F55B5DC060035246D76 9EADB.pygtex)) [357] (./Tutorial/chapter_contributing.tex Chapter 22. [358] (./_minted-Tutorial/7713FA97EA16E9508BA3E6B94494492544BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/61D19A91BF1A1F95030292E40EF87A3644BBF456F55B5DC060035246D76 9EADB.pygtex) [359]) [360] (./Tutorial/chapter_appendix.tex Chapter 23. (./_minted-Tutorial/109DA6882E9B770A79B0E47E5D014D32BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D8DF7F2BE4A1010E81F7C5AD3A4628599543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/268983882DD871BC94F164D025D08B429543DFECA235A69AE23006BA05B 4EB70.pygtex [361]) (./_minted-Tutorial/940D9D0165FD2273E52C2D203CE26C429543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/4B521F4803AD1FD3B86D09A2ECD5A203BD02851C2FB632864165FCA4920 46548.pygtex)) [362] [363] [364] [365] (./Tutorial.aux (./Tutorial/chapter_introduction.aux) (./Tutorial/chapter_quick_start.aux) (./Tutorial/chapter_seq_objects.aux) (./Tutorial/chapter_seq_annot.aux) (./Tutorial/chapter_seqio.aux) (./Tutorial/chapter_align.aux) (./Tutorial/chapter_blast.aux) (./Tutorial/chapter_searchio.aux) (./Tutorial/chapter_entrez.aux) (./Tutorial/chapter_uniprot.aux) (./Tutorial/chapter_pdb.aux) (./Tutorial/chapter_popgen.aux) (./Tutorial/chapter_phylo.aux) (./Tutorial/chapter_motifs.aux) (./Tutorial/chapter_cluster.aux) (./Tutorial/chapter_learning.aux) (./Tutorial/chapter_graphics.aux) (./Tutorial/chapter_kegg.aux) (./Tutorial/chapter_phenotype.aux) (./Tutorial/chapter_cookbook.aux) (./Tutorial/chapter_testing.aux) (./Tutorial/chapter_contributing.aux) (./Tutorial/chapter_appendix.aux)) LaTeX Warning: There were undefined references. LaTeX Warning: There were multiply-defined labels. ) (see the transcript file for additional information) < /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb> Output written on Tutorial.pdf (366 pages, 2520424 bytes). Transcript written on Tutorial.log. pdflatex biopdb_faq.tex This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./biopdb_faq.tex LaTeX2e <2022-11-01> patch level 1 L3 programming layer <2023-01-16> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2022/07/02 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/bookman.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pbk.fd)) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def)) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/generic/iftex/ifvtex.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty)) (/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 56. (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf)) (/usr/share/texlive/texmf-dist/tex/generic/babel/locale/en/babel-english.tex) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) No file biopdb_faq.aux. *geometry* driver: auto-detecting *geometry* detected driver: pdftex *geometry* verbose mode - [ preamble ] result: * driver: pdftex * paper: a4paper * layout: * layoutoffset:(h,v)=(0.0pt,0.0pt) * modes: * h-part:(L,W,R)=(89.62709pt, 418.25368pt, 89.6271pt) * v-part:(T,H,B)=(56.9055pt, 731.23584pt, 56.9055pt) * \paperwidth=597.50787pt * \paperheight=845.04684pt * \textwidth=418.25368pt * \textheight=731.23584pt * \oddsidemargin=17.3571pt * \evensidemargin=17.3571pt * \topmargin=-52.36449pt * \headheight=12.0pt * \headsep=25.0pt * \topskip=10.0pt * \footskip=30.0pt * \marginparwidth=65.0pt * \marginparsep=11.0pt * \columnsep=10.0pt * \skip\footins=9.0pt plus 4.0pt minus 2.0pt * \hoffset=0.0pt * \voffset=0.0pt * \mag=1000 * \@twocolumnfalse * \@twosidefalse * \@mparswitchfalse * \@reversemarginfalse * (1in=72.27pt=25.4mm, 1cm=28.453pt) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) Overfull \hbox (40.90678pt too wide) in paragraph at lines 112--119 []\T1/pbk/l/n/10 However, the [][]\T1/pcr/m/n/10 Bio.PDB.mmCIF.MMCIFlex []\T1/p bk/l/n/10 mod-ule (used in-ter-nally by [][]\T1/pcr/m/n/10 Bio.PDB.MMCIFParser [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pbk.fd) [2] Overfull \hbox (21.75009pt too wide) in paragraph at lines 271--276 \T1/pbk/l/n/10 file to their val-ues. If there are mul-ti-ple val-ues (like in the case of tag \T1/pcr/m/n/10 _atom_site.Cartn_y\T1/pbk/l/n/10 , [3] Overfull \hbox (13.9754pt too wide) in paragraph at lines 312--318 \T1/pbk/l/n/10 The avail-able keys are \T1/pcr/m/n/10 name, head, deposition_-d ate, release_-date, structure_- Overfull \hbox (11.71707pt too wide) in paragraph at lines 312--318 \T1/pcr/m/n/10 method, resolution, structure_-reference \T1/pbk/l/n/10 (maps to a list of ref-er-ences), \T1/pcr/m/n/10 journal_- LaTeX Warning: Reference `sub:The-Structure-object' on page 4 undefined on inpu t line 335. [4] [5] LaTeX Warning: Reference `cap:SMCRA' on page 6 undefined on input line 548. [6] [7 <./images/smcra.png (PNG copy)>] [8] LaTeX Warning: Reference `cap:SMCRA' on page 9 undefined on input line 750. LaTeX Warning: Reference `cap:SMCRA' on page 9 undefined on input line 779. LaTeX Warning: Reference `sub:Analysis' on page 9 undefined on input line 821. [9] LaTeX Warning: Reference `sub:Analysis' on page 10 undefined on input line 826. [10] Overfull \hbox (45.08351pt too wide) in paragraph at lines 1012--1016 \T1/pbk/l/n/10 Note that in the above case only model 0 of the struc-ture is co n-sid-ered by \T1/pcr/m/n/10 PolypeptideBuilder\T1/pbk/l/n/10 . Overfull \hbox (10.80998pt too wide) in paragraph at lines 1020--1024 \T1/pbk/l/n/10 try). The se-quence of each polypep-tide can then eas-ily be ob- tained from the \T1/pcr/m/n/10 Polypeptide [11] LaTeX Warning: Reference `cap:DSSP-codes' on page 12 undefined on input line 10 41. [12] Overfull \hbox (87.74638pt too wide) in paragraph at lines 1148--1149 []\T1/pcr/m/n/10 # Calculate classical coordination number exp_fs=hse.calc_fs_e xposure(model) Overfull \hbox (20.6135pt too wide) in paragraph at lines 1169--1174 \T1/pcr/m/n/10 Atom \T1/pbk/l/n/10 ob-jects re-turn a \T1/pcr/m/n/10 Vector \T1 /pbk/l/n/10 ob-ject rep-re-sen-ta-tion of the co-or-di-nates with the \T1/pcr/m /n/10 get_vector [13] [14] Overfull \hbox (1.21811pt too wide) in paragraph at lines 1345--1353 []\T1/pbk/l/n/10 THE CON-TRIB-U-TORS AND COPY-RIGHT HOLD-ERS OF THIS SOFT-WARE DIS-CLAIM [15] (./biopdb_faq.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. Package rerunfilecheck Warning: File `biopdb_faq.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on biopdb_faq.pdf (15 pages, 163380 bytes). Transcript written on biopdb_faq.log. pdflatex biopdb_faq.tex This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./biopdb_faq.tex LaTeX2e <2022-11-01> patch level 1 L3 programming layer <2023-01-16> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2022/07/02 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/bookman.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pbk.fd)) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def)) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/generic/iftex/ifvtex.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty)) (/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 56. (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf)) (/usr/share/texlive/texmf-dist/tex/generic/babel/locale/en/babel-english.tex) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./biopdb_faq.aux) *geometry* driver: auto-detecting *geometry* detected driver: pdftex *geometry* verbose mode - [ preamble ] result: * driver: pdftex * paper: a4paper * layout: * layoutoffset:(h,v)=(0.0pt,0.0pt) * modes: * h-part:(L,W,R)=(89.62709pt, 418.25368pt, 89.6271pt) * v-part:(T,H,B)=(56.9055pt, 731.23584pt, 56.9055pt) * \paperwidth=597.50787pt * \paperheight=845.04684pt * \textwidth=418.25368pt * \textheight=731.23584pt * \oddsidemargin=17.3571pt * \evensidemargin=17.3571pt * \topmargin=-52.36449pt * \headheight=12.0pt * \headsep=25.0pt * \topskip=10.0pt * \footskip=30.0pt * \marginparwidth=65.0pt * \marginparsep=11.0pt * \columnsep=10.0pt * \skip\footins=9.0pt plus 4.0pt minus 2.0pt * \hoffset=0.0pt * \voffset=0.0pt * \mag=1000 * \@twocolumnfalse * \@twosidefalse * \@mparswitchfalse * \@reversemarginfalse * (1in=72.27pt=25.4mm, 1cm=28.453pt) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx)) (./biopdb_faq.out) (./biopdb_faq.out) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) Overfull \hbox (40.90678pt too wide) in paragraph at lines 112--119 []\T1/pbk/l/n/10 However, the [][]\T1/pcr/m/n/10 Bio.PDB.mmCIF.MMCIFlex []\T1/p bk/l/n/10 mod-ule (used in-ter-nally by [][]\T1/pcr/m/n/10 Bio.PDB.MMCIFParser [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pbk.fd) [2] Overfull \hbox (21.75009pt too wide) in paragraph at lines 271--276 \T1/pbk/l/n/10 file to their val-ues. If there are mul-ti-ple val-ues (like in the case of tag \T1/pcr/m/n/10 _atom_site.Cartn_y\T1/pbk/l/n/10 , [3] Overfull \hbox (13.9754pt too wide) in paragraph at lines 312--318 \T1/pbk/l/n/10 The avail-able keys are \T1/pcr/m/n/10 name, head, deposition_-d ate, release_-date, structure_- Overfull \hbox (11.71707pt too wide) in paragraph at lines 312--318 \T1/pcr/m/n/10 method, resolution, structure_-reference \T1/pbk/l/n/10 (maps to a list of ref-er-ences), \T1/pcr/m/n/10 journal_- [4] [5] [6] [7 <./images/smcra.png (PNG copy)>] [8] [9] [10] Overfull \hbox (45.08351pt too wide) in paragraph at lines 1012--1016 \T1/pbk/l/n/10 Note that in the above case only model 0 of the struc-ture is co n-sid-ered by \T1/pcr/m/n/10 PolypeptideBuilder\T1/pbk/l/n/10 . Overfull \hbox (10.80998pt too wide) in paragraph at lines 1020--1024 \T1/pbk/l/n/10 try). The se-quence of each polypep-tide can then eas-ily be ob- tained from the \T1/pcr/m/n/10 Polypeptide [11] [12] Overfull \hbox (87.74638pt too wide) in paragraph at lines 1148--1149 []\T1/pcr/m/n/10 # Calculate classical coordination number exp_fs=hse.calc_fs_e xposure(model) Overfull \hbox (20.6135pt too wide) in paragraph at lines 1169--1174 \T1/pcr/m/n/10 Atom \T1/pbk/l/n/10 ob-jects re-turn a \T1/pcr/m/n/10 Vector \T1 /pbk/l/n/10 ob-ject rep-re-sen-ta-tion of the co-or-di-nates with the \T1/pcr/m /n/10 get_vector [13] [14] Overfull \hbox (1.21811pt too wide) in paragraph at lines 1345--1353 []\T1/pbk/l/n/10 THE CON-TRIB-U-TORS AND COPY-RIGHT HOLD-ERS OF THIS SOFT-WARE DIS-CLAIM [15] (./biopdb_faq.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on biopdb_faq.pdf (15 pages, 165295 bytes). Transcript written on biopdb_faq.log. pdflatex biopdb_faq.tex This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./biopdb_faq.tex LaTeX2e <2022-11-01> patch level 1 L3 programming layer <2023-01-16> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2022/07/02 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/bookman.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pbk.fd)) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def)) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/generic/iftex/ifvtex.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty)) (/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 56. (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf)) (/usr/share/texlive/texmf-dist/tex/generic/babel/locale/en/babel-english.tex) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./biopdb_faq.aux) *geometry* driver: auto-detecting *geometry* detected driver: pdftex *geometry* verbose mode - [ preamble ] result: * driver: pdftex * paper: a4paper * layout: * layoutoffset:(h,v)=(0.0pt,0.0pt) * modes: * h-part:(L,W,R)=(89.62709pt, 418.25368pt, 89.6271pt) * v-part:(T,H,B)=(56.9055pt, 731.23584pt, 56.9055pt) * \paperwidth=597.50787pt * \paperheight=845.04684pt * \textwidth=418.25368pt * \textheight=731.23584pt * \oddsidemargin=17.3571pt * \evensidemargin=17.3571pt * \topmargin=-52.36449pt * \headheight=12.0pt * \headsep=25.0pt * \topskip=10.0pt * \footskip=30.0pt * \marginparwidth=65.0pt * \marginparsep=11.0pt * \columnsep=10.0pt * \skip\footins=9.0pt plus 4.0pt minus 2.0pt * \hoffset=0.0pt * \voffset=0.0pt * \mag=1000 * \@twocolumnfalse * \@twosidefalse * \@mparswitchfalse * \@reversemarginfalse * (1in=72.27pt=25.4mm, 1cm=28.453pt) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx)) (./biopdb_faq.out) (./biopdb_faq.out) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) Overfull \hbox (40.90678pt too wide) in paragraph at lines 112--119 []\T1/pbk/l/n/10 However, the [][]\T1/pcr/m/n/10 Bio.PDB.mmCIF.MMCIFlex []\T1/p bk/l/n/10 mod-ule (used in-ter-nally by [][]\T1/pcr/m/n/10 Bio.PDB.MMCIFParser [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pbk.fd) [2] Overfull \hbox (21.75009pt too wide) in paragraph at lines 271--276 \T1/pbk/l/n/10 file to their val-ues. If there are mul-ti-ple val-ues (like in the case of tag \T1/pcr/m/n/10 _atom_site.Cartn_y\T1/pbk/l/n/10 , [3] Overfull \hbox (13.9754pt too wide) in paragraph at lines 312--318 \T1/pbk/l/n/10 The avail-able keys are \T1/pcr/m/n/10 name, head, deposition_-d ate, release_-date, structure_- Overfull \hbox (11.71707pt too wide) in paragraph at lines 312--318 \T1/pcr/m/n/10 method, resolution, structure_-reference \T1/pbk/l/n/10 (maps to a list of ref-er-ences), \T1/pcr/m/n/10 journal_- [4] [5] [6] [7 <./images/smcra.png (PNG copy)>] [8] [9] [10] Overfull \hbox (45.08351pt too wide) in paragraph at lines 1012--1016 \T1/pbk/l/n/10 Note that in the above case only model 0 of the struc-ture is co n-sid-ered by \T1/pcr/m/n/10 PolypeptideBuilder\T1/pbk/l/n/10 . Overfull \hbox (10.80998pt too wide) in paragraph at lines 1020--1024 \T1/pbk/l/n/10 try). The se-quence of each polypep-tide can then eas-ily be ob- tained from the \T1/pcr/m/n/10 Polypeptide [11] [12] Overfull \hbox (87.74638pt too wide) in paragraph at lines 1148--1149 []\T1/pcr/m/n/10 # Calculate classical coordination number exp_fs=hse.calc_fs_e xposure(model) Overfull \hbox (20.6135pt too wide) in paragraph at lines 1169--1174 \T1/pcr/m/n/10 Atom \T1/pbk/l/n/10 ob-jects re-turn a \T1/pcr/m/n/10 Vector \T1 /pbk/l/n/10 ob-ject rep-re-sen-ta-tion of the co-or-di-nates with the \T1/pcr/m /n/10 get_vector [13] [14] Overfull \hbox (1.21811pt too wide) in paragraph at lines 1345--1353 []\T1/pbk/l/n/10 THE CON-TRIB-U-TORS AND COPY-RIGHT HOLD-ERS OF THIS SOFT-WARE DIS-CLAIM [15] (./biopdb_faq.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on biopdb_faq.pdf (15 pages, 165295 bytes). Transcript written on biopdb_faq.log. make[2]: Leaving directory '/<>/Doc' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild rm -f -- debian/python3-biopython.substvars rm -fr -- debian/.debhelper/generated/python3-biopython/ debian/python3-biopython/ debian/tmp/ rm -f debian/python3-biopython.debhelper.log debian/rules override_dh_auto_install make[1]: Entering directory '/<>' dh_auto_install install -m0755 -d /<>/python-biopython-1.80\+dfsg/debian/tmp pybuild --install -i python{version} -p 3.11 --dest-dir /<>/python-biopython-1.80\+dfsg/debian/tmp I: pybuild base:275: /usr/bin/python3 setup.py install --root /<>/debian/tmp running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer, pypa/build or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running egg_info writing biopython.egg-info/PKG-INFO writing dependency_links to biopython.egg-info/dependency_links.txt writing requirements to biopython.egg-info/requires.txt writing top-level names to biopython.egg-info/top_level.txt reading manifest file 'biopython.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.py{}' found anywhere in distribution warning: no previously-included files matching '*.py-e' found anywhere in distribution adding license file 'LICENSE' adding license file 'LICENSE.rst' writing manifest file 'biopython.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:201: _Warning: Package 'Bio.Align.substitution_matrices.data' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'Bio.Align.substitution_matrices.data' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'Bio.Align.substitution_matrices.data' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'Bio.Align.substitution_matrices.data' to be distributed and are already explicitly excluding 'Bio.Align.substitution_matrices.data' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:201: _Warning: Package 'Bio.Entrez.DTDs' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'Bio.Entrez.DTDs' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'Bio.Entrez.DTDs' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'Bio.Entrez.DTDs' to be distributed and are already explicitly excluding 'Bio.Entrez.DTDs' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:201: _Warning: Package 'Bio.Entrez.XSDs' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'Bio.Entrez.XSDs' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'Bio.Entrez.XSDs' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'Bio.Entrez.XSDs' to be distributed and are already explicitly excluding 'Bio.Entrez.XSDs' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) running build_ext running install_lib creating /<>/debian/tmp/usr creating /<>/debian/tmp/usr/lib creating /<>/debian/tmp/usr/lib/python3.11 creating /<>/debian/tmp/usr/lib/python3.11/dist-packages creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Nexus copying /<>/.pybuild/cpython3_3.11/build/Bio/Nexus/StandardData.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Nexus copying /<>/.pybuild/cpython3_3.11/build/Bio/Nexus/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Nexus copying /<>/.pybuild/cpython3_3.11/build/Bio/Nexus/Nodes.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Nexus copying /<>/.pybuild/cpython3_3.11/build/Bio/Nexus/Trees.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Nexus copying /<>/.pybuild/cpython3_3.11/build/Bio/Nexus/cnexus.c -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Nexus copying /<>/.pybuild/cpython3_3.11/build/Bio/Nexus/Nexus.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Nexus copying /<>/.pybuild/cpython3_3.11/build/Bio/Nexus/cnexus.cpython-311-riscv64-linux-gnu.so -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Nexus creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Medline copying /<>/.pybuild/cpython3_3.11/build/Bio/Medline/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Medline copying /<>/.pybuild/cpython3_3.11/build/Bio/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SwissProt copying /<>/.pybuild/cpython3_3.11/build/Bio/SwissProt/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SwissProt copying /<>/.pybuild/cpython3_3.11/build/Bio/SwissProt/KeyWList.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SwissProt copying /<>/.pybuild/cpython3_3.11/build/Bio/File.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/TogoWS copying /<>/.pybuild/cpython3_3.11/build/Bio/TogoWS/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/TogoWS creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Wise copying /<>/.pybuild/cpython3_3.11/build/Bio/Wise/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Wise copying /<>/.pybuild/cpython3_3.11/build/Bio/Wise/dnal.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Wise copying /<>/.pybuild/cpython3_3.11/build/Bio/Wise/psw.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Wise creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SVDSuperimposer copying /<>/.pybuild/cpython3_3.11/build/Bio/SVDSuperimposer/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SVDSuperimposer copying /<>/.pybuild/cpython3_3.11/build/Bio/kNN.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio copying /<>/.pybuild/cpython3_3.11/build/Bio/MaxEntropy.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing copying /<>/.pybuild/cpython3_3.11/build/Bio/Sequencing/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing/Applications copying /<>/.pybuild/cpython3_3.11/build/Bio/Sequencing/Applications/_Novoalign.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing/Applications copying /<>/.pybuild/cpython3_3.11/build/Bio/Sequencing/Applications/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing/Applications copying /<>/.pybuild/cpython3_3.11/build/Bio/Sequencing/Applications/_bwa.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing/Applications copying /<>/.pybuild/cpython3_3.11/build/Bio/Sequencing/Applications/_samtools.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing/Applications copying /<>/.pybuild/cpython3_3.11/build/Bio/Sequencing/Ace.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing copying /<>/.pybuild/cpython3_3.11/build/Bio/Sequencing/Phd.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/msf.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/hhr.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/mauve.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/_aligners.cpython-311-riscv64-linux-gnu.so -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/BLOSUM90 -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/BLOSUM80 -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/BLOSUM62 -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/PAM250 -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/HOXD70 -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/PAM30 -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/BLASTN -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/PAM70 -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/GENETIC -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/STR -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/MCLACHLAN -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/RISLER -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/SCHNEIDER -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/BLASTP -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/BENNER22 -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/BLOSUM50 -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/JOHNSON -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/LEVIN -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/BENNER6 -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/JONES -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/MEGABLAST -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/BENNER74 -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/TRANS -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/DAYHOFF -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/FENG -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/BLOSUM45 -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/MDM78 -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/RAO -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/NUC.4.4 -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/GONNET1992 -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/stockholm.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/_aligners.c -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/Applications/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/Applications/_Dialign.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/Applications/_ClustalOmega.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/Applications/_Prank.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/Applications/_Mafft.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/Applications/_TCoffee.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/Applications/_MSAProbs.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/Applications/_Probcons.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/Applications/_Muscle.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/Applications/_Clustalw.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/phylip.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/tabular.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/emboss.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/AlignInfo.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/interfaces.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/nexus.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/exonerate.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/bigpsl.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/maf.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/bed.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/a2m.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/bigbed.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/clustal.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/bigmaf.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/sam.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/fasta.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align copying /<>/.pybuild/cpython3_3.11/build/Bio/Align/psl.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align copying /<>/.pybuild/cpython3_3.11/build/Bio/SeqFeature.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Affy copying /<>/.pybuild/cpython3_3.11/build/Bio/Affy/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Affy copying /<>/.pybuild/cpython3_3.11/build/Bio/Affy/CelFile.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Affy creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP copying /<>/.pybuild/cpython3_3.11/build/Bio/SCOP/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP copying /<>/.pybuild/cpython3_3.11/build/Bio/SCOP/Cla.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP copying /<>/.pybuild/cpython3_3.11/build/Bio/SCOP/Des.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP copying /<>/.pybuild/cpython3_3.11/build/Bio/SCOP/Residues.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP copying /<>/.pybuild/cpython3_3.11/build/Bio/SCOP/Raf.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP copying /<>/.pybuild/cpython3_3.11/build/Bio/SCOP/Hie.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP copying /<>/.pybuild/cpython3_3.11/build/Bio/SCOP/Dom.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP copying /<>/.pybuild/cpython3_3.11/build/Bio/pairwise2.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/GckIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/PdbIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/Interfaces.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/PhdIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/SnapGeneIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/NibIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/_index.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/XdnaIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/QualityIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/PirIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/TabIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/SeqXmlIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/FastaIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/UniprotIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/_twoBitIO.c -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/IgIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/SwissIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/SffIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/AceIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/TwoBitIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/_twoBitIO.cpython-311-riscv64-linux-gnu.so -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/AbiIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Compass copying /<>/.pybuild/cpython3_3.11/build/Bio/Compass/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Compass creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG copying /<>/.pybuild/cpython3_3.11/build/Bio/KEGG/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/Enzyme copying /<>/.pybuild/cpython3_3.11/build/Bio/KEGG/Enzyme/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/Enzyme creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/Map copying /<>/.pybuild/cpython3_3.11/build/Bio/KEGG/Map/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/Map copying /<>/.pybuild/cpython3_3.11/build/Bio/KEGG/REST.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/Gene copying /<>/.pybuild/cpython3_3.11/build/Bio/KEGG/Gene/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/Gene creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/Compound copying /<>/.pybuild/cpython3_3.11/build/Bio/KEGG/Compound/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/Compound creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/KGML copying /<>/.pybuild/cpython3_3.11/build/Bio/KEGG/KGML/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/KGML copying /<>/.pybuild/cpython3_3.11/build/Bio/KEGG/KGML/KGML_pathway.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/KGML copying /<>/.pybuild/cpython3_3.11/build/Bio/KEGG/KGML/KGML_parser.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/KGML creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PopGen copying /<>/.pybuild/cpython3_3.11/build/Bio/PopGen/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PopGen creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PopGen/GenePop copying /<>/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PopGen/GenePop copying /<>/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop/EasyController.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PopGen/GenePop copying /<>/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop/FileParser.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PopGen/GenePop copying /<>/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop/Controller.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PopGen/GenePop copying /<>/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop/LargeFileParser.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PopGen/GenePop creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/UniProt copying /<>/.pybuild/cpython3_3.11/build/Bio/UniProt/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/UniProt copying /<>/.pybuild/cpython3_3.11/build/Bio/UniProt/GOA.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/UniProt copying /<>/.pybuild/cpython3_3.11/build/Bio/bgzf.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Blast copying /<>/.pybuild/cpython3_3.11/build/Bio/Blast/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Blast copying /<>/.pybuild/cpython3_3.11/build/Bio/Blast/NCBIXML.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Blast copying /<>/.pybuild/cpython3_3.11/build/Bio/Blast/ParseBlastTable.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Blast copying /<>/.pybuild/cpython3_3.11/build/Bio/Blast/Applications.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Blast copying /<>/.pybuild/cpython3_3.11/build/Bio/Blast/Record.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Blast copying /<>/.pybuild/cpython3_3.11/build/Bio/Blast/NCBIWWW.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Blast creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/NMR copying /<>/.pybuild/cpython3_3.11/build/Bio/NMR/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/NMR copying /<>/.pybuild/cpython3_3.11/build/Bio/NMR/xpktools.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/NMR copying /<>/.pybuild/cpython3_3.11/build/Bio/NMR/NOEtools.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/NMR creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Geo copying /<>/.pybuild/cpython3_3.11/build/Bio/Geo/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Geo copying /<>/.pybuild/cpython3_3.11/build/Bio/Geo/Record.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Geo creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Application copying /<>/.pybuild/cpython3_3.11/build/Bio/Application/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Application creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics copying /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics copying /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/DisplayRepresentation.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram copying /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram copying /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram/_Track.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram copying /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram/_Feature.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram copying /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram/_Diagram.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram copying /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram/_CrossLink.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram copying /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram/_GraphSet.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram copying /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram copying /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram/_Colors.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram copying /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram/_FeatureSet.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram copying /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram copying /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram copying /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram/_Graph.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram copying /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/KGML_vis.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics copying /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/Comparative.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics copying /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/ColorSpiral.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics copying /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/BasicChromosome.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics copying /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/Distribution.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/Polypeptide.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/PDBExceptions.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/Model.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/Selection.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/mmtf copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/mmtf/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/mmtf copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/mmtf/mmtfio.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/mmtf copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/mmtf/DefaultParser.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/mmtf copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/ccealign.cpython-311-riscv64-linux-gnu.so -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/Atom.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/MMCIF2Dict.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/mmcifio.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/kdtrees.c -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/SASA.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/FragmentMapper.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/Dice.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/ccealignmodule.c -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/Superimposer.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/SCADIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/PDBParser.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/NACCESS.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/MMCIFParser.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/StructureAlignment.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/QCPSuperimposer copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/QCPSuperimposer/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/QCPSuperimposer copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/QCPSuperimposer/qcprotmodule.c -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/QCPSuperimposer copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-riscv64-linux-gnu.so -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/QCPSuperimposer copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/Entity.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/Residue.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/ic_rebuild.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/Chain.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/AbstractPropertyMap.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/qcprot.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/internal_coords.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/HSExposure.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/Structure.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/PICIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/kdtrees.cpython-311-riscv64-linux-gnu.so -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/parse_pdb_header.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/StructureBuilder.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/cealign.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/NeighborSearch.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/PDBList.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/PDBIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/DSSP.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/PSEA.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/ResidueDepth.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/ic_data.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB copying /<>/.pybuild/cpython3_3.11/build/Bio/PDB/vectors.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Emboss copying /<>/.pybuild/cpython3_3.11/build/Bio/Emboss/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Emboss copying /<>/.pybuild/cpython3_3.11/build/Bio/Emboss/PrimerSearch.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Emboss copying /<>/.pybuild/cpython3_3.11/build/Bio/Emboss/Primer3.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Emboss copying /<>/.pybuild/cpython3_3.11/build/Bio/Emboss/Applications.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Emboss copying /<>/.pybuild/cpython3_3.11/build/Bio/Seq.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio copying /<>/.pybuild/cpython3_3.11/build/Bio/_utils.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio copying /<>/.pybuild/cpython3_3.11/build/Bio/MarkovModel.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_legacy copying /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_legacy/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_legacy copying /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_legacy/ParserSupport.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_legacy copying /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_legacy/NCBIStandalone.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_legacy copying /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_index.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/BlastIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/BlastIO/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/BlastIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/BlastIO/blast_xml.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/BlastIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/BlastIO/blast_tab.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/BlastIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/BlastIO/blast_text.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/BlastIO creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HHsuiteIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HHsuiteIO/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HHsuiteIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HHsuiteIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/BlatIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/FastaIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_model copying /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_model copying /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model/query.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_model copying /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model/_base.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_model copying /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model/hit.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_model copying /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model/hsp.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_model copying /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_utils.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/ExonerateIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/ExonerateIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO/_base.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/ExonerateIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/ExonerateIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO/exonerate_text.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/ExonerateIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/ExonerateIO creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HmmerIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HmmerIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO/_base.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HmmerIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO/hmmer3_tab.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HmmerIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HmmerIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO/hmmer2_text.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HmmerIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO/hmmer3_text.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HmmerIO creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/InterproscanIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/InterproscanIO/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/InterproscanIO copying /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/InterproscanIO/interproscan_xml.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/InterproscanIO copying /<>/.pybuild/cpython3_3.11/build/Bio/NaiveBayes.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/ExPASy copying /<>/.pybuild/cpython3_3.11/build/Bio/ExPASy/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/ExPASy copying /<>/.pybuild/cpython3_3.11/build/Bio/ExPASy/Prosite.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/ExPASy copying /<>/.pybuild/cpython3_3.11/build/Bio/ExPASy/ScanProsite.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/ExPASy copying /<>/.pybuild/cpython3_3.11/build/Bio/ExPASy/Enzyme.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/ExPASy copying /<>/.pybuild/cpython3_3.11/build/Bio/ExPASy/cellosaurus.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/ExPASy copying /<>/.pybuild/cpython3_3.11/build/Bio/ExPASy/Prodoc.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/ExPASy creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/UniGene copying /<>/.pybuild/cpython3_3.11/build/Bio/UniGene/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/UniGene creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Alphabet copying /<>/.pybuild/cpython3_3.11/build/Bio/Alphabet/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Alphabet creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils copying /<>/.pybuild/cpython3_3.11/build/Bio/SeqUtils/CheckSum.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils copying /<>/.pybuild/cpython3_3.11/build/Bio/SeqUtils/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils copying /<>/.pybuild/cpython3_3.11/build/Bio/SeqUtils/MeltingTemp.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils copying /<>/.pybuild/cpython3_3.11/build/Bio/SeqUtils/IsoelectricPoint.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils copying /<>/.pybuild/cpython3_3.11/build/Bio/SeqUtils/ProtParam.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils copying /<>/.pybuild/cpython3_3.11/build/Bio/SeqUtils/CodonUsage.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils copying /<>/.pybuild/cpython3_3.11/build/Bio/SeqUtils/lcc.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils copying /<>/.pybuild/cpython3_3.11/build/Bio/SeqUtils/CodonUsageIndices.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils copying /<>/.pybuild/cpython3_3.11/build/Bio/SeqUtils/ProtParamData.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Data copying /<>/.pybuild/cpython3_3.11/build/Bio/Data/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Data copying /<>/.pybuild/cpython3_3.11/build/Bio/Data/SCOPData.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Data copying /<>/.pybuild/cpython3_3.11/build/Bio/Data/IUPACData.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Data copying /<>/.pybuild/cpython3_3.11/build/Bio/Data/PDBData.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Data copying /<>/.pybuild/cpython3_3.11/build/Bio/Data/CodonTable.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Data creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Pathway copying /<>/.pybuild/cpython3_3.11/build/Bio/Pathway/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Pathway creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Pathway/Rep copying /<>/.pybuild/cpython3_3.11/build/Bio/Pathway/Rep/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Pathway/Rep copying /<>/.pybuild/cpython3_3.11/build/Bio/Pathway/Rep/MultiGraph.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Pathway/Rep copying /<>/.pybuild/cpython3_3.11/build/Bio/Pathway/Rep/Graph.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Pathway/Rep copying /<>/.pybuild/cpython3_3.11/build/Bio/cpairwise2.cpython-311-riscv64-linux-gnu.so -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio copying /<>/.pybuild/cpython3_3.11/build/Bio/cpairwise2module.c -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/codonalign copying /<>/.pybuild/cpython3_3.11/build/Bio/codonalign/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/codonalign copying /<>/.pybuild/cpython3_3.11/build/Bio/codonalign/codonseq.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/codonalign copying /<>/.pybuild/cpython3_3.11/build/Bio/codonalign/codonalignment.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/codonalign copying /<>/.pybuild/cpython3_3.11/build/Bio/LogisticRegression.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO copying /<>/.pybuild/cpython3_3.11/build/Bio/AlignIO/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO copying /<>/.pybuild/cpython3_3.11/build/Bio/AlignIO/Interfaces.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO copying /<>/.pybuild/cpython3_3.11/build/Bio/AlignIO/EmbossIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO copying /<>/.pybuild/cpython3_3.11/build/Bio/AlignIO/NexusIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO copying /<>/.pybuild/cpython3_3.11/build/Bio/AlignIO/PhylipIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO copying /<>/.pybuild/cpython3_3.11/build/Bio/AlignIO/FastaIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO copying /<>/.pybuild/cpython3_3.11/build/Bio/AlignIO/ClustalIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO copying /<>/.pybuild/cpython3_3.11/build/Bio/AlignIO/StockholmIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO copying /<>/.pybuild/cpython3_3.11/build/Bio/AlignIO/MafIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO copying /<>/.pybuild/cpython3_3.11/build/Bio/AlignIO/MsfIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO copying /<>/.pybuild/cpython3_3.11/build/Bio/AlignIO/MauveIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/GenBank copying /<>/.pybuild/cpython3_3.11/build/Bio/GenBank/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/GenBank copying /<>/.pybuild/cpython3_3.11/build/Bio/GenBank/Scanner.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/GenBank copying /<>/.pybuild/cpython3_3.11/build/Bio/GenBank/utils.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/GenBank copying /<>/.pybuild/cpython3_3.11/build/Bio/GenBank/Record.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/GenBank copying /<>/.pybuild/cpython3_3.11/build/Bio/SeqRecord.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/CAPS copying /<>/.pybuild/cpython3_3.11/build/Bio/CAPS/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/CAPS creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Cluster copying /<>/.pybuild/cpython3_3.11/build/Bio/Cluster/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Cluster copying /<>/.pybuild/cpython3_3.11/build/Bio/Cluster/clustermodule.c -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Cluster copying /<>/.pybuild/cpython3_3.11/build/Bio/Cluster/cluster.c -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Cluster copying /<>/.pybuild/cpython3_3.11/build/Bio/Cluster/cluster.h -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Cluster copying /<>/.pybuild/cpython3_3.11/build/Bio/Cluster/_cluster.cpython-311-riscv64-linux-gnu.so -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Cluster creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/HMM copying /<>/.pybuild/cpython3_3.11/build/Bio/HMM/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/HMM copying /<>/.pybuild/cpython3_3.11/build/Bio/HMM/MarkovModel.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/HMM copying /<>/.pybuild/cpython3_3.11/build/Bio/HMM/Trainer.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/HMM copying /<>/.pybuild/cpython3_3.11/build/Bio/HMM/Utilities.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/HMM copying /<>/.pybuild/cpython3_3.11/build/Bio/HMM/DynamicProgramming.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/HMM creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-journalmeta1-3.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/esummary-v1.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-references1-3.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_RNA.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_all.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Systems.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/PRF_General.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmcommon_011101.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-common1-3.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isobox.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmmedline_011101.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/xhtml-table-1.mod -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Blast4.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/OMSSA.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/mathml-in-pubmed.mod -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/bookdoc_140101.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/pmc-1.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isodia.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/pubmed_180101.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Biblio.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/pubmed_110101.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/mmlextra.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Access.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/Docsum_3_2.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isocyr2.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/pubmed_020114.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_BioTree.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_BioSource.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/bookdoc_130101.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/PDB_General.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/pubmed_130101.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isoamsa.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/Docsum_3_4.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Submit.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isopub.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/eLink_090910.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/articlemeta.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/notat.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/EMBL_General.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/PIR_General.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/pubmed_180601.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Sequence.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-modules1-3.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Mime.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/modules.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NSE.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/archivecustom-classes.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-display1-3.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Gene.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_TxInit.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/egquery.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/archivecustom-mixes.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/taxon.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/esearch.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/para.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Seqres.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/xmlspecchars.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Remap.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Rsite.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-math1-3.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmcommon_090101.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-para1-3.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/mathmlsetup.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/bookdoc_120101.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Pub.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/Docsum_3_3.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/HomoloGene.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isoamso.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_TSeq.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-link1-3.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-chars1-3.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isogrk1.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isocyr1.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/GenBank_General.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isonum.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isogrk2.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Mim.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/SP_General.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-default-classes1-3.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/mathml2.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isomopf.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/elink_020122.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/EMBL_General.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isogrk3.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/BITS-question-answer2.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/archivecustom-models.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/bookdoc_150101.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/mathml3-qname1.mod -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/bookdoc_110101.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-section1-3.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/eInfo_020511.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-xmlspecchars1-3.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-backmatter1-3.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isogrk4.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Protein.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/MMDB_Features.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/PDB_General.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-funding1-3.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/MMDB.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/default-mixes.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isomscr.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_General.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/GenBank_General.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/list.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-notat1-3.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Cdd.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/section.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isoamsb.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/einfo.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/references.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/chars.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/pubmed_120101.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-related-object1-3.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/bookdoc_100301.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/PIR_General.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/eSearch_020511.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-format1-3.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/pubmed_100301.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/Docsum_3_1.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Organism.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-phrase1-3.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmmedline_090101.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/htmltable.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmserials_100101.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_General.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/pubmed_130501.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/journalmeta.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/pubmed_080101.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isoamsn.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/MMDB.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-articlemeta1-3.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/pubmed_090101.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/format.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/default-classes.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmserials_080101.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/BITS-embedded-index2.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Variation.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/OMSSA.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/common.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/eSummary_041029.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/backmatter.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isoamsr.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isolat2.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Project.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/link.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/ePost_020511.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/math.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/eSpell.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isotech.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-default-mixes1-3.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/archivearticle.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/display.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/phrase.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_PubMed.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/HomoloGene.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isolat1.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isomfrk.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/mmlalias.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/archivecustom-modules.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/pubmed_140101.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/PRF_General.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NSE.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/mathml3.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/pubmed_100101.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-list1-3.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Medline.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-common-atts1-3.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Medlars.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/SP_General.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/eLink_101123.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Seqset.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/XHTMLtablesetup.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isoamsc.ent -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmcommon_080101.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmmedline_080101.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/Docsum_3_0.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/pubmed_150101.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/pubmed_190101.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/XSDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/XSDs/IPGReportSet.xsd -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/XSDs copying /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/Parser.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/phenotype copying /<>/.pybuild/cpython3_3.11/build/Bio/phenotype/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/phenotype copying /<>/.pybuild/cpython3_3.11/build/Bio/phenotype/phen_micro.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/phenotype copying /<>/.pybuild/cpython3_3.11/build/Bio/phenotype/pm_fitting.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/phenotype creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Restriction copying /<>/.pybuild/cpython3_3.11/build/Bio/Restriction/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Restriction copying /<>/.pybuild/cpython3_3.11/build/Bio/Restriction/Restriction_Dictionary.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Restriction copying /<>/.pybuild/cpython3_3.11/build/Bio/Restriction/PrintFormat.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Restriction copying /<>/.pybuild/cpython3_3.11/build/Bio/Restriction/Restriction.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Restriction creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo copying /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo copying /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/NeXML.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo copying /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/BaseTree.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo copying /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/_cdao_owl.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML copying /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML copying /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML/_parse_yn00.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML copying /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML/codeml.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML copying /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML/_paml.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML copying /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML/_parse_baseml.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML copying /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML/chi2.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML copying /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML/_parse_codeml.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML copying /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML/yn00.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML copying /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML/baseml.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML copying /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/Consensus.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/Applications copying /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/Applications/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/Applications copying /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/Applications/_Phyml.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/Applications copying /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/Applications/_Fasttree.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/Applications copying /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/Applications/_Raxml.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/Applications copying /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/NexusIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo copying /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/TreeConstruction.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo copying /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/PhyloXMLIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo copying /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/_utils.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo copying /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/_io.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo copying /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/Newick.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo copying /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/CDAOIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo copying /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/NewickIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo copying /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/PhyloXML.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo copying /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/CDAO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo copying /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/NeXMLIO.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs copying /<>/.pybuild/cpython3_3.11/build/Bio/motifs/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs copying /<>/.pybuild/cpython3_3.11/build/Bio/motifs/transfac.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/applications copying /<>/.pybuild/cpython3_3.11/build/Bio/motifs/applications/_xxmotif.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/applications copying /<>/.pybuild/cpython3_3.11/build/Bio/motifs/applications/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/applications copying /<>/.pybuild/cpython3_3.11/build/Bio/motifs/xms.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs copying /<>/.pybuild/cpython3_3.11/build/Bio/motifs/thresholds.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/jaspar copying /<>/.pybuild/cpython3_3.11/build/Bio/motifs/jaspar/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/jaspar copying /<>/.pybuild/cpython3_3.11/build/Bio/motifs/jaspar/db.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/jaspar copying /<>/.pybuild/cpython3_3.11/build/Bio/motifs/matrix.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs copying /<>/.pybuild/cpython3_3.11/build/Bio/motifs/mast.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs copying /<>/.pybuild/cpython3_3.11/build/Bio/motifs/clusterbuster.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs copying /<>/.pybuild/cpython3_3.11/build/Bio/motifs/meme.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs copying /<>/.pybuild/cpython3_3.11/build/Bio/motifs/pfm.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs copying /<>/.pybuild/cpython3_3.11/build/Bio/motifs/_pwm.c -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs copying /<>/.pybuild/cpython3_3.11/build/Bio/motifs/alignace.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs copying /<>/.pybuild/cpython3_3.11/build/Bio/motifs/_pwm.cpython-311-riscv64-linux-gnu.so -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs copying /<>/.pybuild/cpython3_3.11/build/Bio/motifs/minimal.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/BioSQL copying /<>/.pybuild/cpython3_3.11/build/BioSQL/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/BioSQL copying /<>/.pybuild/cpython3_3.11/build/BioSQL/BioSeq.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/BioSQL copying /<>/.pybuild/cpython3_3.11/build/BioSQL/DBUtils.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/BioSQL copying /<>/.pybuild/cpython3_3.11/build/BioSQL/BioSeqDatabase.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/BioSQL copying /<>/.pybuild/cpython3_3.11/build/BioSQL/Loader.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/BioSQL byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Nexus/StandardData.py to StandardData.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Nexus/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Nexus/Nodes.py to Nodes.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Nexus/Trees.py to Trees.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Nexus/Nexus.py to Nexus.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Medline/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SwissProt/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SwissProt/KeyWList.py to KeyWList.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/File.py to File.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/TogoWS/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Wise/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Wise/dnal.py to dnal.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Wise/psw.py to psw.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SVDSuperimposer/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/kNN.py to kNN.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/MaxEntropy.py to MaxEntropy.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing/Applications/_Novoalign.py to _Novoalign.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing/Applications/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing/Applications/_bwa.py to _bwa.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing/Applications/_samtools.py to _samtools.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing/Ace.py to Ace.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing/Phd.py to Phd.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/msf.py to msf.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/hhr.py to hhr.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/mauve.py to mauve.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/stockholm.py to stockholm.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications/_Dialign.py to _Dialign.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications/_ClustalOmega.py to _ClustalOmega.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications/_Prank.py to _Prank.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications/_Mafft.py to _Mafft.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications/_TCoffee.py to _TCoffee.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications/_MSAProbs.py to _MSAProbs.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications/_Probcons.py to _Probcons.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications/_Muscle.py to _Muscle.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications/_Clustalw.py to _Clustalw.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/phylip.py to phylip.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/tabular.py to tabular.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/emboss.py to emboss.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/AlignInfo.py to AlignInfo.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/interfaces.py to interfaces.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/nexus.py to nexus.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/exonerate.py to exonerate.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/bigpsl.py to bigpsl.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/maf.py to maf.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/bed.py to bed.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/a2m.py to a2m.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/bigbed.py to bigbed.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/clustal.py to clustal.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/bigmaf.py to bigmaf.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/sam.py to sam.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/fasta.py to fasta.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/psl.py to psl.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqFeature.py to SeqFeature.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Affy/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Affy/CelFile.py to CelFile.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP/Cla.py to Cla.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP/Des.py to Des.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP/Residues.py to Residues.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP/Raf.py to Raf.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP/Hie.py to Hie.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP/Dom.py to Dom.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/pairwise2.py to pairwise2.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/GckIO.py to GckIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/PdbIO.py to PdbIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/Interfaces.py to Interfaces.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/PhdIO.py to PhdIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/SnapGeneIO.py to SnapGeneIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/NibIO.py to NibIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/_index.py to _index.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/XdnaIO.py to XdnaIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/QualityIO.py to QualityIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/PirIO.py to PirIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/TabIO.py to TabIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/SeqXmlIO.py to SeqXmlIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/FastaIO.py to FastaIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/UniprotIO.py to UniprotIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/InsdcIO.py to InsdcIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/IgIO.py to IgIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/SwissIO.py to SwissIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/SffIO.py to SffIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/AceIO.py to AceIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/TwoBitIO.py to TwoBitIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/AbiIO.py to AbiIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Compass/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/Enzyme/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/Map/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/REST.py to REST.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/Gene/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/Compound/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/KGML/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/KGML/KGML_pathway.py to KGML_pathway.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/KGML/KGML_parser.py to KGML_parser.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PopGen/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PopGen/GenePop/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PopGen/GenePop/EasyController.py to EasyController.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PopGen/GenePop/FileParser.py to FileParser.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PopGen/GenePop/Controller.py to Controller.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PopGen/GenePop/LargeFileParser.py to LargeFileParser.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/UniProt/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/UniProt/GOA.py to GOA.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/bgzf.py to bgzf.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Blast/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Blast/NCBIXML.py to NCBIXML.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Blast/ParseBlastTable.py to ParseBlastTable.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Blast/Applications.py to Applications.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Blast/Record.py to Record.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Blast/NCBIWWW.py to NCBIWWW.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/NMR/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/NMR/xpktools.py to xpktools.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/NMR/NOEtools.py to NOEtools.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Geo/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Geo/Record.py to Record.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Application/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/DisplayRepresentation.py to DisplayRepresentation.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/_Track.py to _Track.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/_Feature.py to _Feature.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/_Diagram.py to _Diagram.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/_CrossLink.py to _CrossLink.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/_GraphSet.py to _GraphSet.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/_CircularDrawer.py to _CircularDrawer.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/_Colors.py to _Colors.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/_FeatureSet.py to _FeatureSet.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py to _AbstractDrawer.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/_LinearDrawer.py to _LinearDrawer.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/_Graph.py to _Graph.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/KGML_vis.py to KGML_vis.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/Comparative.py to Comparative.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/ColorSpiral.py to ColorSpiral.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/BasicChromosome.py to BasicChromosome.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/Distribution.py to Distribution.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/Polypeptide.py to Polypeptide.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/PDBExceptions.py to PDBExceptions.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/Model.py to Model.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/Selection.py to Selection.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/mmtf/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/mmtf/mmtfio.py to mmtfio.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/mmtf/DefaultParser.py to DefaultParser.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/Atom.py to Atom.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/MMCIF2Dict.py to MMCIF2Dict.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/mmcifio.py to mmcifio.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/SASA.py to SASA.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/FragmentMapper.py to FragmentMapper.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/Dice.py to Dice.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/Superimposer.py to Superimposer.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/SCADIO.py to SCADIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/PDBParser.py to PDBParser.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/NACCESS.py to NACCESS.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/MMCIFParser.py to MMCIFParser.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/StructureAlignment.py to StructureAlignment.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/QCPSuperimposer/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/Entity.py to Entity.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/Residue.py to Residue.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/ic_rebuild.py to ic_rebuild.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/Chain.py to Chain.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/AbstractPropertyMap.py to AbstractPropertyMap.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/qcprot.py to qcprot.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/internal_coords.py to internal_coords.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/HSExposure.py to HSExposure.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/Structure.py to Structure.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/PICIO.py to PICIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/parse_pdb_header.py to parse_pdb_header.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/StructureBuilder.py to StructureBuilder.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/cealign.py to cealign.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/NeighborSearch.py to NeighborSearch.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/PDBList.py to PDBList.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/PDBIO.py to PDBIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/DSSP.py to DSSP.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/PSEA.py to PSEA.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/ResidueDepth.py to ResidueDepth.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/ic_data.py to ic_data.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/vectors.py to vectors.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Emboss/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Emboss/PrimerSearch.py to PrimerSearch.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Emboss/Primer3.py to Primer3.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Emboss/Applications.py to Applications.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Seq.py to Seq.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/_utils.py to _utils.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/MarkovModel.py to MarkovModel.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_legacy/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_legacy/ParserSupport.py to ParserSupport.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_legacy/NCBIStandalone.py to NCBIStandalone.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_index.py to _index.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/BlastIO/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/BlastIO/blast_xml.py to blast_xml.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/BlastIO/blast_tab.py to blast_tab.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/BlastIO/blast_text.py to blast_text.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HHsuiteIO/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HHsuiteIO/hhsuite2_text.py to hhsuite2_text.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/BlatIO.py to BlatIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/FastaIO.py to FastaIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_model/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_model/query.py to query.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_model/_base.py to _base.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_model/hit.py to hit.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_model/hsp.py to hsp.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_utils.py to _utils.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/ExonerateIO/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/ExonerateIO/_base.py to _base.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/ExonerateIO/exonerate_cigar.py to exonerate_cigar.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/ExonerateIO/exonerate_text.py to exonerate_text.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py to exonerate_vulgar.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HmmerIO/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HmmerIO/_base.py to _base.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HmmerIO/hmmer3_tab.py to hmmer3_tab.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HmmerIO/hmmer3_domtab.py to hmmer3_domtab.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HmmerIO/hmmer2_text.py to hmmer2_text.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HmmerIO/hmmer3_text.py to hmmer3_text.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/InterproscanIO/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/InterproscanIO/interproscan_xml.py to interproscan_xml.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/NaiveBayes.py to NaiveBayes.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/ExPASy/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/ExPASy/Prosite.py to Prosite.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/ExPASy/ScanProsite.py to ScanProsite.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/ExPASy/Enzyme.py to Enzyme.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/ExPASy/cellosaurus.py to cellosaurus.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/ExPASy/Prodoc.py to Prodoc.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/UniGene/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Alphabet/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils/CheckSum.py to CheckSum.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils/MeltingTemp.py to MeltingTemp.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils/IsoelectricPoint.py to IsoelectricPoint.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils/ProtParam.py to ProtParam.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils/CodonUsage.py to CodonUsage.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils/lcc.py to lcc.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils/CodonUsageIndices.py to CodonUsageIndices.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils/ProtParamData.py to ProtParamData.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Data/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Data/SCOPData.py to SCOPData.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Data/IUPACData.py to IUPACData.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Data/PDBData.py to PDBData.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Data/CodonTable.py to CodonTable.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Pathway/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Pathway/Rep/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Pathway/Rep/MultiGraph.py to MultiGraph.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Pathway/Rep/Graph.py to Graph.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/codonalign/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/codonalign/codonseq.py to codonseq.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/codonalign/codonalignment.py to codonalignment.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/LogisticRegression.py to LogisticRegression.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO/Interfaces.py to Interfaces.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO/EmbossIO.py to EmbossIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO/NexusIO.py to NexusIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO/PhylipIO.py to PhylipIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO/FastaIO.py to FastaIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO/ClustalIO.py to ClustalIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO/StockholmIO.py to StockholmIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO/MafIO.py to MafIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO/MsfIO.py to MsfIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO/MauveIO.py to MauveIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/GenBank/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/GenBank/Scanner.py to Scanner.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/GenBank/utils.py to utils.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/GenBank/Record.py to Record.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqRecord.py to SeqRecord.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/CAPS/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Cluster/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/HMM/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/HMM/MarkovModel.py to MarkovModel.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/HMM/Trainer.py to Trainer.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/HMM/Utilities.py to Utilities.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/HMM/DynamicProgramming.py to DynamicProgramming.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/Parser.py to Parser.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/phenotype/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/phenotype/phen_micro.py to phen_micro.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/phenotype/pm_fitting.py to pm_fitting.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Restriction/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Restriction/Restriction_Dictionary.py to Restriction_Dictionary.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Restriction/PrintFormat.py to PrintFormat.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Restriction/Restriction.py to Restriction.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/NeXML.py to NeXML.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/BaseTree.py to BaseTree.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/_cdao_owl.py to _cdao_owl.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML/_parse_yn00.py to _parse_yn00.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML/codeml.py to codeml.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML/_paml.py to _paml.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML/_parse_baseml.py to _parse_baseml.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML/chi2.py to chi2.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML/_parse_codeml.py to _parse_codeml.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML/yn00.py to yn00.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML/baseml.py to baseml.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/Consensus.py to Consensus.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/Applications/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/Applications/_Phyml.py to _Phyml.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/Applications/_Fasttree.py to _Fasttree.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/Applications/_Raxml.py to _Raxml.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/NexusIO.py to NexusIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/TreeConstruction.py to TreeConstruction.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PhyloXMLIO.py to PhyloXMLIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/_utils.py to _utils.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/_io.py to _io.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/Newick.py to Newick.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/CDAOIO.py to CDAOIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/NewickIO.py to NewickIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PhyloXML.py to PhyloXML.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/CDAO.py to CDAO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/NeXMLIO.py to NeXMLIO.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/transfac.py to transfac.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/applications/_xxmotif.py to _xxmotif.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/applications/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/xms.py to xms.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/thresholds.py to thresholds.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/jaspar/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/jaspar/db.py to db.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/matrix.py to matrix.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/mast.py to mast.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/clusterbuster.py to clusterbuster.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/meme.py to meme.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/pfm.py to pfm.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/alignace.py to alignace.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/minimal.py to minimal.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/BioSQL/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/BioSQL/BioSeq.py to BioSeq.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/BioSQL/DBUtils.py to DBUtils.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/BioSQL/BioSeqDatabase.py to BioSeqDatabase.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/BioSQL/Loader.py to Loader.cpython-311.pyc running install_egg_info Copying biopython.egg-info to /<>/debian/tmp/usr/lib/python3.11/dist-packages/biopython-1.80.egg-info Skipping SOURCES.txt running install_scripts dh_numpy3 -ppython3-biopython mv debian/python3-biopython.substvars.new debian/python3-biopython.substvars make[1]: Leaving directory '/<>' dh_install -a -O--buildsystem=pybuild install -m0755 -d debian/python3-biopython//usr/lib/python3.11/dist-packages cp --reflink=auto -a debian/tmp/usr/lib/python3.11/dist-packages/Bio debian/tmp/usr/lib/python3.11/dist-packages/biopython-1.80.egg-info debian/python3-biopython//usr/lib/python3.11/dist-packages/ dh_installdocs -a -O--buildsystem=pybuild install -m0755 -d debian/python3-biopython/usr/share/doc/python3-biopython install -m0755 -d debian/python3-biopython/usr/share/doc/python3-biopython cp --reflink=auto -a ./CONTRIB.rst debian/python3-biopython/usr/share/doc/python3-biopython cp --reflink=auto -a ./CONTRIBUTING.rst debian/python3-biopython/usr/share/doc/python3-biopython cp --reflink=auto -a ./DEPRECATED.rst debian/python3-biopython/usr/share/doc/python3-biopython cp --reflink=auto -a ./NEWS.rst debian/python3-biopython/usr/share/doc/python3-biopython chmod -R u\+rw,go=rX debian/python3-biopython/usr/share/doc install -p -m0644 debian/README.Debian debian/python3-biopython/usr/share/doc/python3-biopython/README.Debian install -p -m0644 debian/copyright debian/python3-biopython/usr/share/doc/python3-biopython/copyright dh_installchangelogs -a -O--buildsystem=pybuild install -m0755 -d debian/python3-biopython/usr/share/doc/python3-biopython install -p -m0644 debian/.debhelper/generated/python3-biopython/dh_installchangelogs.dch.trimmed debian/python3-biopython/usr/share/doc/python3-biopython/changelog.Debian install -p -m0644 debian/NEWS debian/python3-biopython/usr/share/doc/python3-biopython/NEWS.Debian dh_python3 -a -O--buildsystem=pybuild D: dh_python3 dh_python3:179: version: 6.20230603 D: dh_python3 dh_python3:180: argv: ['/usr/bin/dh_python3', '-a', '-O--buildsystem=pybuild'] D: dh_python3 dh_python3:181: options: Namespace(guess_deps=True, skip_private=False, verbose=True, arch=True, package=None, no_package=None, remaining_packages=False, compile_all=False, vrange=None, regexpr=None, accept_upstream_versions=False, depends=None, depends_section=None, recommends=None, recommends_section=None, suggests=None, suggests_section=None, requires=None, shebang=None, ignore_shebangs=False, clean_dbg_pkg=True, no_ext_rename=False, no_shebang_rewrite=False, private_dir=None, O=['--buildsystem=pybuild']) D: dh_python3 dh_python3:182: supported Python versions: 3.11 (default=3.11) D: dh_python3 debhelper:149: skipping package: python-biopython-doc D: dh_python3 debhelper:183: source=python-biopython, binary packages=['python3-biopython'] D: dh_python3 dh_python3:204: processing package python3-biopython... D: dh_python3 fs:52: moving files from debian/python3-biopython/usr/lib/python3.11/dist-packages to debian/python3-biopython/usr/lib/python3/dist-packages/ D: dh_python3 fs:408: package python3-biopython details = {'requires.txt': {'debian/python3-biopython/usr/lib/python3/dist-packages/biopython-1.80.egg-info/requires.txt'}, 'egg-info': set(), 'dist-info': set(), 'nsp.txt': set(), 'shebangs': set(), 'public_vers': {Version('3')}, 'private_dirs': {}, 'compile': True, 'ext_vers': {Version('3.11')}, 'ext_no_version': set()} D: dh_python3 depends:117: generating dependencies for package python3-biopython D: dh_python3 pydist:173: trying to find dependency for numpy (python=None) D: dh_python3 pydist:207: dependency: module seems to be installed D: dh_python3 pydist:270: dependency: included in build-deps D: dh_python3 depends:281: D={'python3 (>= 3.11~)', 'python3:any', 'python3-numpy', 'python3 (<< 3.12)'}; R=[]; S=[]; E=[], B=[]; RT=[] dh_installsystemduser -a -O--buildsystem=pybuild dh_lintian -a -O--buildsystem=pybuild install -m0755 -d debian/python3-biopython/usr/share/lintian/overrides install -p -m0644 debian/python3-biopython.lintian-overrides debian/python3-biopython/usr/share/lintian/overrides/python3-biopython dh_perl -a -O--buildsystem=pybuild dh_link -a -O--buildsystem=pybuild install -m0755 -d debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Entrez/DTDs rm -f debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Entrez/DTDs/mathml2.dtd ln -s ../../../../../../share/xml/w3c-sgml-lib/schema/dtd/XX-MathML2-20031104/mathml2.dtd debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Entrez/DTDs/mathml2.dtd dh_strip_nondeterminism -a -O--buildsystem=pybuild dh_compress -a -O--buildsystem=pybuild cd debian/python3-biopython chmod a-x usr/share/doc/python3-biopython/CONTRIB.rst usr/share/doc/python3-biopython/DEPRECATED.rst usr/share/doc/python3-biopython/NEWS.Debian usr/share/doc/python3-biopython/NEWS.rst usr/share/doc/python3-biopython/changelog.Debian gzip -9nf usr/share/doc/python3-biopython/CONTRIB.rst usr/share/doc/python3-biopython/DEPRECATED.rst usr/share/doc/python3-biopython/NEWS.Debian usr/share/doc/python3-biopython/NEWS.rst usr/share/doc/python3-biopython/changelog.Debian cd '/<>' rm -f debian/python3-biopython.debhelper.log debian/rules override_dh_fixperms make[1]: Entering directory '/<>' dh_fixperms find debian/python3-biopython ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/python3-biopython/usr/share/doc -type f -a -true -a ! -regex 'debian/python3-biopython/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-biopython/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/python3-biopython/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-biopython -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-biopython/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian -name "*.dtd" -exec chmod -x \{\} \; chmod: cannot operate on dangling symlink 'debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Entrez/DTDs/mathml2.dtd' make[1]: Leaving directory '/<>' dh_missing -a -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild install -m0755 -d debian/python3-biopython/usr/lib/debug/.dwz/riscv64-linux-gnu dwz -mdebian/python3-biopython/usr/lib/debug/.dwz/riscv64-linux-gnu/python3-biopython.debug -M/usr/lib/debug/.dwz/riscv64-linux-gnu/python3-biopython.debug -- debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Align/_aligners.cpython-311-riscv64-linux-gnu.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Cluster/_cluster.cpython-311-riscv64-linux-gnu.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Nexus/cnexus.cpython-311-riscv64-linux-gnu.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-riscv64-linux-gnu.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/ccealign.cpython-311-riscv64-linux-gnu.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/kdtrees.cpython-311-riscv64-linux-gnu.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/SeqIO/_twoBitIO.cpython-311-riscv64-linux-gnu.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/cpairwise2.cpython-311-riscv64-linux-gnu.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/motifs/_pwm.cpython-311-riscv64-linux-gnu.so objcopy --compress-debug-sections debian/python3-biopython/usr/lib/debug/.dwz/riscv64-linux-gnu/python3-biopython.debug chmod 0644 -- debian/python3-biopython/usr/lib/debug/.dwz/riscv64-linux-gnu/python3-biopython.debug dh_strip -a -O--buildsystem=pybuild debugedit --build-id --build-id-seed=python3-biopython/1.80\+dfsg-4ubuntu1 debian/python3-biopython/usr/lib/python3/dist-packages/Bio/cpairwise2.cpython-311-riscv64-linux-gnu.so debugedit: debian/python3-biopython/usr/lib/python3/dist-packages/Bio/cpairwise2.cpython-311-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 c82cb7511a5a229e9f74a5d01c0ecdcf4d9d9eb5 install -m0755 -d debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/c8 objcopy --only-keep-debug --compress-debug-sections debian/python3-biopython/usr/lib/python3/dist-packages/Bio/cpairwise2.cpython-311-riscv64-linux-gnu.so debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/c8/2cb7511a5a229e9f74a5d01c0ecdcf4d9d9eb5.debug chmod 0644 -- debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/c8/2cb7511a5a229e9f74a5d01c0ecdcf4d9d9eb5.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/jEhEryngS5/stripK5__lZ debian/python3-biopython/usr/lib/python3/dist-packages/Bio/cpairwise2.cpython-311-riscv64-linux-gnu.so chmod --reference debian/python3-biopython/usr/lib/python3/dist-packages/Bio/cpairwise2.cpython-311-riscv64-linux-gnu.so /tmp/jEhEryngS5/stripK5__lZ cat '/tmp/jEhEryngS5/stripK5__lZ' > 'debian/python3-biopython/usr/lib/python3/dist-packages/Bio/cpairwise2.cpython-311-riscv64-linux-gnu.so' chmod --reference /tmp/jEhEryngS5/stripK5__lZ debian/python3-biopython/usr/lib/python3/dist-packages/Bio/cpairwise2.cpython-311-riscv64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/c8/2cb7511a5a229e9f74a5d01c0ecdcf4d9d9eb5.debug debian/python3-biopython/usr/lib/python3/dist-packages/Bio/cpairwise2.cpython-311-riscv64-linux-gnu.so /tmp/jEhEryngS5/objcopy75XLxD chmod --reference debian/python3-biopython/usr/lib/python3/dist-packages/Bio/cpairwise2.cpython-311-riscv64-linux-gnu.so /tmp/jEhEryngS5/objcopy75XLxD cat '/tmp/jEhEryngS5/objcopy75XLxD' > 'debian/python3-biopython/usr/lib/python3/dist-packages/Bio/cpairwise2.cpython-311-riscv64-linux-gnu.so' chmod --reference /tmp/jEhEryngS5/objcopy75XLxD debian/python3-biopython/usr/lib/python3/dist-packages/Bio/cpairwise2.cpython-311-riscv64-linux-gnu.so debugedit --build-id --build-id-seed=python3-biopython/1.80\+dfsg-4ubuntu1 debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Nexus/cnexus.cpython-311-riscv64-linux-gnu.so debugedit: debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Nexus/cnexus.cpython-311-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 67ffbda8195f505f2fb121a0f01dde2bdb78bf5a install -m0755 -d debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/67 objcopy --only-keep-debug --compress-debug-sections debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Nexus/cnexus.cpython-311-riscv64-linux-gnu.so debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/67/ffbda8195f505f2fb121a0f01dde2bdb78bf5a.debug chmod 0644 -- debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/67/ffbda8195f505f2fb121a0f01dde2bdb78bf5a.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/jEhEryngS5/stripPC2tGf debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Nexus/cnexus.cpython-311-riscv64-linux-gnu.so chmod --reference debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Nexus/cnexus.cpython-311-riscv64-linux-gnu.so /tmp/jEhEryngS5/stripPC2tGf cat '/tmp/jEhEryngS5/stripPC2tGf' > 'debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Nexus/cnexus.cpython-311-riscv64-linux-gnu.so' chmod --reference /tmp/jEhEryngS5/stripPC2tGf debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Nexus/cnexus.cpython-311-riscv64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/67/ffbda8195f505f2fb121a0f01dde2bdb78bf5a.debug debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Nexus/cnexus.cpython-311-riscv64-linux-gnu.so /tmp/jEhEryngS5/objcopyYmfBE0 chmod --reference debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Nexus/cnexus.cpython-311-riscv64-linux-gnu.so /tmp/jEhEryngS5/objcopyYmfBE0 cat '/tmp/jEhEryngS5/objcopyYmfBE0' > 'debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Nexus/cnexus.cpython-311-riscv64-linux-gnu.so' chmod --reference /tmp/jEhEryngS5/objcopyYmfBE0 debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Nexus/cnexus.cpython-311-riscv64-linux-gnu.so debugedit --build-id --build-id-seed=python3-biopython/1.80\+dfsg-4ubuntu1 debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Align/_aligners.cpython-311-riscv64-linux-gnu.so debugedit: debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Align/_aligners.cpython-311-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 427e83aa04c0d7a637b2a96c8ffe0afc2b7dd9f8 install -m0755 -d debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/42 objcopy --only-keep-debug --compress-debug-sections debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Align/_aligners.cpython-311-riscv64-linux-gnu.so debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/42/7e83aa04c0d7a637b2a96c8ffe0afc2b7dd9f8.debug chmod 0644 -- debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/42/7e83aa04c0d7a637b2a96c8ffe0afc2b7dd9f8.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/jEhEryngS5/stripc0NUDt debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Align/_aligners.cpython-311-riscv64-linux-gnu.so chmod --reference debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Align/_aligners.cpython-311-riscv64-linux-gnu.so /tmp/jEhEryngS5/stripc0NUDt cat '/tmp/jEhEryngS5/stripc0NUDt' > 'debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Align/_aligners.cpython-311-riscv64-linux-gnu.so' chmod --reference /tmp/jEhEryngS5/stripc0NUDt debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Align/_aligners.cpython-311-riscv64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/42/7e83aa04c0d7a637b2a96c8ffe0afc2b7dd9f8.debug debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Align/_aligners.cpython-311-riscv64-linux-gnu.so /tmp/jEhEryngS5/objcopyE4aPKC chmod --reference debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Align/_aligners.cpython-311-riscv64-linux-gnu.so /tmp/jEhEryngS5/objcopyE4aPKC cat '/tmp/jEhEryngS5/objcopyE4aPKC' > 'debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Align/_aligners.cpython-311-riscv64-linux-gnu.so' chmod --reference /tmp/jEhEryngS5/objcopyE4aPKC debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Align/_aligners.cpython-311-riscv64-linux-gnu.so debugedit --build-id --build-id-seed=python3-biopython/1.80\+dfsg-4ubuntu1 debian/python3-biopython/usr/lib/python3/dist-packages/Bio/SeqIO/_twoBitIO.cpython-311-riscv64-linux-gnu.so debugedit: debian/python3-biopython/usr/lib/python3/dist-packages/Bio/SeqIO/_twoBitIO.cpython-311-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 0894b6c793ebc5656bbc4d7668562c5492f7e486 install -m0755 -d debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/08 objcopy --only-keep-debug --compress-debug-sections debian/python3-biopython/usr/lib/python3/dist-packages/Bio/SeqIO/_twoBitIO.cpython-311-riscv64-linux-gnu.so debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/08/94b6c793ebc5656bbc4d7668562c5492f7e486.debug chmod 0644 -- debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/08/94b6c793ebc5656bbc4d7668562c5492f7e486.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/jEhEryngS5/stripzPkLNk debian/python3-biopython/usr/lib/python3/dist-packages/Bio/SeqIO/_twoBitIO.cpython-311-riscv64-linux-gnu.so chmod --reference debian/python3-biopython/usr/lib/python3/dist-packages/Bio/SeqIO/_twoBitIO.cpython-311-riscv64-linux-gnu.so /tmp/jEhEryngS5/stripzPkLNk cat '/tmp/jEhEryngS5/stripzPkLNk' > 'debian/python3-biopython/usr/lib/python3/dist-packages/Bio/SeqIO/_twoBitIO.cpython-311-riscv64-linux-gnu.so' chmod --reference /tmp/jEhEryngS5/stripzPkLNk debian/python3-biopython/usr/lib/python3/dist-packages/Bio/SeqIO/_twoBitIO.cpython-311-riscv64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/08/94b6c793ebc5656bbc4d7668562c5492f7e486.debug debian/python3-biopython/usr/lib/python3/dist-packages/Bio/SeqIO/_twoBitIO.cpython-311-riscv64-linux-gnu.so /tmp/jEhEryngS5/objcopy8RcBFl chmod --reference debian/python3-biopython/usr/lib/python3/dist-packages/Bio/SeqIO/_twoBitIO.cpython-311-riscv64-linux-gnu.so /tmp/jEhEryngS5/objcopy8RcBFl cat '/tmp/jEhEryngS5/objcopy8RcBFl' > 'debian/python3-biopython/usr/lib/python3/dist-packages/Bio/SeqIO/_twoBitIO.cpython-311-riscv64-linux-gnu.so' chmod --reference /tmp/jEhEryngS5/objcopy8RcBFl debian/python3-biopython/usr/lib/python3/dist-packages/Bio/SeqIO/_twoBitIO.cpython-311-riscv64-linux-gnu.so debugedit --build-id --build-id-seed=python3-biopython/1.80\+dfsg-4ubuntu1 debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/ccealign.cpython-311-riscv64-linux-gnu.so debugedit: debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/ccealign.cpython-311-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 774c209ae135bf71f9be926ababb6732536fe9fe install -m0755 -d debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/77 objcopy --only-keep-debug --compress-debug-sections debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/ccealign.cpython-311-riscv64-linux-gnu.so debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/77/4c209ae135bf71f9be926ababb6732536fe9fe.debug chmod 0644 -- debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/77/4c209ae135bf71f9be926ababb6732536fe9fe.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/jEhEryngS5/strips4pL58 debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/ccealign.cpython-311-riscv64-linux-gnu.so chmod --reference debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/ccealign.cpython-311-riscv64-linux-gnu.so /tmp/jEhEryngS5/strips4pL58 cat '/tmp/jEhEryngS5/strips4pL58' > 'debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/ccealign.cpython-311-riscv64-linux-gnu.so' chmod --reference /tmp/jEhEryngS5/strips4pL58 debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/ccealign.cpython-311-riscv64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/77/4c209ae135bf71f9be926ababb6732536fe9fe.debug debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/ccealign.cpython-311-riscv64-linux-gnu.so /tmp/jEhEryngS5/objcopyncrlen chmod --reference debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/ccealign.cpython-311-riscv64-linux-gnu.so /tmp/jEhEryngS5/objcopyncrlen cat '/tmp/jEhEryngS5/objcopyncrlen' > 'debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/ccealign.cpython-311-riscv64-linux-gnu.so' chmod --reference /tmp/jEhEryngS5/objcopyncrlen debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/ccealign.cpython-311-riscv64-linux-gnu.so debugedit --build-id --build-id-seed=python3-biopython/1.80\+dfsg-4ubuntu1 debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/kdtrees.cpython-311-riscv64-linux-gnu.so debugedit: debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/kdtrees.cpython-311-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 28846c811fbe14ec634ccb42b0d5ce551534eb9f install -m0755 -d debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/28 objcopy --only-keep-debug --compress-debug-sections debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/kdtrees.cpython-311-riscv64-linux-gnu.so debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/28/846c811fbe14ec634ccb42b0d5ce551534eb9f.debug chmod 0644 -- debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/28/846c811fbe14ec634ccb42b0d5ce551534eb9f.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/jEhEryngS5/strip6z6RZz debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/kdtrees.cpython-311-riscv64-linux-gnu.so chmod --reference debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/kdtrees.cpython-311-riscv64-linux-gnu.so /tmp/jEhEryngS5/strip6z6RZz cat '/tmp/jEhEryngS5/strip6z6RZz' > 'debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/kdtrees.cpython-311-riscv64-linux-gnu.so' chmod --reference /tmp/jEhEryngS5/strip6z6RZz debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/kdtrees.cpython-311-riscv64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/28/846c811fbe14ec634ccb42b0d5ce551534eb9f.debug debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/kdtrees.cpython-311-riscv64-linux-gnu.so /tmp/jEhEryngS5/objcopyqqSApG chmod --reference debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/kdtrees.cpython-311-riscv64-linux-gnu.so /tmp/jEhEryngS5/objcopyqqSApG cat '/tmp/jEhEryngS5/objcopyqqSApG' > 'debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/kdtrees.cpython-311-riscv64-linux-gnu.so' chmod --reference /tmp/jEhEryngS5/objcopyqqSApG debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/kdtrees.cpython-311-riscv64-linux-gnu.so debugedit --build-id --build-id-seed=python3-biopython/1.80\+dfsg-4ubuntu1 debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-riscv64-linux-gnu.so debugedit: debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 9506337ba820f17dbb04f584c7bdd17dc1049dc5 install -m0755 -d debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/95 objcopy --only-keep-debug --compress-debug-sections debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-riscv64-linux-gnu.so debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/95/06337ba820f17dbb04f584c7bdd17dc1049dc5.debug chmod 0644 -- debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/95/06337ba820f17dbb04f584c7bdd17dc1049dc5.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/jEhEryngS5/stripQARDmL debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-riscv64-linux-gnu.so chmod --reference debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-riscv64-linux-gnu.so /tmp/jEhEryngS5/stripQARDmL cat '/tmp/jEhEryngS5/stripQARDmL' > 'debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-riscv64-linux-gnu.so' chmod --reference /tmp/jEhEryngS5/stripQARDmL debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-riscv64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/95/06337ba820f17dbb04f584c7bdd17dc1049dc5.debug debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-riscv64-linux-gnu.so /tmp/jEhEryngS5/objcopyJYDgCO chmod --reference debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-riscv64-linux-gnu.so /tmp/jEhEryngS5/objcopyJYDgCO cat '/tmp/jEhEryngS5/objcopyJYDgCO' > 'debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-riscv64-linux-gnu.so' chmod --reference /tmp/jEhEryngS5/objcopyJYDgCO debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-riscv64-linux-gnu.so debugedit --build-id --build-id-seed=python3-biopython/1.80\+dfsg-4ubuntu1 debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Cluster/_cluster.cpython-311-riscv64-linux-gnu.so debugedit: debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Cluster/_cluster.cpython-311-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 0fb1295af51ef79b4086449324a91bc1d275a559 install -m0755 -d debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/0f objcopy --only-keep-debug --compress-debug-sections debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Cluster/_cluster.cpython-311-riscv64-linux-gnu.so debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/0f/b1295af51ef79b4086449324a91bc1d275a559.debug chmod 0644 -- debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/0f/b1295af51ef79b4086449324a91bc1d275a559.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/jEhEryngS5/stripea9XKG debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Cluster/_cluster.cpython-311-riscv64-linux-gnu.so chmod --reference debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Cluster/_cluster.cpython-311-riscv64-linux-gnu.so /tmp/jEhEryngS5/stripea9XKG cat '/tmp/jEhEryngS5/stripea9XKG' > 'debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Cluster/_cluster.cpython-311-riscv64-linux-gnu.so' chmod --reference /tmp/jEhEryngS5/stripea9XKG debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Cluster/_cluster.cpython-311-riscv64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/0f/b1295af51ef79b4086449324a91bc1d275a559.debug debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Cluster/_cluster.cpython-311-riscv64-linux-gnu.so /tmp/jEhEryngS5/objcopyR5LmhX chmod --reference debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Cluster/_cluster.cpython-311-riscv64-linux-gnu.so /tmp/jEhEryngS5/objcopyR5LmhX cat '/tmp/jEhEryngS5/objcopyR5LmhX' > 'debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Cluster/_cluster.cpython-311-riscv64-linux-gnu.so' chmod --reference /tmp/jEhEryngS5/objcopyR5LmhX debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Cluster/_cluster.cpython-311-riscv64-linux-gnu.so debugedit --build-id --build-id-seed=python3-biopython/1.80\+dfsg-4ubuntu1 debian/python3-biopython/usr/lib/python3/dist-packages/Bio/motifs/_pwm.cpython-311-riscv64-linux-gnu.so debugedit: debian/python3-biopython/usr/lib/python3/dist-packages/Bio/motifs/_pwm.cpython-311-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 2069f4c1e6874f74cffbfba381b895bd36e875e7 install -m0755 -d debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/20 objcopy --only-keep-debug --compress-debug-sections debian/python3-biopython/usr/lib/python3/dist-packages/Bio/motifs/_pwm.cpython-311-riscv64-linux-gnu.so debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/20/69f4c1e6874f74cffbfba381b895bd36e875e7.debug chmod 0644 -- debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/20/69f4c1e6874f74cffbfba381b895bd36e875e7.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/jEhEryngS5/stripZfGu3f debian/python3-biopython/usr/lib/python3/dist-packages/Bio/motifs/_pwm.cpython-311-riscv64-linux-gnu.so chmod --reference debian/python3-biopython/usr/lib/python3/dist-packages/Bio/motifs/_pwm.cpython-311-riscv64-linux-gnu.so /tmp/jEhEryngS5/stripZfGu3f cat '/tmp/jEhEryngS5/stripZfGu3f' > 'debian/python3-biopython/usr/lib/python3/dist-packages/Bio/motifs/_pwm.cpython-311-riscv64-linux-gnu.so' chmod --reference /tmp/jEhEryngS5/stripZfGu3f debian/python3-biopython/usr/lib/python3/dist-packages/Bio/motifs/_pwm.cpython-311-riscv64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/20/69f4c1e6874f74cffbfba381b895bd36e875e7.debug debian/python3-biopython/usr/lib/python3/dist-packages/Bio/motifs/_pwm.cpython-311-riscv64-linux-gnu.so /tmp/jEhEryngS5/objcopyn6jKwM chmod --reference debian/python3-biopython/usr/lib/python3/dist-packages/Bio/motifs/_pwm.cpython-311-riscv64-linux-gnu.so /tmp/jEhEryngS5/objcopyn6jKwM cat '/tmp/jEhEryngS5/objcopyn6jKwM' > 'debian/python3-biopython/usr/lib/python3/dist-packages/Bio/motifs/_pwm.cpython-311-riscv64-linux-gnu.so' chmod --reference /tmp/jEhEryngS5/objcopyn6jKwM debian/python3-biopython/usr/lib/python3/dist-packages/Bio/motifs/_pwm.cpython-311-riscv64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/python3-biopython/usr/lib/debug/.dwz/riscv64-linux-gnu debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/python3-biopython/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/python3-biopython/usr/lib/debug install -m0755 -d debian/.debhelper/python3-biopython/dbgsym-root/usr/share/doc ln -s python3-biopython debian/.debhelper/python3-biopython/dbgsym-root/usr/share/doc/python3-biopython-dbgsym install -m0755 -d debian/.debhelper/python3-biopython dh_makeshlibs -a -O--buildsystem=pybuild rm -f debian/python3-biopython/DEBIAN/shlibs dh_shlibdeps -a -O--buildsystem=pybuild install -m0755 -d debian/python3-biopython/DEBIAN dpkg-shlibdeps -Tdebian/python3-biopython.substvars debian/python3-biopython/usr/lib/python3/dist-packages/Bio/cpairwise2.cpython-311-riscv64-linux-gnu.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Nexus/cnexus.cpython-311-riscv64-linux-gnu.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Align/_aligners.cpython-311-riscv64-linux-gnu.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/SeqIO/_twoBitIO.cpython-311-riscv64-linux-gnu.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/ccealign.cpython-311-riscv64-linux-gnu.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/kdtrees.cpython-311-riscv64-linux-gnu.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-riscv64-linux-gnu.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Cluster/_cluster.cpython-311-riscv64-linux-gnu.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/motifs/_pwm.cpython-311-riscv64-linux-gnu.so dh_installdeb -a -O--buildsystem=pybuild install -m0755 -d debian/python3-biopython/DEBIAN printf '#!/bin/sh\nset -e\n' > debian/python3-biopython/DEBIAN/postinst cat debian/python3-biopython.postinst.debhelper >> debian/python3-biopython/DEBIAN/postinst chmod 0755 -- debian/python3-biopython/DEBIAN/postinst printf '#!/bin/sh\nset -e\n' > debian/python3-biopython/DEBIAN/prerm cat debian/python3-biopython.prerm.debhelper >> debian/python3-biopython/DEBIAN/prerm chmod 0755 -- debian/python3-biopython/DEBIAN/prerm dh_gencontrol -a -O--buildsystem=pybuild install -m0755 -d debian/python3-biopython/DEBIAN echo misc:Depends= >> debian/python3-biopython.substvars echo misc:Pre-Depends= >> debian/python3-biopython.substvars install -m0755 -d debian/.debhelper/python3-biopython/dbgsym-root/DEBIAN dpkg-gencontrol -ppython3-biopython -ldebian/changelog -Tdebian/python3-biopython.substvars -Pdebian/.debhelper/python3-biopython/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=python3-biopython-dbgsym "-DDepends=python3-biopython (= \${binary:Version})" "-DDescription=debug symbols for python3-biopython" "-DBuild-Ids=0894b6c793ebc5656bbc4d7668562c5492f7e486 0fb1295af51ef79b4086449324a91bc1d275a559 2069f4c1e6874f74cffbfba381b895bd36e875e7 28846c811fbe14ec634ccb42b0d5ce551534eb9f 427e83aa04c0d7a637b2a96c8ffe0afc2b7dd9f8 67ffbda8195f505f2fb121a0f01dde2bdb78bf5a 774c209ae135bf71f9be926ababb6732536fe9fe 9506337ba820f17dbb04f584c7bdd17dc1049dc5 c82cb7511a5a229e9f74a5d01c0ecdcf4d9d9eb5" -DSection=debug -DPackage-Type=ddeb -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/python3-biopython/dbgsym-root/DEBIAN/control dpkg-gencontrol -ppython3-biopython -ldebian/changelog -Tdebian/python3-biopython.substvars -Pdebian/python3-biopython chmod 0644 -- debian/python3-biopython/DEBIAN/control dh_md5sums -a -O--buildsystem=pybuild install -m0755 -d debian/python3-biopython/DEBIAN cd debian/python3-biopython >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/python3-biopython/DEBIAN/md5sums install -m0755 -d debian/.debhelper/python3-biopython/dbgsym-root/DEBIAN cd debian/.debhelper/python3-biopython/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/python3-biopython/dbgsym-root/DEBIAN/md5sums dh_builddeb -a -O--buildsystem=pybuild dpkg-deb --root-owner-group --build debian/python3-biopython .. dpkg-deb --root-owner-group --build debian/.debhelper/python3-biopython/dbgsym-root debian/.debhelper/scratch-space/build-python3-biopython INFO: pkgstriptranslations version 153 INFO: pkgstriptranslations version 153 pkgstriptranslations: processing python3-biopython-dbgsym (in debian/.debhelper/python3-biopython/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing python3-biopython (in debian/python3-biopython); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/.debhelper/python3-biopython/dbgsym-root/DEBIAN/control, package python3-biopython-dbgsym, directory debian/.debhelper/python3-biopython/dbgsym-root dpkg-deb: building package 'python3-biopython-dbgsym' in 'debian/.debhelper/scratch-space/build-python3-biopython/python3-biopython-dbgsym_1.80+dfsg-4ubuntu1_riscv64.deb'. pkgstripfiles: processing control file: debian/python3-biopython/DEBIAN/control, package python3-biopython, directory debian/python3-biopython pkgstripfiles: Running PNG optimization (using 8 cpus) for package python3-biopython ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python3-biopython' in '../python3-biopython_1.80+dfsg-4ubuntu1_riscv64.deb'. Renaming python3-biopython-dbgsym_1.80+dfsg-4ubuntu1_riscv64.deb to python3-biopython-dbgsym_1.80+dfsg-4ubuntu1_riscv64.ddeb mv debian/.debhelper/scratch-space/build-python3-biopython/python3-biopython-dbgsym_1.80\+dfsg-4ubuntu1_riscv64.deb ../python3-biopython-dbgsym_1.80\+dfsg-4ubuntu1_riscv64.ddeb dpkg-genbuildinfo --build=any -O../python-biopython_1.80+dfsg-4ubuntu1_riscv64.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../python-biopython_1.80+dfsg-4ubuntu1_riscv64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2023-06-27T10:46:44Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ python-biopython_1.80+dfsg-4ubuntu1_riscv64.changes: ---------------------------------------------------- Format: 1.8 Date: Tue, 27 Jun 2023 11:17:19 +0200 Source: python-biopython Binary: python3-biopython Built-For-Profiles: noudeb Architecture: riscv64 Version: 1.80+dfsg-4ubuntu1 Distribution: mantic-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Lukas Märdian Description: python3-biopython - Python3 library for bioinformatics Launchpad-Bugs-Fixed: 2025133 Changes: python-biopython (1.80+dfsg-4ubuntu1) mantic; urgency=medium . * Drop python3-renderpm dependency, as this binary got dropped from src:python-reportlab by its (new) maintainer. (LP: #2025133) Checksums-Sha1: df775b10ab6d4684f881bceb5264d14728a4465c 13603 python-biopython_1.80+dfsg-4ubuntu1_riscv64.buildinfo 90fd8248eae3656273321b9f1e0bbb5f1ee72356 272168 python3-biopython-dbgsym_1.80+dfsg-4ubuntu1_riscv64.ddeb efb7c9dcea01a907c4068298b4cce3b1fbacd1a6 1622564 python3-biopython_1.80+dfsg-4ubuntu1_riscv64.deb Checksums-Sha256: f682465c72558b8f7b3f83dd54b58e891dbe5796c4d741d08570cc61b69f32eb 13603 python-biopython_1.80+dfsg-4ubuntu1_riscv64.buildinfo 4d347c8b7602694fea4adfe0dca9c34fb5a8af8b2d1fd5b6102eeb62588744de 272168 python3-biopython-dbgsym_1.80+dfsg-4ubuntu1_riscv64.ddeb cd70b24a94165610158fb08ae893bae86ba653a295d80a9592e5e7784aeaebcb 1622564 python3-biopython_1.80+dfsg-4ubuntu1_riscv64.deb Files: abcad3c94b5a9c44f96076caaea4057f 13603 python optional python-biopython_1.80+dfsg-4ubuntu1_riscv64.buildinfo 4225e7ad46ef9dea9c858d76d7cd9ca0 272168 debug optional python3-biopython-dbgsym_1.80+dfsg-4ubuntu1_riscv64.ddeb 3586c40b3b89419111396afbe6dec1f4 1622564 python optional python3-biopython_1.80+dfsg-4ubuntu1_riscv64.deb Original-Maintainer: Debian Med Packaging Team /<>/python-biopython_1.80+dfsg-4ubuntu1_riscv64.changes.new could not be renamed to /<>/python-biopython_1.80+dfsg-4ubuntu1_riscv64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: python-biopython Binary: python3-biopython python3-biopython-dbgsym Architecture: riscv64 Version: 1.80+dfsg-4ubuntu1 Checksums-Md5: 4225e7ad46ef9dea9c858d76d7cd9ca0 272168 python3-biopython-dbgsym_1.80+dfsg-4ubuntu1_riscv64.ddeb 3586c40b3b89419111396afbe6dec1f4 1622564 python3-biopython_1.80+dfsg-4ubuntu1_riscv64.deb Checksums-Sha1: 90fd8248eae3656273321b9f1e0bbb5f1ee72356 272168 python3-biopython-dbgsym_1.80+dfsg-4ubuntu1_riscv64.ddeb efb7c9dcea01a907c4068298b4cce3b1fbacd1a6 1622564 python3-biopython_1.80+dfsg-4ubuntu1_riscv64.deb Checksums-Sha256: 4d347c8b7602694fea4adfe0dca9c34fb5a8af8b2d1fd5b6102eeb62588744de 272168 python3-biopython-dbgsym_1.80+dfsg-4ubuntu1_riscv64.ddeb cd70b24a94165610158fb08ae893bae86ba653a295d80a9592e5e7784aeaebcb 1622564 python3-biopython_1.80+dfsg-4ubuntu1_riscv64.deb Build-Origin: Ubuntu Build-Architecture: riscv64 Build-Date: Tue, 27 Jun 2023 10:46:39 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.21-12), autotools-dev (= 20220109.1), base-files (= 13ubuntu1), base-passwd (= 3.6.1), bash (= 5.2.15-2ubuntu1), binutils (= 2.40.50.20230622-1ubuntu1), binutils-common (= 2.40.50.20230622-1ubuntu1), binutils-riscv64-linux-gnu (= 2.40.50.20230622-1ubuntu1), blt (= 2.5.3+dfsg-4.1build2), bsdextrautils (= 2.38.1-5ubuntu2), bsdutils (= 1:2.38.1-5ubuntu2), build-essential (= 12.9ubuntu3), bwa (= 0.7.17-7), bzip2 (= 1.0.8-5build1), clustalo (= 1.2.4-7), clustalw (= 2.1+lgpl-7), coreutils (= 9.1-1ubuntu2), cpp (= 4:12.2.0-3ubuntu1), cpp-12 (= 12.3.0-3ubuntu1), dash (= 0.5.12-2ubuntu1), debconf (= 1.5.82), debhelper (= 13.11.4ubuntu3), debianutils (= 5.7-0.4), debugedit (= 1:5.0-5), dh-autoreconf (= 20), dh-python (= 6.20230603), dh-strip-nondeterminism (= 1.13.1-1), dialign (= 2.2.1-11), diffutils (= 1:3.8-4), dpkg (= 1.21.22ubuntu1), dpkg-dev (= 1.21.22ubuntu1), dssp (= 4.2.2-2), dwz (= 0.15-1), emboss (= 6.6.0+dfsg-12ubuntu1), emboss-data (= 6.6.0+dfsg-12ubuntu1), emboss-lib (= 6.6.0+dfsg-12ubuntu1), fasttree (= 2.1.11-2), file (= 1:5.44-3), findutils (= 4.9.0-4ubuntu1), flex (= 2.6.4-8.2), fontconfig-config (= 2.14.1-4ubuntu1), fonts-dejavu-core (= 2.37-6), fonts-lmodern (= 2.005-1), fonts-lyx (= 2.3.7-1), fonts-urw-base35 (= 20200910-7), g++ (= 4:12.2.0-3ubuntu1), g++-12 (= 12.3.0-3ubuntu1), gcc (= 4:12.2.0-3ubuntu1), gcc-12 (= 12.3.0-3ubuntu1), gcc-12-base (= 12.3.0-3ubuntu1), gcc-13-base (= 13.1.0-6ubuntu1), gettext (= 0.21-12), gettext-base (= 0.21-12), ghostscript (= 10.0.0~dfsg1-0ubuntu1.1), grep (= 3.8-5), groff-base (= 1.22.4-10), gzip (= 1.12-1ubuntu1), hevea (= 2.36-1build1), hicolor-icon-theme (= 0.17-2), hostname (= 3.23+nmu1ubuntu1), imagemagick (= 8:6.9.11.60+dfsg-1.6), imagemagick-6-common (= 8:6.9.11.60+dfsg-1.6), imagemagick-6.q16 (= 8:6.9.11.60+dfsg-1.6), init-system-helpers (= 1.65.2), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.1-3), libaom3 (= 3.6.1-1), libapache-pom-java (= 29-2), libarchive-zip-perl (= 1.68-1), libargtable2-0 (= 13-1.1), libasan8 (= 13.1.0-6ubuntu1), libatomic1 (= 13.1.0-6ubuntu1), libattr1 (= 1:2.5.1-4), libaudit-common (= 1:3.0.9-1), libaudit1 (= 1:3.0.9-1), libavahi-client3 (= 0.8-10ubuntu1), libavahi-common-data (= 0.8-10ubuntu1), libavahi-common3 (= 0.8-10ubuntu1), libbinutils (= 2.40.50.20230622-1ubuntu1), libblas3 (= 3.11.0-2), libblkid1 (= 2.38.1-5ubuntu2), libboost-dev (= 1.74.0.3ubuntu7), libboost-regex1.74.0 (= 1.74.0+ds1-21.1ubuntu1), libboost1.74-dev (= 1.74.0+ds1-21.1ubuntu1), libbrotli1 (= 1.0.9-2build8), libbsd0 (= 0.11.7-4), libbz2-1.0 (= 1.0.8-5build1), libc-bin (= 2.37-0ubuntu2), libc-dev-bin (= 2.37-0ubuntu2), libc6 (= 2.37-0ubuntu2), libc6-dev (= 2.37-0ubuntu2), libcairo2 (= 1.16.0-7), libcap-ng0 (= 0.8.3-1build2), libcap2 (= 1:2.66-4ubuntu1), libcc1-0 (= 13.1.0-6ubuntu1), libcifpp-data (= 5.0.7.1-1build1), libcifpp5 (= 5.0.7.1-1build1), libcom-err2 (= 1.47.0-1ubuntu1), libcommons-logging-java (= 1.2-3), libcommons-parent-java (= 56-1), libcrypt-dev (= 1:4.4.35-1), libcrypt1 (= 1:4.4.35-1), libctf-nobfd0 (= 2.40.50.20230622-1ubuntu1), libctf0 (= 2.40.50.20230622-1ubuntu1), libcups2 (= 2.4.5-0ubuntu2), libcurl3-gnutls (= 7.88.1-10ubuntu1), libdav1d6 (= 1.2.1-2), libdb5.3 (= 5.3.28+dfsg2-1), libdbus-1-3 (= 1.14.6-1ubuntu1), libde265-0 (= 1.0.12-1), libdebconfclient0 (= 0.267ubuntu1), libdebhelper-perl (= 13.11.4ubuntu3), libdeflate0 (= 1.15-1), libdpkg-perl (= 1.21.22ubuntu1), libdw1 (= 0.188-2.1), libelf1 (= 0.188-2.1), libexpat1 (= 2.5.0-2), libexpat1-dev (= 2.5.0-2), libffi8 (= 3.4.4-1), libfftw3-double3 (= 3.3.10-1ubuntu1), libfile-stripnondeterminism-perl (= 1.13.1-1), libfontbox-java (= 1:1.8.16-2), libfontconfig1 (= 2.14.1-4ubuntu1), libfontenc1 (= 1:1.1.4-1build3), libfreetype6 (= 2.12.1+dfsg-5), libfribidi0 (= 1.0.13-3), libgcc-12-dev (= 12.3.0-3ubuntu1), libgcc-s1 (= 13.1.0-6ubuntu1), libgcrypt20 (= 1.10.1-3ubuntu1), libgd3 (= 2.3.3-9ubuntu1), libgdbm-compat4 (= 1.23-3), libgdbm6 (= 1.23-3), libgfortran5 (= 13.1.0-6ubuntu1), libglib2.0-0 (= 2.76.3-1ubuntu1), libgmp10 (= 2:6.2.1+dfsg1-1.1ubuntu1), libgnutls30 (= 3.7.9-2ubuntu1), libgomp1 (= 13.1.0-6ubuntu1), libgpg-error0 (= 1.46-1), libgraphite2-3 (= 1.3.14-1build2), libgs-common (= 10.0.0~dfsg1-0ubuntu1.1), libgs10 (= 10.0.0~dfsg1-0ubuntu1.1), libgs10-common (= 10.0.0~dfsg1-0ubuntu1.1), libgssapi-krb5-2 (= 1.20.1-2), libharfbuzz0b (= 6.0.0+dfsg-3build1), libheif1 (= 1.15.1-1), libhogweed6 (= 3.8.1-2), libhpdf-2.3.0 (= 2.3.0+dfsg-1build1), libhts3 (= 1.17+ds-1), libhtscodecs2 (= 1.5.0-1), libice6 (= 2:1.0.10-1build2), libicu72 (= 72.1-3ubuntu2), libidn12 (= 1.41-1), libidn2-0 (= 2.3.3-1build1), libijs-0.35 (= 0.35-15.1), libimagequant0 (= 2.17.0-1), libisl23 (= 0.26-3), libjansson4 (= 2.14-2), libjbig0 (= 2.1-6.1ubuntu1), libjbig2dec0 (= 0.19-3build2), libjpeg-turbo8 (= 2.1.5-2ubuntu1), libjpeg8 (= 8c-2ubuntu11), libjs-jquery (= 3.6.1+dfsg+~3.5.14-1), libjs-jquery-ui (= 1.13.2+dfsg-1), libjs-sphinxdoc (= 5.3.0-4), libjs-underscore (= 1.13.4~dfsg+~1.11.4-3), libk5crypto3 (= 1.20.1-2), libkeyutils1 (= 1.6.3-2), libkpathsea6 (= 2022.20220321.62855-5.1), libkrb5-3 (= 1.20.1-2), libkrb5support0 (= 1.20.1-2), liblapack3 (= 3.11.0-2), liblbfgsb0 (= 3.0+dfsg.4-1), liblcms2-2 (= 2.14-2), libldap2 (= 2.6.3+dfsg-1~exp1ubuntu2), liblerc4 (= 4.0.0+ds-2ubuntu2), liblmdb0 (= 0.9.24-1build2), liblqr-1-0 (= 0.4.2-2.1), libltdl7 (= 2.4.7-5), liblz4-1 (= 1.9.4-1), liblzma5 (= 5.4.1-0.2), libmagic-mgc (= 1:5.44-3), libmagic1 (= 1:5.44-3), libmagickcore-6.q16-6 (= 8:6.9.11.60+dfsg-1.6), libmagickwand-6.q16-6 (= 8:6.9.11.60+dfsg-1.6), libmbedcrypto7 (= 2.28.3-1), libmbedtls14 (= 2.28.3-1), libmbedx509-1 (= 2.28.3-1), libmd0 (= 1.1.0-1), libmount1 (= 2.38.1-5ubuntu2), libmpc3 (= 1.3.1-1), libmpfr6 (= 4.2.0-1), libmysqlclient21 (= 8.0.33-2), libncurses6 (= 6.4-4), libncursesw6 (= 6.4-4), libnetpbm11 (= 2:11.01.00-2build1), libnettle8 (= 3.8.1-2), libnghttp2-14 (= 1.54.0-1), libnsl-dev (= 1.3.0-2build2), libnsl2 (= 1.3.0-2build2), libopenblas-dev (= 0.3.23+ds-2), libopenblas-pthread-dev (= 0.3.23+ds-2), libopenblas0 (= 0.3.23+ds-2), libopenblas0-pthread (= 0.3.23+ds-2), libopenjp2-7 (= 2.5.0-2), libp11-kit0 (= 0.24.1-2ubuntu1), libpam-modules (= 1.5.2-6ubuntu1), libpam-modules-bin (= 1.5.2-6ubuntu1), libpam-runtime (= 1.5.2-6ubuntu1), libpam0g (= 1.5.2-6ubuntu1), libpaper-utils (= 1.1.29), libpaper1 (= 1.1.29), libpcre2-8-0 (= 10.42-1), libpcre3 (= 2:8.39-15), libpdfbox-java (= 1:1.8.16-2), libperl5.36 (= 5.36.0-7ubuntu1), libpipeline1 (= 1.5.7-1), libpixman-1-0 (= 0.42.2-1), libpng16-16 (= 1.6.40-1), libpq5 (= 15.3-1), libpsl5 (= 0.21.2-1), libptexenc1 (= 2022.20220321.62855-5.1), libpython3-all-dev (= 3.11.4-1), libpython3-dev (= 3.11.4-1), libpython3-stdlib (= 3.11.4-1), libpython3.11 (= 3.11.4-1), libpython3.11-dev (= 3.11.4-1), libpython3.11-minimal (= 3.11.4-1), libpython3.11-stdlib (= 3.11.4-1), libqhull-r8.0 (= 2020.2-5), libraqm0 (= 0.10.1-1), libreadline8 (= 8.2-1.3), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build4), libsasl2-2 (= 2.1.28+dfsg1-1), libsasl2-modules-db (= 2.1.28+dfsg1-1), libselinux1 (= 3.4-1build4), libsm6 (= 2:1.2.3-1build2), libsmartcols1 (= 2.38.1-5ubuntu2), libsqlite3-0 (= 3.42.0-1), libssh-4 (= 0.10.5-2), libssl3 (= 3.0.9-1ubuntu1), libstdc++-12-dev (= 12.3.0-3ubuntu1), libstdc++6 (= 13.1.0-6ubuntu1), libsub-override-perl (= 0.09-4), libsynctex2 (= 2022.20220321.62855-5.1), libsystemd0 (= 252.5-2ubuntu3), libtasn1-6 (= 4.19.0-2), libtcl8.6 (= 8.6.13+dfsg-2), libteckit0 (= 2.5.11+ds1-1), libtexlua53-5 (= 2022.20220321.62855-5.1), libtiff6 (= 4.5.0-6ubuntu1), libtinfo6 (= 6.4-4), libtirpc-common (= 1.3.3+ds-1), libtirpc-dev (= 1.3.3+ds-1), libtirpc3 (= 1.3.3+ds-1), libtk8.6 (= 8.6.13-2), libtool (= 2.4.7-5), libuchardet0 (= 0.0.7-1build2), libudev1 (= 252.5-2ubuntu3), libunistring2 (= 1.0-2), libuuid1 (= 2.38.1-5ubuntu2), libwebp7 (= 1.2.4-0.2), libwebpdemux2 (= 1.2.4-0.2), libwebpmux3 (= 1.2.4-0.2), libx11-6 (= 2:1.8.6-1), libx11-data (= 2:1.8.6-1), libx265-199 (= 3.5-2), libxau6 (= 1:1.0.9-1build5), libxaw7 (= 2:1.0.14-1), libxcb-render0 (= 1.15-1), libxcb-shm0 (= 1.15-1), libxcb1 (= 1.15-1), libxdmcp6 (= 1:1.1.3-0ubuntu5), libxext6 (= 2:1.3.4-1build1), libxft2 (= 2.3.6-1), libxi6 (= 2:1.8-1build1), libxml2 (= 2.9.14+dfsg-1.2), libxmu6 (= 2:1.1.3-3), libxpm4 (= 1:3.5.12-1.1), libxrender1 (= 1:0.9.10-1.1), libxsimd-dev (= 8.1.0-7), libxslt1.1 (= 1.1.35-1), libxss1 (= 1:1.2.3-1build2), libxt6 (= 1:1.2.1-1.1), libzstd1 (= 1.5.5+dfsg2-1), libzzip-0-13 (= 0.13.72+dfsg.1-1.1), linux-libc-dev (= 6.3.0-7.7), login (= 1:4.13+dfsg1-1ubuntu1), lsb-base (= 11.6), lto-disabled-list (= 41), m4 (= 1.4.19-3), mafft (= 7.505-1), mailcap (= 3.70+nmu1ubuntu1), make (= 4.3-4.1build1), man-db (= 2.11.2-2), mawk (= 1.3.4.20230525-1), media-types (= 10.0.0), mime-support (= 3.66), mysql-common (= 5.8+1.1.0), ncbi-blast+ (= 2.12.0+ds-3build1), ncbi-data (= 6.1.20170106+dfsg1-10), ncurses-base (= 6.4-4), ncurses-bin (= 6.4-4), netpbm (= 2:11.01.00-2build1), patch (= 2.7.6-7build2), perl (= 5.36.0-7ubuntu1), perl-base (= 5.36.0-7ubuntu1), perl-modules-5.36 (= 5.36.0-7ubuntu1), phylip (= 1:3.697+dfsg-2), po-debconf (= 1.0.21+nmu1), poppler-data (= 0.4.12-1), prank (= 0.0.170427+dfsg-3), preview-latex-style (= 12.2-1ubuntu1), probcons (= 1.12-14), python-matplotlib-data (= 3.6.3-1ubuntu2), python3 (= 3.11.4-1), python3-all (= 3.11.4-1), python3-all-dev (= 3.11.4-1), python3-appdirs (= 1.4.4-3), python3-attr (= 23.1.0-1), python3-beniget (= 0.4.1-3), python3-brotli (= 1.0.9-2build8), python3-contourpy (= 1.0.7-1build1), python3-cycler (= 0.11.0-1), python3-dateutil (= 2.8.2-2), python3-decorator (= 5.1.1-3), python3-dev (= 3.11.4-1), python3-distutils (= 3.11.4-1), python3-fonttools (= 4.38.0-1build1), python3-fs (= 2.4.16-2), python3-gast (= 0.5.2-2), python3-isodate (= 0.6.1-1), python3-kiwisolver (= 1.4.4-1build1), python3-lib2to3 (= 3.11.4-1), python3-lxml (= 4.9.2-1build1), python3-lz4 (= 4.0.2+dfsg-1build1), python3-matplotlib (= 3.6.3-1ubuntu2), python3-minimal (= 3.11.4-1), python3-mmtf (= 1.1.3-1), python3-mpmath (= 1.2.1-2), python3-msgpack (= 1.0.3-2build1), python3-mysqldb (= 1.4.6-2build1), python3-networkx (= 2.8.8-1ubuntu1), python3-numpy (= 1:1.24.2-1), python3-packaging (= 23.1-1), python3-pil (= 9.5.0-1), python3-pil.imagetk (= 9.5.0-1), python3-pkg-resources (= 67.8.0-1), python3-ply (= 3.11-5), python3-psycopg2 (= 2.9.5-1build1), python3-pygments (= 2.15.1+dfsg-1), python3-pyparsing (= 3.0.9-1), python3-pythran (= 0.11.0+ds-7), python3-rdflib (= 6.1.1-1), python3-reportlab (= 4.0.4-1), python3-scipy (= 1.10.1-2), python3-setuptools (= 67.8.0-1), python3-six (= 1.16.0-4), python3-sympy (= 1.12-2), python3-tk (= 3.11.4-1), python3-tz (= 2023.3-3), python3-ufolib2 (= 0.14.0+dfsg1-1), python3-unittest2 (= 1.1.0-9), python3.11 (= 3.11.4-1), python3.11-dev (= 3.11.4-1), python3.11-minimal (= 3.11.4-1), readline-common (= 8.2-1.3), rpcsvc-proto (= 1.4.2-0ubuntu6), samtools (= 1.17-1), sed (= 4.9-1), sensible-utils (= 0.0.20), sysvinit-utils (= 3.06-4ubuntu1), t-coffee (= 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1), t1utils (= 1.41-4build2), tar (= 1.34+dfsg-1.2ubuntu1), tex-common (= 6.18), texlive-base (= 2022.20230122-3), texlive-binaries (= 2022.20220321.62855-5.1), texlive-fonts-recommended (= 2022.20230122-3), texlive-latex-base (= 2022.20230122-3), texlive-latex-extra (= 2022.20230122-4), texlive-latex-recommended (= 2022.20230122-3), texlive-pictures (= 2022.20230122-3), tk8.6-blt2.5 (= 2.5.3+dfsg-4.1build2), tzdata (= 2023c-4exp1ubuntu1), ucf (= 3.0043+nmu1), unicode-data (= 15.0.0-1), usrmerge (= 35ubuntu1), util-linux (= 2.38.1-5ubuntu2), util-linux-extra (= 2.38.1-5ubuntu2), wise (= 2.4.1-23), wise-data (= 2.4.1-23), x11-common (= 1:7.7+23ubuntu2), xdg-utils (= 1.1.3-4.1ubuntu3), xfonts-encodings (= 1:1.0.5-0ubuntu2), xfonts-utils (= 1:7.7+6build2), xz-utils (= 5.4.1-0.2), zlib1g (= 1:1.2.13.dfsg-1ubuntu4), zlib1g-dev (= 1:1.2.13.dfsg-1ubuntu4) Environment: DEB_BUILD_OPTIONS="nocheck parallel=8" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1687857439" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ python3-biopython_1.80+dfsg-4ubuntu1_riscv64.deb ------------------------------------------------ new Debian package, version 2.0. size 1622564 bytes: control archive=18217 bytes. 1568 bytes, 27 lines control 63673 bytes, 674 lines md5sums 285 bytes, 12 lines * postinst #!/bin/sh 398 bytes, 12 lines * prerm #!/bin/sh Package: python3-biopython Source: python-biopython Version: 1.80+dfsg-4ubuntu1 Architecture: riscv64 Maintainer: Ubuntu Developers Installed-Size: 11192 Depends: python3-numpy (>= 1:1.22.0), python3-numpy-abi9, python3 (<< 3.12), python3 (>= 3.11~), python3:any, libc6 (>= 2.27), python3-reportlab, w3c-sgml-lib Recommends: python-biopython-doc (= 1.80+dfsg-4ubuntu1), ncbi-blast+ (>= 2.10.1-3) Suggests: python3-tk, bwa, clustalo, clustalw, dialign, dssp (>= 4.0.0), emboss, fasttree, mafft, muscle3, phylip, phyml, prank, probcons, python3-mysqldb, python3-matplotlib, python3-mmtf, python3-pil, python3-rdflib, python3-psycopg2, python3-scipy, raxml, samtools, t-coffee, wise Breaks: cnvkit (<< 0.9.7-1~), ncbi-acc-download (<< 0.2.7-2~) Section: python Priority: optional Homepage: https://biopython.org Description: Python3 library for bioinformatics The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology. . It is a distributed collaborative effort to develop Python3 libraries and applications which address the needs of current and future work in bioinformatics. The source code is made available under the Biopython License, which is extremely liberal and compatible with almost every license in the world. The project works along with the Open Bioinformatics Foundation, who generously provide web and CVS space for the project. Original-Maintainer: Debian Med Packaging Team drwxr-xr-x root/root 0 2023-06-27 09:17 ./ drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/ drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/ drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/ drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/ drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/ drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/Affy/ -rw-r--r-- root/root 23670 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Affy/CelFile.py -rw-r--r-- root/root 296 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Affy/__init__.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/Align/ -rw-r--r-- root/root 22468 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/AlignInfo.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/Align/Applications/ -rw-r--r-- root/root 10012 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/Applications/_ClustalOmega.py -rw-r--r-- root/root 20228 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/Applications/_Clustalw.py -rw-r--r-- root/root 10101 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/Applications/_Dialign.py -rw-r--r-- root/root 3444 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/Applications/_MSAProbs.py -rw-r--r-- root/root 19884 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/Applications/_Mafft.py -rw-r--r-- root/root 36013 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/Align/Applications/_Muscle.py -rw-r--r-- root/root 10544 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/Applications/_Prank.py -rw-r--r-- root/root 5238 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/Applications/_Probcons.py -rw-r--r-- root/root 4588 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/Applications/_TCoffee.py -rw-r--r-- root/root 1193 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/Applications/__init__.py -rw-r--r-- root/root 127623 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/__init__.py -rw-r--r-- root/root 235976 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/_aligners.c -rw-r--r-- root/root 101432 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/Align/_aligners.cpython-311-riscv64-linux-gnu.so -rw-r--r-- root/root 4544 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/a2m.py -rw-r--r-- root/root 9367 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/bed.py -rw-r--r-- root/root 26722 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/bigbed.py -rw-r--r-- root/root 2042 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/bigmaf.py -rw-r--r-- root/root 7928 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/bigpsl.py -rw-r--r-- root/root 9649 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/clustal.py -rw-r--r-- root/root 10434 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/emboss.py -rw-r--r-- root/root 25364 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/exonerate.py -rw-r--r-- root/root 3161 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/fasta.py -rw-r--r-- root/root 9699 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/hhr.py -rw-r--r-- root/root 7086 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/interfaces.py -rw-r--r-- root/root 17848 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/maf.py -rw-r--r-- root/root 10005 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/mauve.py -rw-r--r-- root/root 9546 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/msf.py -rw-r--r-- root/root 6086 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/nexus.py -rw-r--r-- root/root 6419 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/phylip.py -rw-r--r-- root/root 21842 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/psl.py -rw-r--r-- root/root 29932 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/sam.py -rw-r--r-- root/root 25757 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/stockholm.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/ -rw-r--r-- root/root 17844 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/__init__.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/ -rw-r--r-- root/root 2387 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22 -rw-r--r-- root/root 2387 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6 -rw-r--r-- root/root 2387 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74 -rw-r--r-- root/root 1715 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN -rw-r--r-- root/root 4009 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP -rw-r--r-- root/root 2122 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45 -rw-r--r-- root/root 2122 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50 -rw-r--r-- root/root 2122 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62 -rw-r--r-- root/root 2124 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80 -rw-r--r-- root/root 2122 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90 -rw-r--r-- root/root 2451 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF -rw-r--r-- root/root 1120 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG -rw-r--r-- root/root 2380 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC -rw-r--r-- root/root 2351 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992 -rw-r--r-- root/root 275 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70 -rw-r--r-- root/root 2818 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON -rw-r--r-- root/root 2413 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES -rw-r--r-- root/root 1542 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN -rw-r--r-- root/root 1092 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN -rw-r--r-- root/root 2859 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78 -rw-r--r-- root/root 1730 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST -rw-r--r-- root/root 1171 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4 -rw-r--r-- root/root 2068 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250 -rw-r--r-- root/root 2666 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30 -rw-r--r-- root/root 2666 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70 -rw-r--r-- root/root 1581 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO -rw-r--r-- root/root 2456 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER -rw-r--r-- root/root 25459 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER -rw-r--r-- root/root 1543 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR -rw-r--r-- root/root 402 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS -rw-r--r-- root/root 16125 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Align/tabular.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/AlignIO/ -rw-r--r-- root/root 12151 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/AlignIO/ClustalIO.py -rw-r--r-- root/root 8748 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/AlignIO/EmbossIO.py -rw-r--r-- root/root 13353 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/AlignIO/FastaIO.py -rw-r--r-- root/root 5624 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/AlignIO/Interfaces.py -rw-r--r-- root/root 34268 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/AlignIO/MafIO.py -rw-r--r-- root/root 13287 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/AlignIO/MauveIO.py -rw-r--r-- root/root 14119 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/AlignIO/MsfIO.py -rw-r--r-- root/root 6024 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/AlignIO/NexusIO.py -rw-r--r-- root/root 17141 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/AlignIO/PhylipIO.py -rw-r--r-- root/root 26397 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/AlignIO/StockholmIO.py -rw-r--r-- root/root 18615 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/AlignIO/__init__.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/Alphabet/ -rw-r--r-- root/root 1200 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Alphabet/__init__.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/Application/ -rw-r--r-- root/root 32073 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Application/__init__.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/Blast/ -rw-r--r-- root/root 67007 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Blast/Applications.py -rw-r--r-- root/root 14043 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Blast/NCBIWWW.py -rw-r--r-- root/root 33437 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py -rw-r--r-- root/root 4403 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Blast/ParseBlastTable.py -rw-r--r-- root/root 15835 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Blast/Record.py -rw-r--r-- root/root 350 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Blast/__init__.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/CAPS/ -rw-r--r-- root/root 4041 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/CAPS/__init__.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/Cluster/ -rw-r--r-- root/root 50797 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Cluster/__init__.py -rw-r--r-- root/root 76904 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/Cluster/_cluster.cpython-311-riscv64-linux-gnu.so -rw-r--r-- root/root 169203 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Cluster/cluster.c -rw-r--r-- root/root 4135 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Cluster/cluster.h -rw-r--r-- root/root 77865 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Cluster/clustermodule.c drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/Compass/ -rw-r--r-- root/root 6954 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Compass/__init__.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/Data/ -rw-r--r-- root/root 50327 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Data/CodonTable.py -rw-r--r-- root/root 9224 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Data/IUPACData.py -rw-r--r-- root/root 22893 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Data/PDBData.py -rw-r--r-- root/root 17579 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Data/SCOPData.py -rw-r--r-- root/root 353 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Data/__init__.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/Emboss/ -rw-r--r-- root/root 49096 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Emboss/Applications.py -rw-r--r-- root/root 5593 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Emboss/Primer3.py -rw-r--r-- root/root 2521 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Emboss/PrimerSearch.py -rw-r--r-- root/root 355 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Emboss/__init__.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/Entrez/ drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/ -rw-r--r-- root/root 16498 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/BITS-embedded-index2.ent -rw-r--r-- root/root 26770 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/BITS-question-answer2.ent -rw-r--r-- root/root 660 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/Docsum_3_0.dtd -rw-r--r-- root/root 33675 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -rw-r--r-- root/root 660 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/Docsum_3_1.dtd -rw-r--r-- root/root 33691 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -rw-r--r-- root/root 660 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/Docsum_3_2.dtd -rw-r--r-- root/root 36007 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -rw-r--r-- root/root 660 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/Docsum_3_3.dtd -rw-r--r-- root/root 41304 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -rw-r--r-- root/root 660 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/Docsum_3_4.dtd -rw-r--r-- root/root 41537 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -rw-r--r-- root/root 792 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/EMBL_General.dtd -rw-r--r-- root/root 2871 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/EMBL_General.mod.dtd -rw-r--r-- root/root 807 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/GenBank_General.dtd -rw-r--r-- root/root 1743 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/GenBank_General.mod.dtd -rw-r--r-- root/root 3500 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/HomoloGene.dtd -rw-r--r-- root/root 6460 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/HomoloGene.mod.dtd -rw-r--r-- root/root 671 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/INSD_INSDSeq.dtd -rw-r--r-- root/root 14705 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -rw-r--r-- root/root 31246 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent -rw-r--r-- root/root 15260 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent -rw-r--r-- root/root 51353 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd -rw-r--r-- root/root 20885 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent -rw-r--r-- root/root 31272 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent -rw-r--r-- root/root 78956 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent -rw-r--r-- root/root 20899 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent -rw-r--r-- root/root 128551 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-articlemeta1-3.ent -rw-r--r-- root/root 26909 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-backmatter1-3.ent -rw-r--r-- root/root 35219 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-chars1-3.ent -rw-r--r-- root/root 18691 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-common-atts1-3.ent -rw-r--r-- root/root 237581 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-common1-3.ent -rw-r--r-- root/root 75822 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-default-classes1-3.ent -rw-r--r-- root/root 32971 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-default-mixes1-3.ent -rw-r--r-- root/root 65828 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-display1-3.ent -rw-r--r-- root/root 50729 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-format1-3.ent -rw-r--r-- root/root 56436 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-funding1-3.ent -rw-r--r-- root/root 29732 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-journalmeta1-3.ent -rw-r--r-- root/root 30254 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-link1-3.ent -rw-r--r-- root/root 32721 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-list1-3.ent -rw-r--r-- root/root 27873 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-math1-3.ent -rw-r--r-- root/root 23901 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent -rw-r--r-- root/root 16430 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent -rw-r--r-- root/root 37192 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-modules1-3.ent -rw-r--r-- root/root 21564 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent -rw-r--r-- root/root 20223 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-notat1-3.ent -rw-r--r-- root/root 32349 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-para1-3.ent -rw-r--r-- root/root 33583 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-phrase1-3.ent -rw-r--r-- root/root 73018 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-references1-3.ent -rw-r--r-- root/root 21380 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-related-object1-3.ent -rw-r--r-- root/root 23664 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-section1-3.ent -rw-r--r-- root/root 24007 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-xmlspecchars1-3.ent -rw-r--r-- root/root 3893 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/MMDB.dtd -rw-r--r-- root/root 9382 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/MMDB.mod.dtd -rw-r--r-- root/root 3908 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -rw-r--r-- root/root 17213 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -rw-r--r-- root/root 3902 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/MMDB_Features.dtd -rw-r--r-- root/root 28680 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/MMDB_Features.mod.dtd -rw-r--r-- root/root 3910 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/MMDB_Structural_model.dtd -rw-r--r-- root/root 25075 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -rw-r--r-- root/root 665 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Access.dtd -rw-r--r-- root/root 1221 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Access.mod.dtd -rw-r--r-- root/root 785 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Biblio.dtd -rw-r--r-- root/root 15918 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -rw-r--r-- root/root 925 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_BioSource.dtd -rw-r--r-- root/root 4641 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -rw-r--r-- root/root 671 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_BioTree.dtd -rw-r--r-- root/root 2444 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -rw-r--r-- root/root 3740 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Blast4.dtd -rw-r--r-- root/root 39597 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -rw-r--r-- root/root 3507 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_BlastDL.dtd -rw-r--r-- root/root 4281 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -rw-r--r-- root/root 692 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -rw-r--r-- root/root 6579 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -rw-r--r-- root/root 4347 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Cdd.dtd -rw-r--r-- root/root 28292 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -rw-r--r-- root/root 4005 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Cn3d.dtd -rw-r--r-- root/root 16758 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -rw-r--r-- root/root 410 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -rw-r--r-- root/root 671 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Entrez2.dtd -rw-r--r-- root/root 21922 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -rw-r--r-- root/root 3525 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -rw-r--r-- root/root 10316 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -rw-r--r-- root/root 671 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_FeatDef.dtd -rw-r--r-- root/root 2358 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -rw-r--r-- root/root 659 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_GBSeq.dtd -rw-r--r-- root/root 11502 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -rw-r--r-- root/root 776 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Gene.dtd -rw-r--r-- root/root 2381 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -rw-r--r-- root/root 671 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_General.dtd -rw-r--r-- root/root 8215 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_General.mod.dtd -rw-r--r-- root/root 3629 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_ID1Access.dtd -rw-r--r-- root/root 5733 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -rw-r--r-- root/root 3757 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_ID2Access.dtd -rw-r--r-- root/root 23205 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -rw-r--r-- root/root 1378 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_MedArchive.dtd -rw-r--r-- root/root 6931 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -rw-r--r-- root/root 907 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Medlars.dtd -rw-r--r-- root/root 1617 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -rw-r--r-- root/root 907 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Medline.dtd -rw-r--r-- root/root 5757 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -rw-r--r-- root/root 647 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Mim.dtd -rw-r--r-- root/root 8395 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -rw-r--r-- root/root 4461 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Mime.dtd -rw-r--r-- root/root 7270 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -rw-r--r-- root/root 665 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -rw-r--r-- root/root 3131 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -rw-r--r-- root/root 796 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Organism.dtd -rw-r--r-- root/root 5250 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -rw-r--r-- root/root 1519 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_PCAssay.dtd -rw-r--r-- root/root 31800 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -rw-r--r-- root/root 1155 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -rw-r--r-- root/root 43623 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -rw-r--r-- root/root 3736 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Project.dtd -rw-r--r-- root/root 3769 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Project.mod.dtd -rw-r--r-- root/root 791 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Protein.dtd -rw-r--r-- root/root 1791 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -rw-r--r-- root/root 1003 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Pub.dtd -rw-r--r-- root/root 2700 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -rw-r--r-- root/root 1021 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_PubMed.dtd -rw-r--r-- root/root 1698 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -rw-r--r-- root/root 3383 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_RNA.dtd -rw-r--r-- root/root 3379 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -rw-r--r-- root/root 3495 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Remap.dtd -rw-r--r-- root/root 4064 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -rw-r--r-- root/root 781 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Rsite.dtd -rw-r--r-- root/root 1044 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -rw-r--r-- root/root 3629 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -rw-r--r-- root/root 19503 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -rw-r--r-- root/root 671 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_SeqCode.dtd -rw-r--r-- root/root 4231 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -rw-r--r-- root/root 3389 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_SeqTable.dtd -rw-r--r-- root/root 9912 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -rw-r--r-- root/root 3634 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Seq_split.dtd -rw-r--r-- root/root 11475 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -rw-r--r-- root/root 3389 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Seqalign.dtd -rw-r--r-- root/root 15026 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -rw-r--r-- root/root 3387 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -rw-r--r-- root/root 19204 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -rw-r--r-- root/root 3385 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Seqloc.dtd -rw-r--r-- root/root 7383 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -rw-r--r-- root/root 3385 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Seqres.dtd -rw-r--r-- root/root 3149 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -rw-r--r-- root/root 3501 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Seqset.dtd -rw-r--r-- root/root 3479 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -rw-r--r-- root/root 3384 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Sequence.dtd -rw-r--r-- root/root 26293 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -rw-r--r-- root/root 3617 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Submit.dtd -rw-r--r-- root/root 4130 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -rw-r--r-- root/root 3379 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Systems.dtd -rw-r--r-- root/root 656 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_TSeq.dtd -rw-r--r-- root/root 1660 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -rw-r--r-- root/root 1138 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_TxInit.dtd -rw-r--r-- root/root 4625 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -rw-r--r-- root/root 3389 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Variation.dtd -rw-r--r-- root/root 27155 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -rw-r--r-- root/root 7893 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_all.dtd -rw-r--r-- root/root 625 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NSE.dtd -rw-r--r-- root/root 26853 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NSE.mod.dtd -rw-r--r-- root/root 3470 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/OMSSA.dtd -rw-r--r-- root/root 34917 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/OMSSA.mod.dtd -rw-r--r-- root/root 787 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/PDB_General.dtd -rw-r--r-- root/root 1815 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/PDB_General.mod.dtd -rw-r--r-- root/root 3387 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/PIR_General.dtd -rw-r--r-- root/root 2076 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/PIR_General.mod.dtd -rw-r--r-- root/root 667 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/PRF_General.dtd -rw-r--r-- root/root 1535 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/PRF_General.mod.dtd -rw-r--r-- root/root 3386 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/SP_General.dtd -rw-r--r-- root/root 2375 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/SP_General.mod.dtd -rw-r--r-- root/root 17329 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/XHTMLtablesetup.ent -rw-r--r-- root/root 51298 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/archivearticle.dtd -rw-r--r-- root/root 8304 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/archivecustom-classes.ent -rw-r--r-- root/root 16646 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/archivecustom-mixes.ent -rw-r--r-- root/root 38921 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/archivecustom-models.ent -rw-r--r-- root/root 6412 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/archivecustom-modules.ent -rw-r--r-- root/root 98004 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/articlemeta.ent -rw-r--r-- root/root 15090 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/backmatter.ent -rw-r--r-- root/root 2645 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/bookdoc_100301.dtd -rw-r--r-- root/root 2645 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/bookdoc_110101.dtd -rw-r--r-- root/root 2645 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/bookdoc_120101.dtd -rw-r--r-- root/root 2756 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/bookdoc_130101.dtd -rw-r--r-- root/root 2756 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/bookdoc_140101.dtd -rw-r--r-- root/root 2756 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/bookdoc_150101.dtd -rw-r--r-- root/root 21412 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/chars.ent -rw-r--r-- root/root 152388 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/common.ent -rw-r--r-- root/root 33182 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/default-classes.ent -rw-r--r-- root/root 19402 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/default-mixes.ent -rw-r--r-- root/root 82067 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/display.ent -rw-r--r-- root/root 1655 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/eInfo_020511.dtd -rw-r--r-- root/root 2299 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/eLink_090910.dtd -rw-r--r-- root/root 2447 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/eLink_101123.dtd -rw-r--r-- root/root 520 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/ePost_020511.dtd -rw-r--r-- root/root 2392 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/eSearch_020511.dtd -rw-r--r-- root/root 736 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/eSpell.dtd -rw-r--r-- root/root 602 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/eSummary_041029.dtd -rw-r--r-- root/root 851 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/egquery.dtd -rw-r--r-- root/root 1715 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/einfo.dtd -rw-r--r-- root/root 466 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/elink_020122.dtd -rw-r--r-- root/root 3337 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/esearch.dtd -rw-r--r-- root/root 602 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/esummary-v1.dtd -rw-r--r-- root/root 22746 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/format.ent -rw-r--r-- root/root 9849 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/htmltable.dtd -rw-r--r-- root/root 11589 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isoamsa.ent -rw-r--r-- root/root 9556 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isoamsb.ent -rw-r--r-- root/root 2254 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isoamsc.ent -rw-r--r-- root/root 7945 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isoamsn.ent -rw-r--r-- root/root 4432 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isoamso.ent -rw-r--r-- root/root 14133 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isoamsr.ent -rw-r--r-- root/root 3507 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isobox.ent -rw-r--r-- root/root 5257 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isocyr1.ent -rw-r--r-- root/root 2457 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isocyr2.ent -rw-r--r-- root/root 1473 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isodia.ent -rw-r--r-- root/root 4102 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isogrk1.ent -rw-r--r-- root/root 2389 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isogrk2.ent -rw-r--r-- root/root 3699 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isogrk3.ent -rw-r--r-- root/root 3591 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isogrk4.ent -rw-r--r-- root/root 5199 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isolat1.ent -rw-r--r-- root/root 8865 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isolat2.ent -rw-r--r-- root/root 4478 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isomfrk.ent -rw-r--r-- root/root 2522 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isomopf.ent -rw-r--r-- root/root 4557 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isomscr.ent -rw-r--r-- root/root 5816 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isonum.ent -rw-r--r-- root/root 6594 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isopub.ent -rw-r--r-- root/root 12399 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isotech.ent -rw-r--r-- root/root 18988 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/journalmeta.ent -rw-r--r-- root/root 28360 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/link.ent -rw-r--r-- root/root 25663 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/list.ent -rw-r--r-- root/root 18334 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/math.ent -rw-r--r-- root/root 6820 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/mathml-in-pubmed.mod lrwxrwxrwx root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/mathml2.dtd -> ../../../../../../share/xml/w3c-sgml-lib/schema/dtd/XX-MathML2-20031104/mathml2.dtd -rw-r--r-- root/root 12255 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/mathml3-qname1.mod -rw-r--r-- root/root 42407 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/mathml3.dtd -rw-r--r-- root/root 10452 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/mathmlsetup.ent -rw-r--r-- root/root 37695 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/mmlalias.ent -rw-r--r-- root/root 7776 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/mmlextra.ent -rw-r--r-- root/root 21313 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/modules.ent -rw-r--r-- root/root 35333 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -rw-r--r-- root/root 12369 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -rw-r--r-- root/root 5839 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmcommon_011101.dtd -rw-r--r-- root/root 7946 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmcommon_080101.dtd -rw-r--r-- root/root 8638 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmcommon_090101.dtd -rw-r--r-- root/root 2053 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedline_011101.dtd -rw-r--r-- root/root 3017 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedline_080101.dtd -rw-r--r-- root/root 3195 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedline_090101.dtd -rw-r--r-- root/root 6760 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -rw-r--r-- root/root 5001 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -rw-r--r-- root/root 5262 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -rw-r--r-- root/root 9322 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -rw-r--r-- root/root 9618 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -rw-r--r-- root/root 9308 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -rw-r--r-- root/root 8829 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -rw-r--r-- root/root 8995 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -rw-r--r-- root/root 9033 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -rw-r--r-- root/root 9112 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -rw-r--r-- root/root 8947 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -rw-r--r-- root/root 5672 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmserials_080101.dtd -rw-r--r-- root/root 6703 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmserials_100101.dtd -rw-r--r-- root/root 3185 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -rw-r--r-- root/root 3317 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -rw-r--r-- root/root 9656 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/notat.ent -rw-r--r-- root/root 23807 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/para.ent -rw-r--r-- root/root 15750 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/phrase.ent -rw-r--r-- root/root 25142 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pmc-1.dtd -rw-r--r-- root/root 2714 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_020114.dtd -rw-r--r-- root/root 3045 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_080101.dtd -rw-r--r-- root/root 3059 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_090101.dtd -rw-r--r-- root/root 3126 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_100101.dtd -rw-r--r-- root/root 3434 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_100301.dtd -rw-r--r-- root/root 3434 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_110101.dtd -rw-r--r-- root/root 3434 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_120101.dtd -rw-r--r-- root/root 3434 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_130101.dtd -rw-r--r-- root/root 3445 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_130501.dtd -rw-r--r-- root/root 3445 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_140101.dtd -rw-r--r-- root/root 3445 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_150101.dtd -rw-r--r-- root/root 13062 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_180101.dtd -rw-r--r-- root/root 13869 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_180601.dtd -rw-r--r-- root/root 14576 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_190101.dtd -rw-r--r-- root/root 40015 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/references.ent -rw-r--r-- root/root 13173 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/section.ent -rw-r--r-- root/root 4003 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/taxon.dtd -rw-r--r-- root/root 1141 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -rw-r--r-- root/root 9503 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/xhtml-table-1.mod -rw-r--r-- root/root 13595 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/xmlspecchars.ent -rw-r--r-- root/root 43778 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/Parser.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/Entrez/XSDs/ -rw-r--r-- root/root 3536 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/XSDs/IPGReportSet.xsd -rw-r--r-- root/root 29439 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Entrez/__init__.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/ExPASy/ -rw-r--r-- root/root 4570 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/ExPASy/Enzyme.py -rw-r--r-- root/root 5009 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/ExPASy/Prodoc.py -rw-r--r-- root/root 11495 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/ExPASy/Prosite.py -rw-r--r-- root/root 5146 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/ExPASy/ScanProsite.py -rw-r--r-- root/root 4097 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/ExPASy/__init__.py -rw-r--r-- root/root 5735 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/ExPASy/cellosaurus.py -rw-r--r-- root/root 24673 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/File.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/GenBank/ -rw-r--r-- root/root 23278 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/GenBank/Record.py -rw-r--r-- root/root 85906 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/GenBank/Scanner.py -rw-r--r-- root/root 43868 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/GenBank/__init__.py -rw-r--r-- root/root 2229 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/GenBank/utils.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/Geo/ -rw-r--r-- root/root 3025 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Geo/Record.py -rw-r--r-- root/root 2176 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Geo/__init__.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/Graphics/ -rw-r--r-- root/root 31404 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Graphics/BasicChromosome.py -rw-r--r-- root/root 7371 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Graphics/ColorSpiral.py -rw-r--r-- root/root 6472 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Graphics/Comparative.py -rw-r--r-- root/root 6775 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Graphics/DisplayRepresentation.py -rw-r--r-- root/root 9334 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Graphics/Distribution.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/ -rw-r--r-- root/root 18530 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -rw-r--r-- root/root 68538 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/_CircularDrawer.py -rw-r--r-- root/root 9678 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/_Colors.py -rw-r--r-- root/root 3309 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/_CrossLink.py -rw-r--r-- root/root 15633 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/_Diagram.py -rw-r--r-- root/root 8047 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/_Feature.py -rw-r--r-- root/root 7802 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/_FeatureSet.py -rw-r--r-- root/root 6861 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/_Graph.py -rw-r--r-- root/root 5634 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/_GraphSet.py -rw-r--r-- root/root 63150 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/_LinearDrawer.py -rw-r--r-- root/root 11663 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/_Track.py -rw-r--r-- root/root 1172 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/__init__.py -rw-r--r-- root/root 17644 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Graphics/KGML_vis.py -rw-r--r-- root/root 3232 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Graphics/__init__.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/HMM/ -rw-r--r-- root/root 12483 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/HMM/DynamicProgramming.py -rw-r--r-- root/root 26511 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/HMM/MarkovModel.py -rw-r--r-- root/root 16472 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/HMM/Trainer.py -rw-r--r-- root/root 2106 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/HMM/Utilities.py -rw-r--r-- root/root 283 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/HMM/__init__.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/KEGG/ drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/KEGG/Compound/ -rw-r--r-- root/root 5412 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/KEGG/Compound/__init__.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/KEGG/Enzyme/ -rw-r--r-- root/root 11127 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/KEGG/Enzyme/__init__.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/KEGG/Gene/ -rw-r--r-- root/root 4250 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/KEGG/Gene/__init__.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/KEGG/KGML/ -rw-r--r-- root/root 6195 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/KEGG/KGML/KGML_parser.py -rw-r--r-- root/root 27604 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/KEGG/KGML/KGML_pathway.py -rw-r--r-- root/root 516 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/KEGG/KGML/__init__.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/KEGG/Map/ -rw-r--r-- root/root 1642 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/KEGG/Map/__init__.py -rw-r--r-- root/root 10967 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/KEGG/REST.py -rw-r--r-- root/root 3039 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/KEGG/__init__.py -rw-r--r-- root/root 4259 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/LogisticRegression.py -rw-r--r-- root/root 23626 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/MarkovModel.py -rw-r--r-- root/root 10881 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/MaxEntropy.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/Medline/ -rw-r--r-- root/root 5913 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Medline/__init__.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/NMR/ -rw-r--r-- root/root 3353 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/NMR/NOEtools.py -rw-r--r-- root/root 332 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/NMR/__init__.py -rw-r--r-- root/root 9276 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/NMR/xpktools.py -rw-r--r-- root/root 7962 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/NaiveBayes.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/Nexus/ -rw-r--r-- root/root 84818 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Nexus/Nexus.py -rw-r--r-- root/root 5745 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Nexus/Nodes.py -rw-r--r-- root/root 4006 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Nexus/StandardData.py -rw-r--r-- root/root 39870 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Nexus/Trees.py -rw-r--r-- root/root 388 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Nexus/__init__.py -rw-r--r-- root/root 3737 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Nexus/cnexus.c -rw-r--r-- root/root 6312 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/Nexus/cnexus.cpython-311-riscv64-linux-gnu.so drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/PDB/ -rw-r--r-- root/root 4083 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/AbstractPropertyMap.py -rw-r--r-- root/root 18337 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/Atom.py -rw-r--r-- root/root 6767 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/Chain.py -rw-r--r-- root/root 20286 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/DSSP.py -rw-r--r-- root/root 2315 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/Dice.py -rw-r--r-- root/root 15259 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/Entity.py -rw-r--r-- root/root 9640 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/FragmentMapper.py -rw-r--r-- root/root 11321 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/HSExposure.py -rw-r--r-- root/root 4883 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/MMCIF2Dict.py -rw-r--r-- root/root 24301 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/MMCIFParser.py -rw-r--r-- root/root 2203 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/Model.py -rw-r--r-- root/root 7182 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/NACCESS.py -rw-r--r-- root/root 4437 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/NeighborSearch.py -rw-r--r-- root/root 897 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/PDBExceptions.py -rw-r--r-- root/root 13808 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/PDBIO.py -rw-r--r-- root/root 30861 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/PDBList.py -rw-r--r-- root/root 17451 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/PDBParser.py -rw-r--r-- root/root 39862 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/PICIO.py -rw-r--r-- root/root 3100 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/PSEA.py -rw-r--r-- root/root 15215 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/Polypeptide.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/PDB/QCPSuperimposer/ -rw-r--r-- root/root 5590 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/QCPSuperimposer/__init__.py -rw-r--r-- root/root 9125 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.c -rw-r--r-- root/root 10392 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-riscv64-linux-gnu.so -rw-r--r-- root/root 5262 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/Residue.py -rw-r--r-- root/root 22268 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/ResidueDepth.py -rw-r--r-- root/root 8435 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/PDB/SASA.py -rw-r--r-- root/root 34578 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/SCADIO.py -rw-r--r-- root/root 2591 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/Selection.py -rw-r--r-- root/root 2043 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/Structure.py -rw-r--r-- root/root 3340 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/StructureAlignment.py -rw-r--r-- root/root 11708 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py -rw-r--r-- root/root 1947 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/Superimposer.py -rw-r--r-- root/root 2499 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/__init__.py -rw-r--r-- root/root 10456 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/PDB/ccealign.cpython-311-riscv64-linux-gnu.so -rw-r--r-- root/root 23585 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/ccealignmodule.c -rw-r--r-- root/root 5513 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/cealign.py -rw-r--r-- root/root 59010 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/ic_data.py -rw-r--r-- root/root 16973 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/ic_rebuild.py -rw-r--r-- root/root 176751 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/PDB/internal_coords.py -rw-r--r-- root/root 42796 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/kdtrees.c -rw-r--r-- root/root 20576 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/PDB/kdtrees.cpython-311-riscv64-linux-gnu.so -rw-r--r-- root/root 15410 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/mmcifio.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/PDB/mmtf/ -rw-r--r-- root/root 8949 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/mmtf/DefaultParser.py -rw-r--r-- root/root 1546 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/mmtf/__init__.py -rw-r--r-- root/root 10193 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/mmtf/mmtfio.py -rw-r--r-- root/root 11694 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/parse_pdb_header.py -rw-r--r-- root/root 11906 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/qcprot.py -rw-r--r-- root/root 20603 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PDB/vectors.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/Pathway/ drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/Pathway/Rep/ -rw-r--r-- root/root 5865 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Pathway/Rep/Graph.py -rw-r--r-- root/root 6779 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Pathway/Rep/MultiGraph.py -rw-r--r-- root/root 575 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Pathway/Rep/__init__.py -rw-r--r-- root/root 10763 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Pathway/__init__.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/Phylo/ drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/Phylo/Applications/ -rw-r--r-- root/root 27405 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Phylo/Applications/_Fasttree.py -rw-r--r-- root/root 10846 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Phylo/Applications/_Phyml.py -rw-r--r-- root/root 18861 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Phylo/Applications/_Raxml.py -rw-r--r-- root/root 751 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Phylo/Applications/__init__.py -rw-r--r-- root/root 45363 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Phylo/BaseTree.py -rw-r--r-- root/root 1662 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Phylo/CDAO.py -rw-r--r-- root/root 16045 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py -rw-r--r-- root/root 23544 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Phylo/Consensus.py -rw-r--r-- root/root 1404 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Phylo/NeXML.py -rw-r--r-- root/root 11326 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Phylo/NeXMLIO.py -rw-r--r-- root/root 1298 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Phylo/Newick.py -rw-r--r-- root/root 12517 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Phylo/NewickIO.py -rw-r--r-- root/root 2652 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Phylo/NexusIO.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/Phylo/PAML/ -rw-r--r-- root/root 325 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Phylo/PAML/__init__.py -rw-r--r-- root/root 5145 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Phylo/PAML/_paml.py -rw-r--r-- root/root 11409 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Phylo/PAML/_parse_baseml.py -rw-r--r-- root/root 21155 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Phylo/PAML/_parse_codeml.py -rw-r--r-- root/root 6820 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Phylo/PAML/_parse_yn00.py -rw-r--r-- root/root 8272 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Phylo/PAML/baseml.py -rw-r--r-- root/root 3727 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Phylo/PAML/chi2.py -rw-r--r-- root/root 8844 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Phylo/PAML/codeml.py -rw-r--r-- root/root 5731 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Phylo/PAML/yn00.py -rw-r--r-- root/root 45957 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Phylo/PhyloXML.py -rw-r--r-- root/root 32752 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Phylo/PhyloXMLIO.py -rw-r--r-- root/root 42927 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Phylo/TreeConstruction.py -rw-r--r-- root/root 513 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Phylo/__init__.py -rw-r--r-- root/root 109268 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Phylo/_cdao_owl.py -rw-r--r-- root/root 2595 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Phylo/_io.py -rw-r--r-- root/root 17879 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Phylo/_utils.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/PopGen/ drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/PopGen/GenePop/ -rw-r--r-- root/root 34382 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PopGen/GenePop/Controller.py -rw-r--r-- root/root 7789 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PopGen/GenePop/EasyController.py -rw-r--r-- root/root 11860 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PopGen/GenePop/FileParser.py -rw-r--r-- root/root 3919 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PopGen/GenePop/LargeFileParser.py -rw-r--r-- root/root 7461 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PopGen/GenePop/__init__.py -rw-r--r-- root/root 359 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/PopGen/__init__.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/Restriction/ -rw-r--r-- root/root 16299 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Restriction/PrintFormat.py -rw-r--r-- root/root 85184 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Restriction/Restriction.py -rw-r--r-- root/root 550284 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Restriction/Restriction_Dictionary.py -rw-r--r-- root/root 7837 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Restriction/__init__.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/SCOP/ -rw-r--r-- root/root 3922 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SCOP/Cla.py -rw-r--r-- root/root 3004 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SCOP/Des.py -rw-r--r-- root/root 2466 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SCOP/Dom.py -rw-r--r-- root/root 2963 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SCOP/Hie.py -rw-r--r-- root/root 10338 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SCOP/Raf.py -rw-r--r-- root/root 3084 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SCOP/Residues.py -rw-r--r-- root/root 32757 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SCOP/__init__.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/SVDSuperimposer/ -rw-r--r-- root/root 6211 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SVDSuperimposer/__init__.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/SearchIO/ drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/SearchIO/BlastIO/ -rw-r--r-- root/root 23895 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SearchIO/BlastIO/__init__.py -rw-r--r-- root/root 33733 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SearchIO/BlastIO/blast_tab.py -rw-r--r-- root/root 5610 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SearchIO/BlastIO/blast_text.py -rw-r--r-- root/root 36938 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SearchIO/BlastIO/blast_xml.py -rw-r--r-- root/root 31231 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SearchIO/BlatIO.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/SearchIO/ExonerateIO/ -rw-r--r-- root/root 12964 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SearchIO/ExonerateIO/__init__.py -rw-r--r-- root/root 20876 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SearchIO/ExonerateIO/_base.py -rw-r--r-- root/root 4089 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SearchIO/ExonerateIO/exonerate_cigar.py -rw-r--r-- root/root 20434 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SearchIO/ExonerateIO/exonerate_text.py -rw-r--r-- root/root 8244 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -rw-r--r-- root/root 25906 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SearchIO/FastaIO.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/SearchIO/HHsuiteIO/ -rw-r--r-- root/root 639 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SearchIO/HHsuiteIO/__init__.py -rw-r--r-- root/root 9261 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SearchIO/HHsuiteIO/hhsuite2_text.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/SearchIO/HmmerIO/ -rw-r--r-- root/root 20309 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SearchIO/HmmerIO/__init__.py -rw-r--r-- root/root 1482 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SearchIO/HmmerIO/_base.py -rw-r--r-- root/root 12839 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SearchIO/HmmerIO/hmmer2_text.py -rw-r--r-- root/root 13956 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SearchIO/HmmerIO/hmmer3_domtab.py -rw-r--r-- root/root 12818 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SearchIO/HmmerIO/hmmer3_tab.py -rw-r--r-- root/root 18733 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SearchIO/HmmerIO/hmmer3_text.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/SearchIO/InterproscanIO/ -rw-r--r-- root/root 5155 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SearchIO/InterproscanIO/__init__.py -rw-r--r-- root/root 7455 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SearchIO/InterproscanIO/interproscan_xml.py -rw-r--r-- root/root 28939 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SearchIO/__init__.py -rw-r--r-- root/root 1213 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SearchIO/_index.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/SearchIO/_legacy/ -rw-r--r-- root/root 74634 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SearchIO/_legacy/NCBIStandalone.py -rw-r--r-- root/root 12123 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SearchIO/_legacy/ParserSupport.py -rw-r--r-- root/root 690 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SearchIO/_legacy/__init__.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/SearchIO/_model/ -rw-r--r-- root/root 2464 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SearchIO/_model/__init__.py -rw-r--r-- root/root 2626 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SearchIO/_model/_base.py -rw-r--r-- root/root 17335 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SearchIO/_model/hit.py -rw-r--r-- root/root 48190 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SearchIO/_model/hsp.py -rw-r--r-- root/root 30200 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SearchIO/_model/query.py -rw-r--r-- root/root 5584 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SearchIO/_utils.py -rw-r--r-- root/root 142690 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Seq.py -rw-r--r-- root/root 94308 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SeqFeature.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/SeqIO/ -rw-r--r-- root/root 26087 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SeqIO/AbiIO.py -rw-r--r-- root/root 4091 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SeqIO/AceIO.py -rw-r--r-- root/root 16504 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SeqIO/FastaIO.py -rw-r--r-- root/root 8069 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SeqIO/GckIO.py -rw-r--r-- root/root 4433 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SeqIO/IgIO.py -rw-r--r-- root/root 57064 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py -rw-r--r-- root/root 9168 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SeqIO/Interfaces.py -rw-r--r-- root/root 5841 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SeqIO/NibIO.py -rw-r--r-- root/root 20579 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SeqIO/PdbIO.py -rw-r--r-- root/root 6059 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SeqIO/PhdIO.py -rw-r--r-- root/root 10295 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SeqIO/PirIO.py -rw-r--r-- root/root 91857 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SeqIO/QualityIO.py -rw-r--r-- root/root 27430 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SeqIO/SeqXmlIO.py -rw-r--r-- root/root 55688 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SeqIO/SffIO.py -rw-r--r-- root/root 10473 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SeqIO/SnapGeneIO.py -rw-r--r-- root/root 4817 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SeqIO/SwissIO.py -rw-r--r-- root/root 5014 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SeqIO/TabIO.py -rw-r--r-- root/root 11060 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py -rw-r--r-- root/root 25411 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SeqIO/UniprotIO.py -rw-r--r-- root/root 12533 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SeqIO/XdnaIO.py -rw-r--r-- root/root 43507 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py -rw-r--r-- root/root 27381 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SeqIO/_index.py -rw-r--r-- root/root 21992 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SeqIO/_twoBitIO.c -rw-r--r-- root/root 10680 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/SeqIO/_twoBitIO.cpython-311-riscv64-linux-gnu.so -rw-r--r-- root/root 55510 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SeqRecord.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/SeqUtils/ -rw-r--r-- root/root 3511 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SeqUtils/CheckSum.py -rw-r--r-- root/root 7199 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SeqUtils/CodonUsage.py -rw-r--r-- root/root 1983 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SeqUtils/CodonUsageIndices.py -rw-r--r-- root/root 6470 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SeqUtils/IsoelectricPoint.py -rw-r--r-- root/root 43662 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SeqUtils/MeltingTemp.py -rw-r--r-- root/root 13021 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SeqUtils/ProtParam.py -rw-r--r-- root/root 18172 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SeqUtils/ProtParamData.py -rw-r--r-- root/root 23125 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SeqUtils/__init__.py -rw-r--r-- root/root 5502 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SeqUtils/lcc.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/Sequencing/ -rw-r--r-- root/root 20710 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Sequencing/Ace.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/Sequencing/Applications/ -rw-r--r-- root/root 8586 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Sequencing/Applications/_Novoalign.py -rw-r--r-- root/root 2189 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Sequencing/Applications/__init__.py -rw-r--r-- root/root 28256 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Sequencing/Applications/_bwa.py -rw-r--r-- root/root 36658 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Sequencing/Applications/_samtools.py -rw-r--r-- root/root 5598 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Sequencing/Phd.py -rw-r--r-- root/root 530 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Sequencing/__init__.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/SwissProt/ -rw-r--r-- root/root 3488 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SwissProt/KeyWList.py -rw-r--r-- root/root 32734 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/SwissProt/__init__.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/TogoWS/ -rw-r--r-- root/root 13889 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/TogoWS/__init__.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/UniGene/ -rw-r--r-- root/root 12738 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/UniGene/__init__.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/UniProt/ -rw-r--r-- root/root 15792 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/UniProt/GOA.py -rw-r--r-- root/root 722 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/UniProt/__init__.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/Wise/ -rw-r--r-- root/root 4909 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Wise/__init__.py -rw-r--r-- root/root 4802 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Wise/dnal.py -rw-r--r-- root/root 4604 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/Wise/psw.py -rw-r--r-- root/root 5399 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/__init__.py -rw-r--r-- root/root 2095 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/_utils.py -rw-r--r-- root/root 39444 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/bgzf.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/codonalign/ -rw-r--r-- root/root 30013 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/codonalign/__init__.py -rw-r--r-- root/root 18030 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/codonalign/codonalignment.py -rw-r--r-- root/root 47867 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/codonalign/codonseq.py -rw-r--r-- root/root 10712 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/cpairwise2.cpython-311-riscv64-linux-gnu.so -rw-r--r-- root/root 16043 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/cpairwise2module.c -rw-r--r-- root/root 4296 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/kNN.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/motifs/ -rw-r--r-- root/root 21230 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/motifs/__init__.py -rw-r--r-- root/root 5800 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/motifs/_pwm.c -rw-r--r-- root/root 10680 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/motifs/_pwm.cpython-311-riscv64-linux-gnu.so -rw-r--r-- root/root 2107 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/motifs/alignace.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/motifs/applications/ -rw-r--r-- root/root 582 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/motifs/applications/__init__.py -rw-r--r-- root/root 10382 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/motifs/applications/_xxmotif.py -rw-r--r-- root/root 2609 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/motifs/clusterbuster.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/motifs/jaspar/ -rw-r--r-- root/root 11305 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/motifs/jaspar/__init__.py -rw-r--r-- root/root 27920 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/motifs/jaspar/db.py -rw-r--r-- root/root 4828 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/motifs/mast.py -rw-r--r-- root/root 20572 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/motifs/matrix.py -rw-r--r-- root/root 6716 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/motifs/meme.py -rw-r--r-- root/root 5768 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/motifs/minimal.py -rw-r--r-- root/root 16521 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/motifs/pfm.py -rw-r--r-- root/root 4530 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/motifs/thresholds.py -rw-r--r-- root/root 11897 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/motifs/transfac.py -rw-r--r-- root/root 3924 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/motifs/xms.py -rw-r--r-- root/root 53156 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/pairwise2.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/Bio/phenotype/ -rw-r--r-- root/root 7921 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/phenotype/__init__.py -rw-r--r-- root/root 37605 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/phenotype/phen_micro.py -rw-r--r-- root/root 4062 2022-11-18 14:54 ./usr/lib/python3/dist-packages/Bio/phenotype/pm_fitting.py drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/biopython-1.80.egg-info/ -rw-r--r-- root/root 13112 2023-06-27 09:17 ./usr/lib/python3/dist-packages/biopython-1.80.egg-info/PKG-INFO -rw-r--r-- root/root 1 2023-06-27 09:17 ./usr/lib/python3/dist-packages/biopython-1.80.egg-info/dependency_links.txt -rw-r--r-- root/root 0 2023-06-27 09:17 ./usr/lib/python3/dist-packages/biopython-1.80.egg-info/requires.txt -rw-r--r-- root/root 11 2023-06-27 09:17 ./usr/lib/python3/dist-packages/biopython-1.80.egg-info/top_level.txt drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/share/ drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/share/doc/ drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/share/doc/python3-biopython/ -rw-r--r-- root/root 5530 2022-11-18 14:54 ./usr/share/doc/python3-biopython/CONTRIB.rst.gz -rw-r--r-- root/root 3957 2022-11-18 14:54 ./usr/share/doc/python3-biopython/CONTRIBUTING.rst -rw-r--r-- root/root 8935 2022-11-18 14:54 ./usr/share/doc/python3-biopython/DEPRECATED.rst.gz -rw-r--r-- root/root 429 2023-06-27 08:00 ./usr/share/doc/python3-biopython/NEWS.Debian.gz -rw-r--r-- root/root 37909 2022-11-18 14:54 ./usr/share/doc/python3-biopython/NEWS.rst.gz -rw-r--r-- root/root 273 2023-06-27 08:00 ./usr/share/doc/python3-biopython/README.Debian -rw-r--r-- root/root 4072 2023-06-27 09:17 ./usr/share/doc/python3-biopython/changelog.Debian.gz -rw-r--r-- root/root 2117 2023-06-27 08:00 ./usr/share/doc/python3-biopython/copyright drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/share/lintian/ drwxr-xr-x root/root 0 2023-06-27 09:17 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 345 2023-06-27 08:00 ./usr/share/lintian/overrides/python3-biopython +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: riscv64 Build Type: any Build-Space: 142684 Build-Time: 2696 Distribution: mantic-proposed Host Architecture: riscv64 Install-Time: 1903 Job: python-biopython_1.80+dfsg-4ubuntu1.dsc Machine Architecture: riscv64 Package: python-biopython Package-Time: 4631 Source-Version: 1.80+dfsg-4ubuntu1 Space: 142684 Status: successful Version: 1.80+dfsg-4ubuntu1 -------------------------------------------------------------------------------- Finished at 2023-06-27T10:46:44Z Build needed 01:17:11, 142684k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=mantic --arch=riscv64 PACKAGEBUILD-26341718 Scanning for processes to kill in build PACKAGEBUILD-26341718 RUN: /usr/share/launchpad-buildd/bin/in-target umount-chroot --backend=chroot --series=mantic --arch=riscv64 PACKAGEBUILD-26341718 Stopping target for build PACKAGEBUILD-26341718 RUN: /usr/share/launchpad-buildd/bin/in-target remove-build --backend=chroot --series=mantic --arch=riscv64 PACKAGEBUILD-26341718 Removing build PACKAGEBUILD-26341718