https://launchpad.net/ubuntu/+source/python-biopython/1.73+dfsg-1ubuntu2/+build/17940165 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-009 4.4.0-166-generic #195-Ubuntu SMP Tue Oct 1 09:36:37 UTC 2019 aarch64 Buildd toolchain package versions: launchpad-buildd_178 python-lpbuildd_178 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.6 dpkg-dev_1.18.4ubuntu1.6 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 3 Nov 09:54:05 ntpdate[1922]: adjust time server 10.211.37.1 offset 0.007969 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=focal --arch=armhf PACKAGEBUILD-17940165 --image-type chroot /home/buildd/filecache-default/f005b6164729459c78307140747b338a2f357aa2 Creating target for build PACKAGEBUILD-17940165 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=focal --arch=armhf PACKAGEBUILD-17940165 Starting target for build PACKAGEBUILD-17940165 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=focal --arch=armhf PACKAGEBUILD-17940165 'deb http://ftpmaster.internal/ubuntu focal main universe' 'deb http://ftpmaster.internal/ubuntu focal-security main universe' 'deb http://ftpmaster.internal/ubuntu focal-updates main universe' 'deb http://ftpmaster.internal/ubuntu focal-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-17940165 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=focal --arch=armhf PACKAGEBUILD-17940165 Updating target for build PACKAGEBUILD-17940165 Get:1 http://ftpmaster.internal/ubuntu focal InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu focal-security InRelease [79.7 kB] Get:3 http://ftpmaster.internal/ubuntu focal-updates InRelease [79.7 kB] Get:4 http://ftpmaster.internal/ubuntu focal-proposed InRelease [107 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main armhf Packages [936 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main Translation-en [505 kB] Get:7 http://ftpmaster.internal/ubuntu focal/universe armhf Packages [8510 kB] Get:8 http://ftpmaster.internal/ubuntu focal/universe Translation-en [5200 kB] Get:9 http://ftpmaster.internal/ubuntu focal-proposed/main armhf Packages [66.4 kB] Get:10 http://ftpmaster.internal/ubuntu focal-proposed/main Translation-en [43.4 kB] Get:11 http://ftpmaster.internal/ubuntu focal-proposed/universe armhf Packages [368 kB] Get:12 http://ftpmaster.internal/ubuntu focal-proposed/universe Translation-en [269 kB] Fetched 16.4 MB in 7s (2422 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libhogweed4 libnettle6 libperl5.28 perl-modules-5.28 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libhogweed5 libnettle7 libperl5.30 perl-modules-5.30 The following packages will be upgraded: base-files binutils binutils-arm-linux-gnueabihf binutils-common bzip2 cpp-9 debianutils g++-9 gcc-9 gcc-9-base libacl1 libapparmor1 libasan5 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libbz2-1.0 libcap-ng0 libcc1-0 libcryptsetup12 libdebconfclient0 libgcc-9-dev libgcc1 libgcrypt20 libgnutls30 libgomp1 libjson-c4 libkmod2 liblockfile-bin liblockfile1 liblz4-1 libncurses6 libncursesw6 libp11-kit0 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsqlite3-0 libstdc++-9-dev libstdc++6 libsystemd0 libtinfo6 libubsan1 libudev1 linux-libc-dev lsb-base ncurses-base ncurses-bin perl perl-base systemd systemd-sysv sysvinit-utils 56 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 44.4 MB of archives. After this operation, 39.4 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu focal/main armhf base-files armhf 11ubuntu1 [60.1 kB] Get:2 http://ftpmaster.internal/ubuntu focal-proposed/main armhf debianutils armhf 4.9 [84.7 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main armhf ncurses-bin armhf 6.1+20191019-1ubuntu1 [163 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main armhf perl-modules-5.30 all 5.30.0-9 [2739 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main armhf libperl5.30 armhf 5.30.0-9 [3286 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main armhf perl armhf 5.30.0-9 [224 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main armhf perl-base armhf 5.30.0-9 [1408 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main armhf bzip2 armhf 1.0.8-2 [32.4 kB] Get:9 http://ftpmaster.internal/ubuntu focal/main armhf libbz2-1.0 armhf 1.0.8-2 [31.0 kB] Get:10 http://ftpmaster.internal/ubuntu focal/main armhf ncurses-base all 6.1+20191019-1ubuntu1 [17.9 kB] Get:11 http://ftpmaster.internal/ubuntu focal/main armhf lsb-base all 11.1.0ubuntu1 [12.2 kB] Get:12 http://ftpmaster.internal/ubuntu focal/main armhf sysvinit-utils armhf 2.96-1ubuntu1 [19.2 kB] Get:13 http://ftpmaster.internal/ubuntu focal-proposed/main armhf systemd-sysv armhf 243-3ubuntu1 [9364 B] Get:14 http://ftpmaster.internal/ubuntu focal/main armhf libacl1 armhf 2.2.53-5 [15.9 kB] Get:15 http://ftpmaster.internal/ubuntu focal/main armhf libapparmor1 armhf 2.13.3-5ubuntu5 [29.7 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main armhf libaudit-common all 1:2.8.5-2ubuntu2 [4080 B] Get:17 http://ftpmaster.internal/ubuntu focal/main armhf libcap-ng0 armhf 0.7.9-2.1 [9692 B] Get:18 http://ftpmaster.internal/ubuntu focal/main armhf libaudit1 armhf 1:2.8.5-2ubuntu2 [36.0 kB] Get:19 http://ftpmaster.internal/ubuntu focal/main armhf libjson-c4 armhf 0.13.1+dfsg-6 [25.6 kB] Get:20 http://ftpmaster.internal/ubuntu focal/main armhf libcryptsetup12 armhf 2:2.2.1-1ubuntu1 [163 kB] Get:21 http://ftpmaster.internal/ubuntu focal-proposed/main armhf libnettle7 armhf 3.5.1+really3.5.1-2 [126 kB] Get:22 http://ftpmaster.internal/ubuntu focal-proposed/main armhf libhogweed5 armhf 3.5.1+really3.5.1-2 [127 kB] Get:23 http://ftpmaster.internal/ubuntu focal/main armhf libp11-kit0 armhf 0.23.18.1-2 [166 kB] Get:24 http://ftpmaster.internal/ubuntu focal-proposed/main armhf libgnutls30 armhf 3.6.9-5ubuntu2 [730 kB] Get:25 http://ftpmaster.internal/ubuntu focal/main armhf libkmod2 armhf 26-3ubuntu1 [37.0 kB] Get:26 http://ftpmaster.internal/ubuntu focal/main armhf liblz4-1 armhf 1.9.1-2 [50.3 kB] Get:27 http://ftpmaster.internal/ubuntu focal-proposed/main armhf libseccomp2 armhf 2.4.1-0ubuntu0.19.10.4 [30.8 kB] Get:28 http://ftpmaster.internal/ubuntu focal-proposed/main armhf systemd armhf 243-3ubuntu1 [3479 kB] Get:29 http://ftpmaster.internal/ubuntu focal-proposed/main armhf libsystemd0 armhf 243-3ubuntu1 [243 kB] Get:30 http://ftpmaster.internal/ubuntu focal/main armhf libcc1-0 armhf 9.2.1-16ubuntu1 [41.6 kB] Get:31 http://ftpmaster.internal/ubuntu focal/main armhf binutils-arm-linux-gnueabihf armhf 2.33.1-1ubuntu1 [2101 kB] Get:32 http://ftpmaster.internal/ubuntu focal/main armhf libbinutils armhf 2.33.1-1ubuntu1 [315 kB] Get:33 http://ftpmaster.internal/ubuntu focal/main armhf binutils-common armhf 2.33.1-1ubuntu1 [203 kB] Get:34 http://ftpmaster.internal/ubuntu focal/main armhf binutils armhf 2.33.1-1ubuntu1 [3348 B] Get:35 http://ftpmaster.internal/ubuntu focal/main armhf libgomp1 armhf 9.2.1-16ubuntu1 [77.4 kB] Get:36 http://ftpmaster.internal/ubuntu focal/main armhf libatomic1 armhf 9.2.1-16ubuntu1 [7092 B] Get:37 http://ftpmaster.internal/ubuntu focal/main armhf libasan5 armhf 9.2.1-16ubuntu1 [386 kB] Get:38 http://ftpmaster.internal/ubuntu focal/main armhf libubsan1 armhf 9.2.1-16ubuntu1 [118 kB] Get:39 http://ftpmaster.internal/ubuntu focal/main armhf gcc-9-base armhf 9.2.1-16ubuntu1 [19.3 kB] Get:40 http://ftpmaster.internal/ubuntu focal/main armhf libstdc++6 armhf 9.2.1-16ubuntu1 [451 kB] Get:41 http://ftpmaster.internal/ubuntu focal/main armhf g++-9 armhf 9.2.1-16ubuntu1 [7911 kB] Get:42 http://ftpmaster.internal/ubuntu focal/main armhf libstdc++-9-dev armhf 9.2.1-16ubuntu1 [1777 kB] Get:43 http://ftpmaster.internal/ubuntu focal/main armhf libgcc-9-dev armhf 9.2.1-16ubuntu1 [685 kB] Get:44 http://ftpmaster.internal/ubuntu focal/main armhf gcc-9 armhf 9.2.1-16ubuntu1 [7587 kB] Get:45 http://ftpmaster.internal/ubuntu focal/main armhf cpp-9 armhf 9.2.1-16ubuntu1 [6890 kB] Get:46 http://ftpmaster.internal/ubuntu focal/main armhf libgcc1 armhf 1:9.2.1-16ubuntu1 [37.4 kB] Get:47 http://ftpmaster.internal/ubuntu focal/main armhf libattr1 armhf 1:2.4.48-5 [11.5 kB] Get:48 http://ftpmaster.internal/ubuntu focal-proposed/main armhf libdebconfclient0 armhf 0.250ubuntu1 [5820 B] Get:49 http://ftpmaster.internal/ubuntu focal/main armhf libgcrypt20 armhf 1.8.5-3ubuntu1 [364 kB] Get:50 http://ftpmaster.internal/ubuntu focal/main armhf libncurses6 armhf 6.1+20191019-1ubuntu1 [79.7 kB] Get:51 http://ftpmaster.internal/ubuntu focal/main armhf libtinfo6 armhf 6.1+20191019-1ubuntu1 [72.8 kB] Get:52 http://ftpmaster.internal/ubuntu focal/main armhf libncursesw6 armhf 6.1+20191019-1ubuntu1 [106 kB] Get:53 http://ftpmaster.internal/ubuntu focal/main armhf libselinux1 armhf 2.9-2build1 [60.7 kB] Get:54 http://ftpmaster.internal/ubuntu focal/main armhf libsemanage-common all 2.9-3build1 [9736 B] Get:55 http://ftpmaster.internal/ubuntu focal/main armhf libsemanage1 armhf 2.9-3build1 [73.7 kB] Get:56 http://ftpmaster.internal/ubuntu focal-proposed/main armhf libudev1 armhf 243-3ubuntu1 [71.0 kB] Get:57 http://ftpmaster.internal/ubuntu focal-proposed/main armhf libsqlite3-0 armhf 3.30.1-1 [460 kB] Get:58 http://ftpmaster.internal/ubuntu focal/main armhf liblockfile-bin armhf 1.16-1.1 [10.5 kB] Get:59 http://ftpmaster.internal/ubuntu focal/main armhf liblockfile1 armhf 1.16-1.1 [5620 B] Get:60 http://ftpmaster.internal/ubuntu focal-proposed/main armhf linux-libc-dev armhf 5.3.0-21.22 [1067 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 44.4 MB in 2s (21.9 MB/s) (Reading database ... 12487 files and directories currently installed.) 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Setting up libatomic1:armhf (9.2.1-16ubuntu1) ... Setting up libubsan1:armhf (9.2.1-16ubuntu1) ... Setting up cpp-9 (9.2.1-16ubuntu1) ... Setting up libperl5.30:armhf (5.30.0-9) ... Setting up liblockfile1:armhf (1.16-1.1) ... Setting up libjson-c4:armhf (0.13.1+dfsg-6) ... Setting up libbinutils:armhf (2.33.1-1ubuntu1) ... Setting up binutils-arm-linux-gnueabihf (2.33.1-1ubuntu1) ... Setting up libcc1-0:armhf (9.2.1-16ubuntu1) ... Setting up libkmod2:armhf (26-3ubuntu1) ... Setting up binutils (2.33.1-1ubuntu1) ... Setting up libgcc-9-dev:armhf (9.2.1-16ubuntu1) ... Setting up perl (5.30.0-9) ... Setting up libcryptsetup12:armhf (2:2.2.1-1ubuntu1) ... Setting up gcc-9 (9.2.1-16ubuntu1) ... Setting up libstdc++-9-dev:armhf (9.2.1-16ubuntu1) ... Setting up systemd (243-3ubuntu1) ... Installing new version of config file /etc/dhcp/dhclient-enter-hooks.d/resolved ... Installing new version of config file /etc/systemd/networkd.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 KVM UUID. Setting up g++-9 (9.2.1-16ubuntu1) ... Setting up systemd-sysv (243-3ubuntu1) ... Processing triggers for libc-bin (2.30-0ubuntu2) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-17940165 armhf focal-proposed -c chroot:build-PACKAGEBUILD-17940165 --arch=armhf --dist=focal-proposed --nolog python-biopython_1.73+dfsg-1ubuntu2.dsc Initiating build PACKAGEBUILD-17940165 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-166-generic #195-Ubuntu SMP Tue Oct 1 09:36:37 UTC 2019 armv7l sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-arm64-009.buildd +==============================================================================+ | python-biopython 1.73+dfsg-1ubuntu2 (armhf) 03 Nov 2019 09:54 | +==============================================================================+ Package: python-biopython Version: 1.73+dfsg-1ubuntu2 Source Version: 1.73+dfsg-1ubuntu2 Distribution: focal-proposed Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf I: NOTICE: Log filtering will replace 'build/python-biopython-zuwbf6/python-biopython-1.73+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/python-biopython-zuwbf6' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-17940165/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- python-biopython_1.73+dfsg-1ubuntu2.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-AAB_gD/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-AAB_gD/apt_archive ./ InRelease Get:2 copy:/<>/resolver-AAB_gD/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-AAB_gD/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-AAB_gD/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-AAB_gD/apt_archive ./ Packages [526 B] Fetched 2859 B in 0s (87.8 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libhogweed4 libnettle6 libperl5.28 perl-modules-5.28 Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-AAB_gD/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14415 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 12~), dh-python, python-all-dev, python3-all-dev, python-numpy, python3-numpy, flex, python-reportlab, python3-reportlab, hevea, texlive-latex-base, texlive-latex-extra, texlive-fonts-recommended, clustalo, clustalw, dialign, dssp, emboss, fasttree, mafft, muscle, ncbi-blast+, phylip, phyml, prank, probcons, python-mysqldb, python3-mysqldb, python-matplotlib, python3-matplotlib, python-pil, python3-pil, python-rdflib (>= 4), python3-rdflib, python-renderpm, python3-renderpm, python-psycopg2, python3-psycopg2, python-scipy, python3-scipy, python-setuptools, python3-setuptools, t-coffee, wise (>= 2.4.1-16) Filtered Build-Depends: debhelper (>= 12~), dh-python, python-all-dev, python3-all-dev, python-numpy, python3-numpy, flex, python-reportlab, python3-reportlab, hevea, texlive-latex-base, texlive-latex-extra, texlive-fonts-recommended, clustalo, clustalw, dialign, dssp, emboss, fasttree, mafft, muscle, ncbi-blast+, phylip, phyml, prank, probcons, python-mysqldb, python3-mysqldb, python-matplotlib, python3-matplotlib, python-pil, python3-pil, python-rdflib (>= 4), python3-rdflib, python-renderpm, python3-renderpm, python-psycopg2, python3-psycopg2, python-scipy, python3-scipy, python-setuptools, python3-setuptools, t-coffee, wise (>= 2.4.1-16) dpkg-deb: building package 'sbuild-build-depends-python-biopython-dummy' in '/<>/resolver-UtwJqf/apt_archive/sbuild-build-depends-python-biopython-dummy.deb'. Ign:1 copy:/<>/resolver-UtwJqf/apt_archive ./ InRelease Get:2 copy:/<>/resolver-UtwJqf/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-UtwJqf/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-UtwJqf/apt_archive ./ Sources [493 B] Get:5 copy:/<>/resolver-UtwJqf/apt_archive ./ Packages [781 B] Fetched 3393 B in 0s (133 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install python-biopython build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libhogweed4 libnettle6 libperl5.28 perl-modules-5.28 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils clustalo clustalw debhelper 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 gettext gettext-base ghostscript groff-base gsfonts hevea intltool-debian libarchive-zip-perl libargtable2-0 libasn1-8-heimdal libavahi-client3 libavahi-common-data libavahi-common3 libblas3 libboost-program-options1.67.0 libboost-system1.67.0 libboost-thread1.67.0 libbsd0 libcairo2 libcroco3 libcups2 libcupsimage2 libdbus-1-3 libdebhelper-perl libedit2 libelf1 libevent-2.1-7 libevent-core-2.1-7 libevent-pthreads-2.1-7 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgd3 libgfortran5 libglib2.0-0 libgraphite2-3 libgs9 libgs9-common libgssapi-krb5-2 libgssapi3-heimdal libharfbuzz-icu0 libharfbuzz0b libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhpdf-2.3.0 libhwloc-plugins libhwloc5 libhx509-5-heimdal libibverbs1 libice6 libicu63 libidn11 libijs-0.35 libimagequant0 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkpathsea6 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.4-2 libldap-common liblmdb0 libltdl7 libmagic-mgc libmagic1 libmbedcrypto3 libmbedtls12 libmbedx509-0 libmpdec2 libmysqlclient21 libnetpbm10 libnl-3-200 libnl-route-3-200 libopenmpi3 libpaper-utils libpaper1 libpciaccess0 libpipeline1 libpixman-1-0 libpmix2 libpq5 libptexenc1 libpython-all-dev libpython-dev libpython-stdlib libpython2-dev libpython2-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.7 libpython3.7-dev libpython3.7-minimal libpython3.7-stdlib libpython3.8 libpython3.8-dev libpython3.8-minimal libpython3.8-stdlib libroken18-heimdal libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libsub-override-perl libsynctex2 libteckit0 libtexlua53 libtexluajit2 libtiff5 libtool libuchardet0 libwebp6 libwebpdemux2 libwebpmux3 libwind0-heimdal libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxt6 libzzip-0-13 m4 mafft man-db mime-support muscle mysql-common ncbi-blast+ ncbi-data netpbm ocaml-base-nox ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client phylip phyml po-debconf poppler-data prank preview-latex-style probcons python python-all python-all-dev python-backports.functools-lru-cache python-cycler python-dateutil python-decorator python-dev python-isodate python-kiwisolver python-matplotlib python-matplotlib-data python-matplotlib2-data python-minimal python-mysqldb python-numpy python-pil python-pkg-resources python-psycopg2 python-pyparsing python-rdflib python-renderpm python-reportlab python-reportlab-accel python-scipy python-setuptools python-six python-subprocess32 python-tz python2 python2-dev python2-minimal python2.7 python2.7-dev python2.7-minimal python3 python3-all python3-all-dev python3-cycler python3-dateutil python3-decorator python3-dev python3-distutils python3-isodate python3-kiwisolver python3-lib2to3 python3-matplotlib python3-minimal python3-mysqldb python3-numpy python3-pil python3-pkg-resources python3-psycopg2 python3-pyparsing python3-rdflib python3-renderpm python3-reportlab python3-reportlab-accel python3-scipy python3-setuptools python3-six python3.7 python3.7-dev python3.7-minimal python3.8 python3.8-dev python3.8-minimal t-coffee t1utils tex-common texlive-base texlive-binaries texlive-fonts-recommended texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures ttf-bitstream-vera ucf wise wise-data x11-common xdg-utils zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation clustalx seaview dh-make emboss-doc emboss-test embassy bison flex-doc gettext-doc libasprintf-dev libgettextpo-dev ghostscript-x groff hevea-doc cups-common libgd-tools krb5-doc krb5-user libhwloc-contrib-plugins libjs-jquery-ui-docs liblcms2-utils pciutils libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser opencl-icd gfortran | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass 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 python-doc python-tk python-cycler-doc dvipng ffmpeg gir1.2-gtk-3.0 inkscape ipython librsvg2-common python-cairocffi python-configobj python-excelerator python-gi python-gobject-2 python-matplotlib2-doc python-nose python-qt4 python-sip python-tornado python-traits python-wxgtk3.0 texlive-extra-utils ttf-staypuft default-mysql-server | virtual-mysql-server python-egenix-mxdatetime python-mysqldb-dbg gfortran python-pytest python-numpy-dbg python-numpy-doc python-pil-doc python-pil-dbg python-psycopg2-doc python-pyparsing-doc python-rdflib-doc python-rdflib-tools python-renderpm-dbg pdf-viewer python-egenix-mxtexttools python-reportlab-doc python-scipy-doc python-setuptools-doc python2-doc python2.7-doc binfmt-support python3-doc python3-tk python3-venv ipython3 python-matplotlib-doc python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-nose python3-pyqt4 python3-sip python3-tornado python3-mysqldb-dbg python3-pytest python3-numpy-dbg python3-pil-dbg python3-renderpm-dbg python3-egenix-mxtexttools python3.7-venv python3.7-doc python3.8-venv python3.8-doc boxshade t-coffee-examples perl-tk xpdf | pdf-viewer xzdec texlive-fonts-recommended-doc texlive-latex-base-doc python-pygments icc-profiles libfile-which-perl libspreadsheet-parseexcel-perl texlive-latex-extra-doc texlive-latex-recommended-doc texlive-luatex texlive-pstricks dot2tex prerex ruby-tcltk | libtcltk-ruby texlive-pictures-doc vprerex wise-doc Recommended packages: primer3 libfl-dev curl | wget | lynx libcupsfilters1 dbus libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs fonts-droid-fallback ibverbs-providers javascript-common krb5-locales libsasl2-modules libltdl-dev blast2 libwww-perl lynx ruby libopenmpi-dev xauth libmail-sendmail-perl python-tk python-olefile python-egenix-mxdatetime python-sparqlwrapper python-html5lib python3-tk python3-olefile python3-sparqlwrapper python3-html5lib amap-align dialign-tx fsa kalign libsoap-lite-perl libxml-simple-perl mustang poa proda tm-align lmodern dvisvgm tex-gyre tipa texlive-plain-generic ruby | ruby-interpreter 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 bsdmainutils clustalo clustalw debhelper 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 gettext gettext-base ghostscript groff-base gsfonts hevea intltool-debian libarchive-zip-perl libargtable2-0 libasn1-8-heimdal libavahi-client3 libavahi-common-data libavahi-common3 libblas3 libboost-program-options1.67.0 libboost-system1.67.0 libboost-thread1.67.0 libbsd0 libcairo2 libcroco3 libcups2 libcupsimage2 libdbus-1-3 libdebhelper-perl libedit2 libelf1 libevent-2.1-7 libevent-core-2.1-7 libevent-pthreads-2.1-7 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgd3 libgfortran5 libglib2.0-0 libgraphite2-3 libgs9 libgs9-common libgssapi-krb5-2 libgssapi3-heimdal libharfbuzz-icu0 libharfbuzz0b libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhpdf-2.3.0 libhwloc-plugins libhwloc5 libhx509-5-heimdal libibverbs1 libice6 libicu63 libidn11 libijs-0.35 libimagequant0 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkpathsea6 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.4-2 libldap-common liblmdb0 libltdl7 libmagic-mgc libmagic1 libmbedcrypto3 libmbedtls12 libmbedx509-0 libmpdec2 libmysqlclient21 libnetpbm10 libnl-3-200 libnl-route-3-200 libopenmpi3 libpaper-utils libpaper1 libpciaccess0 libpipeline1 libpixman-1-0 libpmix2 libpq5 libptexenc1 libpython-all-dev libpython-dev libpython-stdlib libpython2-dev libpython2-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.7 libpython3.7-dev libpython3.7-minimal libpython3.7-stdlib libpython3.8 libpython3.8-dev libpython3.8-minimal libpython3.8-stdlib libroken18-heimdal libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libsub-override-perl libsynctex2 libteckit0 libtexlua53 libtexluajit2 libtiff5 libtool libuchardet0 libwebp6 libwebpdemux2 libwebpmux3 libwind0-heimdal libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxt6 libzzip-0-13 m4 mafft man-db mime-support muscle mysql-common ncbi-blast+ ncbi-data netpbm ocaml-base-nox ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client phylip phyml po-debconf poppler-data prank preview-latex-style probcons python python-all python-all-dev python-backports.functools-lru-cache python-cycler python-dateutil python-decorator python-dev python-isodate python-kiwisolver python-matplotlib python-matplotlib-data python-matplotlib2-data python-minimal python-mysqldb python-numpy python-pil python-pkg-resources python-psycopg2 python-pyparsing python-rdflib python-renderpm python-reportlab python-reportlab-accel python-scipy python-setuptools python-six python-subprocess32 python-tz python2 python2-dev python2-minimal python2.7 python2.7-dev python2.7-minimal python3 python3-all python3-all-dev python3-cycler python3-dateutil python3-decorator python3-dev python3-distutils python3-isodate python3-kiwisolver python3-lib2to3 python3-matplotlib python3-minimal python3-mysqldb python3-numpy python3-pil python3-pkg-resources python3-psycopg2 python3-pyparsing python3-rdflib python3-renderpm python3-reportlab python3-reportlab-accel python3-scipy python3-setuptools python3-six python3.7 python3.7-dev python3.7-minimal python3.8 python3.8-dev python3.8-minimal sbuild-build-depends-python-biopython-dummy t-coffee t1utils tex-common texlive-base texlive-binaries texlive-fonts-recommended texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures ttf-bitstream-vera ucf wise wise-data x11-common xdg-utils zlib1g-dev 0 upgraded, 278 newly installed, 0 to remove and 0 not upgraded. Need to get 282 MB of archives. After this operation, 1309 MB of additional disk space will be used. Get:1 copy:/<>/resolver-UtwJqf/apt_archive ./ sbuild-build-depends-python-biopython-dummy 0.invalid.0 [1104 B] Get:2 http://ftpmaster.internal/ubuntu focal-proposed/main armhf libpython3.7-minimal armhf 3.7.5-2 [539 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main armhf libexpat1 armhf 2.2.9-1 [53.2 kB] Get:4 http://ftpmaster.internal/ubuntu focal-proposed/main armhf python3.7-minimal armhf 3.7.5-2 [1469 kB] Get:5 http://ftpmaster.internal/ubuntu focal-proposed/main armhf python3-minimal armhf 3.7.5-1ubuntu1 [23.3 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main armhf mime-support all 3.64ubuntu1 [30.6 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main armhf libmpdec2 armhf 2.4.2-2 [66.4 kB] Get:8 http://ftpmaster.internal/ubuntu focal-proposed/main armhf libpython3.7-stdlib armhf 3.7.5-2 [1664 kB] Get:9 http://ftpmaster.internal/ubuntu focal-proposed/main armhf python3.7 armhf 3.7.5-2 [301 kB] Get:10 http://ftpmaster.internal/ubuntu focal-proposed/main armhf libpython3-stdlib armhf 3.7.5-1ubuntu1 [6844 B] Get:11 http://ftpmaster.internal/ubuntu focal-proposed/main armhf python3 armhf 3.7.5-1ubuntu1 [47.2 kB] Get:12 http://ftpmaster.internal/ubuntu focal/main armhf libbsd0 armhf 0.10.0-1 [49.8 kB] Get:13 http://ftpmaster.internal/ubuntu focal/main armhf bsdmainutils armhf 11.1.2ubuntu2 [176 kB] Get:14 http://ftpmaster.internal/ubuntu focal/main armhf libuchardet0 armhf 0.0.6-3 [62.1 kB] Get:15 http://ftpmaster.internal/ubuntu focal/main armhf groff-base armhf 1.22.4-3 [772 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main armhf libpipeline1 armhf 1.5.1-2 [21.6 kB] Get:17 http://ftpmaster.internal/ubuntu focal-proposed/main armhf man-db armhf 2.9.0-1 [1079 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main armhf libsigsegv2 armhf 2.12-2 [13.1 kB] Get:19 http://ftpmaster.internal/ubuntu focal/main armhf m4 armhf 1.4.18-2 [186 kB] Get:20 http://ftpmaster.internal/ubuntu focal/main armhf flex armhf 2.6.4-6.2 [298 kB] Get:21 http://ftpmaster.internal/ubuntu focal/main armhf poppler-data all 0.4.9-2 [1475 kB] Get:22 http://ftpmaster.internal/ubuntu focal/universe armhf libpython2.7-minimal armhf 2.7.17-1 [335 kB] Get:23 http://ftpmaster.internal/ubuntu focal/universe armhf python2.7-minimal armhf 2.7.17-1 [1088 kB] Get:24 http://ftpmaster.internal/ubuntu focal/universe armhf python2-minimal armhf 2.7.17-1 [27.8 kB] Get:25 http://ftpmaster.internal/ubuntu focal/universe armhf python-minimal armhf 2.7.17-1 [5996 B] Get:26 http://ftpmaster.internal/ubuntu focal/universe armhf libpython2.7-stdlib armhf 2.7.17-1 [1812 kB] Get:27 http://ftpmaster.internal/ubuntu focal/universe armhf python2.7 armhf 2.7.17-1 [248 kB] Get:28 http://ftpmaster.internal/ubuntu focal/universe armhf libpython2-stdlib armhf 2.7.17-1 [7400 B] Get:29 http://ftpmaster.internal/ubuntu focal/universe armhf libpython-stdlib armhf 2.7.17-1 [5836 B] Get:30 http://ftpmaster.internal/ubuntu focal/universe armhf python2 armhf 2.7.17-1 [26.5 kB] Get:31 http://ftpmaster.internal/ubuntu focal/universe armhf python armhf 2.7.17-1 [7836 B] Get:32 http://ftpmaster.internal/ubuntu focal/main armhf libpython3.8-minimal armhf 3.8.0-3 [696 kB] Get:33 http://ftpmaster.internal/ubuntu focal/main armhf python3.8-minimal armhf 3.8.0-3 [1576 kB] Get:34 http://ftpmaster.internal/ubuntu focal/main armhf ucf all 3.0038+nmu1 [51.6 kB] Get:35 http://ftpmaster.internal/ubuntu focal/main armhf tex-common all 6.12 [32.7 kB] Get:36 http://ftpmaster.internal/ubuntu focal-proposed/main armhf libmagic-mgc armhf 1:5.37-6 [209 kB] Get:37 http://ftpmaster.internal/ubuntu focal-proposed/main armhf libmagic1 armhf 1:5.37-6 [67.7 kB] Get:38 http://ftpmaster.internal/ubuntu focal-proposed/main armhf file armhf 1:5.37-6 [22.2 kB] Get:39 http://ftpmaster.internal/ubuntu focal/main armhf libdbus-1-3 armhf 1.12.14-1ubuntu2 [155 kB] Get:40 http://ftpmaster.internal/ubuntu focal/main armhf libelf1 armhf 0.176-1.1 [40.9 kB] Get:41 http://ftpmaster.internal/ubuntu focal-proposed/main armhf libglib2.0-0 armhf 2.62.2-2 [1104 kB] Get:42 http://ftpmaster.internal/ubuntu focal/main armhf libicu63 armhf 63.2-2 [8002 kB] Get:43 http://ftpmaster.internal/ubuntu focal/main armhf libxml2 armhf 2.9.4+dfsg1-7ubuntu5 [554 kB] Get:44 http://ftpmaster.internal/ubuntu focal-proposed/main armhf python3-pkg-resources all 41.4.0-1 [100 kB] Get:45 http://ftpmaster.internal/ubuntu focal/main armhf python3-six all 1.12.0-2build1 [11.7 kB] Get:46 http://ftpmaster.internal/ubuntu focal/main armhf gettext-base armhf 0.19.8.1-9 [46.0 kB] Get:47 http://ftpmaster.internal/ubuntu focal-proposed/main armhf libedit2 armhf 3.1-20191025-1 [71.6 kB] Get:48 http://ftpmaster.internal/ubuntu focal/main armhf libevent-2.1-7 armhf 2.1.11-stable-1~exp0 [119 kB] Get:49 http://ftpmaster.internal/ubuntu focal/main armhf libkrb5support0 armhf 1.17-6 [28.5 kB] Get:50 http://ftpmaster.internal/ubuntu focal/main armhf libk5crypto3 armhf 1.17-6 [78.9 kB] Get:51 http://ftpmaster.internal/ubuntu focal/main armhf libkeyutils1 armhf 1.6-6ubuntu1 [9172 B] Get:52 http://ftpmaster.internal/ubuntu focal/main armhf libkrb5-3 armhf 1.17-6 [287 kB] Get:53 http://ftpmaster.internal/ubuntu focal/main armhf libgssapi-krb5-2 armhf 1.17-6 [101 kB] Get:54 http://ftpmaster.internal/ubuntu focal/main armhf libxau6 armhf 1:1.0.9-0ubuntu1 [6612 B] Get:55 http://ftpmaster.internal/ubuntu focal/main armhf libxdmcp6 armhf 1:1.1.3-0ubuntu1 [9160 B] Get:56 http://ftpmaster.internal/ubuntu focal/main armhf libxcb1 armhf 1.13.1-2 [40.8 kB] Get:57 http://ftpmaster.internal/ubuntu focal/main armhf libx11-data all 2:1.6.8-1 [113 kB] Get:58 http://ftpmaster.internal/ubuntu focal/main armhf libx11-6 armhf 2:1.6.8-1 [517 kB] Get:59 http://ftpmaster.internal/ubuntu focal/main armhf libxext6 armhf 2:1.3.4-0ubuntu1 [24.2 kB] Get:60 http://ftpmaster.internal/ubuntu focal/main armhf openssh-client armhf 1:8.1p1-1 [555 kB] Get:61 http://ftpmaster.internal/ubuntu focal/main armhf autoconf all 2.69-11ubuntu1 [321 kB] Get:62 http://ftpmaster.internal/ubuntu focal/main armhf autotools-dev all 20180224.1 [39.6 kB] Get:63 http://ftpmaster.internal/ubuntu focal/main armhf automake all 1:1.16.1-4ubuntu3 [522 kB] Get:64 http://ftpmaster.internal/ubuntu focal/main armhf autopoint all 0.19.8.1-9 [412 kB] Get:65 http://ftpmaster.internal/ubuntu focal/universe armhf libargtable2-0 armhf 13-1 [12.0 kB] Get:66 http://ftpmaster.internal/ubuntu focal/universe armhf clustalo armhf 1.2.4-2 [229 kB] Get:67 http://ftpmaster.internal/ubuntu focal/universe armhf clustalw armhf 2.1+lgpl-6 [242 kB] Get:68 http://ftpmaster.internal/ubuntu focal/main armhf libtool all 2.4.6-11 [194 kB] Get:69 http://ftpmaster.internal/ubuntu focal/main armhf dh-autoreconf all 19 [16.1 kB] Get:70 http://ftpmaster.internal/ubuntu focal/main armhf libdebhelper-perl all 12.7.1ubuntu1 [52.0 kB] Get:71 http://ftpmaster.internal/ubuntu focal-proposed/main armhf libarchive-zip-perl all 1.67-1 [90.4 kB] Get:72 http://ftpmaster.internal/ubuntu focal/main armhf libsub-override-perl all 0.09-2 [9532 B] Get:73 http://ftpmaster.internal/ubuntu focal/main armhf libfile-stripnondeterminism-perl all 1.6.2-1 [16.1 kB] Get:74 http://ftpmaster.internal/ubuntu focal/main armhf dh-strip-nondeterminism all 1.6.2-1 [5228 B] Get:75 http://ftpmaster.internal/ubuntu focal/main armhf dwz armhf 0.13-1 [74.2 kB] Get:76 http://ftpmaster.internal/ubuntu focal/main armhf libcroco3 armhf 0.6.13-1 [70.5 kB] Get:77 http://ftpmaster.internal/ubuntu focal/main armhf gettext armhf 0.19.8.1-9 [833 kB] Get:78 http://ftpmaster.internal/ubuntu focal/main armhf intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:79 http://ftpmaster.internal/ubuntu focal/main armhf po-debconf all 1.0.21 [233 kB] Get:80 http://ftpmaster.internal/ubuntu focal/main armhf debhelper all 12.7.1ubuntu1 [875 kB] Get:81 http://ftpmaster.internal/ubuntu focal-proposed/main armhf python3-lib2to3 all 3.8.0-1 [75.6 kB] Get:82 http://ftpmaster.internal/ubuntu focal-proposed/main armhf python3-distutils all 3.8.0-1 [142 kB] Get:83 http://ftpmaster.internal/ubuntu focal/main armhf dh-python all 4.20191017ubuntu1 [88.5 kB] Get:84 http://ftpmaster.internal/ubuntu focal/universe armhf dialign armhf 2.2.1-10 [139 kB] Get:85 http://ftpmaster.internal/ubuntu focal/main armhf libboost-program-options1.67.0 armhf 1.67.0-13ubuntu2 [312 kB] Get:86 http://ftpmaster.internal/ubuntu focal/main armhf libboost-system1.67.0 armhf 1.67.0-13ubuntu2 [204 kB] Get:87 http://ftpmaster.internal/ubuntu focal/main armhf libboost-thread1.67.0 armhf 1.67.0-13ubuntu2 [237 kB] Get:88 http://ftpmaster.internal/ubuntu focal/universe armhf dssp armhf 3.0.0-3 [223 kB] Get:89 http://ftpmaster.internal/ubuntu focal/main armhf libfreetype6 armhf 2.10.1-2 [283 kB] Get:90 http://ftpmaster.internal/ubuntu focal/main armhf fonts-dejavu-core all 2.37-1 [1041 kB] Get:91 http://ftpmaster.internal/ubuntu focal/universe armhf ttf-bitstream-vera all 1.10-8 [352 kB] Get:92 http://ftpmaster.internal/ubuntu focal/main armhf fontconfig-config all 2.13.1-2ubuntu2 [28.9 kB] Get:93 http://ftpmaster.internal/ubuntu focal/main armhf libfontconfig1 armhf 2.13.1-2ubuntu2 [95.8 kB] Get:94 http://ftpmaster.internal/ubuntu focal/main armhf libjpeg-turbo8 armhf 2.0.3-0ubuntu1 [90.4 kB] Get:95 http://ftpmaster.internal/ubuntu focal/main armhf libjpeg8 armhf 8c-2ubuntu8 [2202 B] Get:96 http://ftpmaster.internal/ubuntu focal/main armhf libjbig0 armhf 2.1-3.1build1 [23.9 kB] Get:97 http://ftpmaster.internal/ubuntu focal/main armhf libwebp6 armhf 0.6.1-2 [152 kB] Get:98 http://ftpmaster.internal/ubuntu focal/main armhf libtiff5 armhf 4.0.10+git191003-1 [143 kB] Get:99 http://ftpmaster.internal/ubuntu focal/main armhf libxpm4 armhf 1:3.5.12-1 [29.0 kB] Get:100 http://ftpmaster.internal/ubuntu focal/main armhf libgd3 armhf 2.2.5-5.2 [98.7 kB] Get:101 http://ftpmaster.internal/ubuntu focal/universe armhf libhpdf-2.3.0 armhf 2.3.0+dfsg-1 [327 kB] Get:102 http://ftpmaster.internal/ubuntu focal/main armhf mysql-common all 5.8+1.0.5ubuntu2 [7496 B] Get:103 http://ftpmaster.internal/ubuntu focal/main armhf libmysqlclient21 armhf 8.0.17-0ubuntu3 [1036 kB] Get:104 http://ftpmaster.internal/ubuntu focal/main armhf libroken18-heimdal armhf 7.5.0+dfsg-3build1 [34.5 kB] Get:105 http://ftpmaster.internal/ubuntu focal/main armhf libasn1-8-heimdal armhf 7.5.0+dfsg-3build1 [140 kB] Get:106 http://ftpmaster.internal/ubuntu focal/main armhf libheimbase1-heimdal armhf 7.5.0+dfsg-3build1 [24.3 kB] Get:107 http://ftpmaster.internal/ubuntu focal/main armhf libhcrypto4-heimdal armhf 7.5.0+dfsg-3build1 [78.0 kB] Get:108 http://ftpmaster.internal/ubuntu focal/main armhf libwind0-heimdal armhf 7.5.0+dfsg-3build1 [46.9 kB] Get:109 http://ftpmaster.internal/ubuntu focal/main armhf libhx509-5-heimdal armhf 7.5.0+dfsg-3build1 [88.9 kB] Get:110 http://ftpmaster.internal/ubuntu focal/main armhf libkrb5-26-heimdal armhf 7.5.0+dfsg-3build1 [170 kB] Get:111 http://ftpmaster.internal/ubuntu focal/main armhf libheimntlm0-heimdal armhf 7.5.0+dfsg-3build1 [13.2 kB] Get:112 http://ftpmaster.internal/ubuntu focal/main armhf libgssapi3-heimdal armhf 7.5.0+dfsg-3build1 [79.7 kB] Get:113 http://ftpmaster.internal/ubuntu focal/main armhf libsasl2-modules-db armhf 2.1.27+dfsg-1build3 [13.1 kB] Get:114 http://ftpmaster.internal/ubuntu focal/main armhf libsasl2-2 armhf 2.1.27+dfsg-1build3 [42.7 kB] Get:115 http://ftpmaster.internal/ubuntu focal-proposed/main armhf libldap-common all 2.4.48+dfsg-1ubuntu3 [17.3 kB] Get:116 http://ftpmaster.internal/ubuntu focal-proposed/main armhf libldap-2.4-2 armhf 2.4.48+dfsg-1ubuntu3 [133 kB] Get:117 http://ftpmaster.internal/ubuntu focal-proposed/main armhf libpq5 armhf 12.0-1 [155 kB] Get:118 http://ftpmaster.internal/ubuntu focal/universe armhf emboss-lib armhf 6.6.0+dfsg-7ubuntu2 [2361 kB] Get:119 http://ftpmaster.internal/ubuntu focal/universe armhf emboss-data all 6.6.0+dfsg-7ubuntu2 [61.0 MB] Get:120 http://ftpmaster.internal/ubuntu focal/universe armhf emboss armhf 6.6.0+dfsg-7ubuntu2 [943 kB] Get:121 http://ftpmaster.internal/ubuntu focal/main armhf fonts-lmodern all 2.004.5-6 [4532 kB] Get:122 http://ftpmaster.internal/ubuntu focal/universe armhf fonts-lyx all 2.3.3-2 [154 kB] Get:123 http://ftpmaster.internal/ubuntu focal/main armhf libavahi-common-data armhf 0.7-4ubuntu5 [21.4 kB] Get:124 http://ftpmaster.internal/ubuntu focal/main armhf libavahi-common3 armhf 0.7-4ubuntu5 [18.2 kB] Get:125 http://ftpmaster.internal/ubuntu focal/main armhf libavahi-client3 armhf 0.7-4ubuntu5 [21.8 kB] Get:126 http://ftpmaster.internal/ubuntu focal/main armhf libcups2 armhf 2.3.0-6 [196 kB] Get:127 http://ftpmaster.internal/ubuntu focal/main armhf libcupsimage2 armhf 2.3.0-6 [5688 B] Get:128 http://ftpmaster.internal/ubuntu focal/main armhf libidn11 armhf 1.33-2.2ubuntu2 [43.1 kB] Get:129 http://ftpmaster.internal/ubuntu focal/main armhf libijs-0.35 armhf 0.35-15 [14.0 kB] Get:130 http://ftpmaster.internal/ubuntu focal/main armhf libjbig2dec0 armhf 0.17-1 [51.8 kB] Get:131 http://ftpmaster.internal/ubuntu focal/main armhf libpaper1 armhf 1.1.28 [12.1 kB] Get:132 http://ftpmaster.internal/ubuntu focal/main armhf libgs9-common all 9.27~dfsg+0-0ubuntu3 [5092 kB] Get:133 http://ftpmaster.internal/ubuntu focal/main armhf libgs9 armhf 9.27~dfsg+0-0ubuntu3 [2069 kB] Get:134 http://ftpmaster.internal/ubuntu focal/main armhf ghostscript armhf 9.27~dfsg+0-0ubuntu3 [51.3 kB] Get:135 http://ftpmaster.internal/ubuntu focal/main armhf gsfonts all 1:8.11+urwcyr1.0.7~pre44-4.4 [3120 kB] Get:136 http://ftpmaster.internal/ubuntu focal/universe armhf libnetpbm10 armhf 2:10.0-15.3build1 [47.5 kB] Get:137 http://ftpmaster.internal/ubuntu focal/universe armhf netpbm armhf 2:10.0-15.3build1 [891 kB] Get:138 http://ftpmaster.internal/ubuntu focal/main armhf libpaper-utils armhf 1.1.28 [7960 B] Get:139 http://ftpmaster.internal/ubuntu focal/main armhf libkpathsea6 armhf 2019.20190605.51237-3 [48.8 kB] Get:140 http://ftpmaster.internal/ubuntu focal/main armhf libptexenc1 armhf 2019.20190605.51237-3 [34.9 kB] Get:141 http://ftpmaster.internal/ubuntu focal/main armhf libsynctex2 armhf 2019.20190605.51237-3 [42.9 kB] Get:142 http://ftpmaster.internal/ubuntu focal/main armhf libtexlua53 armhf 2019.20190605.51237-3 [81.8 kB] Get:143 http://ftpmaster.internal/ubuntu focal/main armhf libtexluajit2 armhf 2019.20190605.51237-3 [181 kB] Get:144 http://ftpmaster.internal/ubuntu focal/main armhf t1utils armhf 1.41-3 [48.2 kB] Get:145 http://ftpmaster.internal/ubuntu focal/main armhf libpixman-1-0 armhf 0.38.4-0ubuntu1 [159 kB] Get:146 http://ftpmaster.internal/ubuntu focal/main armhf libxcb-render0 armhf 1.13.1-2 [13.9 kB] Get:147 http://ftpmaster.internal/ubuntu focal/main armhf libxcb-shm0 armhf 1.13.1-2 [5380 B] Get:148 http://ftpmaster.internal/ubuntu focal/main armhf libxrender1 armhf 1:0.9.10-1 [15.6 kB] Get:149 http://ftpmaster.internal/ubuntu focal/main armhf libcairo2 armhf 1.16.0-4 [510 kB] Get:150 http://ftpmaster.internal/ubuntu focal/main armhf libgraphite2-3 armhf 1.3.13-11 [62.7 kB] Get:151 http://ftpmaster.internal/ubuntu focal/main armhf libharfbuzz0b armhf 2.6.2-1 [333 kB] Get:152 http://ftpmaster.internal/ubuntu focal/main armhf libharfbuzz-icu0 armhf 2.6.2-1 [5012 B] Get:153 http://ftpmaster.internal/ubuntu focal/main armhf libteckit0 armhf 2.5.8+ds2-5ubuntu1 [245 kB] Get:154 http://ftpmaster.internal/ubuntu focal/main armhf x11-common all 1:7.7+19ubuntu12 [22.4 kB] Get:155 http://ftpmaster.internal/ubuntu focal/main armhf libice6 armhf 2:1.0.10-0ubuntu1 [34.1 kB] Get:156 http://ftpmaster.internal/ubuntu focal/main armhf libsm6 armhf 2:1.2.3-1 [14.1 kB] Get:157 http://ftpmaster.internal/ubuntu focal/main armhf libxt6 armhf 1:1.1.5-1 [129 kB] Get:158 http://ftpmaster.internal/ubuntu focal/main armhf libxmu6 armhf 2:1.1.3-0ubuntu1 [38.3 kB] Get:159 http://ftpmaster.internal/ubuntu focal/main armhf libxaw7 armhf 2:1.0.13-1 [141 kB] Get:160 http://ftpmaster.internal/ubuntu focal/main armhf libxi6 armhf 2:1.7.10-0ubuntu1 [25.0 kB] Get:161 http://ftpmaster.internal/ubuntu focal/main armhf libzzip-0-13 armhf 0.13.62-3.2 [22.0 kB] Get:162 http://ftpmaster.internal/ubuntu focal/main armhf texlive-binaries armhf 2019.20190605.51237-3 [6306 kB] Get:163 http://ftpmaster.internal/ubuntu focal/main armhf xdg-utils all 1.1.3-1ubuntu2 [60.5 kB] Get:164 http://ftpmaster.internal/ubuntu focal-proposed/main armhf texlive-base all 2019.20191030-1 [20.5 MB] Get:165 http://ftpmaster.internal/ubuntu focal/universe armhf ocaml-base-nox armhf 4.05.0-12ubuntu3 [481 kB] Get:166 http://ftpmaster.internal/ubuntu focal/universe armhf hevea all 2.32-2 [884 kB] Get:167 http://ftpmaster.internal/ubuntu focal-proposed/main armhf libblas3 armhf 3.8.0-8 [101 kB] Get:168 http://ftpmaster.internal/ubuntu focal/main armhf libevent-core-2.1-7 armhf 2.1.11-stable-1~exp0 [77.8 kB] Get:169 http://ftpmaster.internal/ubuntu focal/main armhf libevent-pthreads-2.1-7 armhf 2.1.11-stable-1~exp0 [6952 B] Get:170 http://ftpmaster.internal/ubuntu focal/main armhf libexpat1-dev armhf 2.2.9-1 [99.9 kB] Get:171 http://ftpmaster.internal/ubuntu focal/main armhf libgfortran5 armhf 9.2.1-16ubuntu1 [252 kB] Get:172 http://ftpmaster.internal/ubuntu focal/main armhf libimagequant0 armhf 2.12.2-1.1 [26.2 kB] Get:173 http://ftpmaster.internal/ubuntu focal/main armhf libjs-jquery all 3.3.1~dfsg-3 [329 kB] Get:174 http://ftpmaster.internal/ubuntu focal/universe armhf libjs-jquery-ui all 1.12.1+dfsg-5 [232 kB] Get:175 http://ftpmaster.internal/ubuntu focal-proposed/main armhf liblapack3 armhf 3.8.0-8 [1704 kB] Get:176 http://ftpmaster.internal/ubuntu focal/universe armhf liblbfgsb0 armhf 3.0+dfsg.3-7 [26.2 kB] Get:177 http://ftpmaster.internal/ubuntu focal/main armhf liblcms2-2 armhf 2.9-4 [115 kB] Get:178 http://ftpmaster.internal/ubuntu focal/main armhf liblmdb0 armhf 0.9.23-0ubuntu1 [37.8 kB] Get:179 http://ftpmaster.internal/ubuntu focal/main armhf libltdl7 armhf 2.4.6-11 [35.2 kB] Get:180 http://ftpmaster.internal/ubuntu focal-proposed/universe armhf libmbedcrypto3 armhf 2.16.3-1 [134 kB] Get:181 http://ftpmaster.internal/ubuntu focal-proposed/universe armhf libmbedx509-0 armhf 2.16.3-1 [38.3 kB] Get:182 http://ftpmaster.internal/ubuntu focal-proposed/universe armhf libmbedtls12 armhf 2.16.3-1 [64.7 kB] Get:183 http://ftpmaster.internal/ubuntu focal/main armhf libnl-3-200 armhf 3.4.0-1 [46.1 kB] Get:184 http://ftpmaster.internal/ubuntu focal/main armhf libnl-route-3-200 armhf 3.4.0-1 [124 kB] Get:185 http://ftpmaster.internal/ubuntu focal/universe armhf libhwloc5 armhf 1.11.13-1 [85.8 kB] Get:186 http://ftpmaster.internal/ubuntu focal/main armhf libibverbs1 armhf 26.0-2 [46.2 kB] Get:187 http://ftpmaster.internal/ubuntu focal/main armhf libpciaccess0 armhf 0.16-0ubuntu1 [15.4 kB] Get:188 http://ftpmaster.internal/ubuntu focal/main armhf ocl-icd-libopencl1 armhf 2.2.11-1ubuntu1 [28.7 kB] Get:189 http://ftpmaster.internal/ubuntu focal/universe armhf libhwloc-plugins armhf 1.11.13-1 [11.4 kB] Get:190 http://ftpmaster.internal/ubuntu focal/universe armhf libpmix2 armhf 3.1.4-1build1 [386 kB] Get:191 http://ftpmaster.internal/ubuntu focal/universe armhf libopenmpi3 armhf 3.1.3-11build2 [1831 kB] Get:192 http://ftpmaster.internal/ubuntu focal/universe armhf libpython2.7 armhf 2.7.17-1 [901 kB] Get:193 http://ftpmaster.internal/ubuntu focal/universe armhf libpython2.7-dev armhf 2.7.17-1 [2152 kB] Get:194 http://ftpmaster.internal/ubuntu focal/universe armhf libpython2-dev armhf 2.7.17-1 [7460 B] Get:195 http://ftpmaster.internal/ubuntu focal/universe armhf libpython-dev armhf 2.7.17-1 [5892 B] Get:196 http://ftpmaster.internal/ubuntu focal/universe armhf libpython-all-dev armhf 2.7.17-1 [1112 B] Get:197 http://ftpmaster.internal/ubuntu focal-proposed/main armhf libpython3.7 armhf 3.7.5-2 [1279 kB] Get:198 http://ftpmaster.internal/ubuntu focal-proposed/main armhf libpython3.7-dev armhf 3.7.5-2 [2774 kB] Get:199 http://ftpmaster.internal/ubuntu focal-proposed/main armhf libpython3-dev armhf 3.7.5-1ubuntu1 [6940 B] Get:200 http://ftpmaster.internal/ubuntu focal/main armhf libpython3.8-stdlib armhf 3.8.0-3 [1590 kB] Get:201 http://ftpmaster.internal/ubuntu focal/main armhf libpython3.8 armhf 3.8.0-3 [1389 kB] Get:202 http://ftpmaster.internal/ubuntu focal/main armhf libpython3.8-dev armhf 3.8.0-3 [3109 kB] Get:203 http://ftpmaster.internal/ubuntu focal-proposed/main armhf libpython3-all-dev armhf 3.7.5-1ubuntu1 [1124 B] Get:204 http://ftpmaster.internal/ubuntu focal/main armhf libwebpdemux2 armhf 0.6.1-2 [8760 B] Get:205 http://ftpmaster.internal/ubuntu focal/main armhf libwebpmux3 armhf 0.6.1-2 [16.0 kB] Get:206 http://ftpmaster.internal/ubuntu focal/universe armhf mafft armhf 7.429-1 [753 kB] Get:207 http://ftpmaster.internal/ubuntu focal/universe armhf muscle armhf 1:3.8.1551-2 [201 kB] Get:208 http://ftpmaster.internal/ubuntu focal/universe armhf ncbi-data all 6.1.20170106+dfsg1-7 [3518 kB] Get:209 http://ftpmaster.internal/ubuntu focal-proposed/universe armhf ncbi-blast+ armhf 2.9.0-2 [9438 kB] Get:210 http://ftpmaster.internal/ubuntu focal/universe armhf openmpi-common all 3.1.3-11build2 [147 kB] Get:211 http://ftpmaster.internal/ubuntu focal/universe armhf openmpi-bin armhf 3.1.3-11build2 [85.4 kB] Get:212 http://ftpmaster.internal/ubuntu focal/universe armhf phylip armhf 1:3.697+dfsg-1 [774 kB] Get:213 http://ftpmaster.internal/ubuntu focal/universe armhf phyml armhf 3:3.3.20190321-2 [1564 kB] Get:214 http://ftpmaster.internal/ubuntu focal/universe armhf prank armhf 0.0.170427+dfsg-2 [333 kB] Get:215 http://ftpmaster.internal/ubuntu focal/main armhf preview-latex-style all 11.91-2ubuntu1 [185 kB] Get:216 http://ftpmaster.internal/ubuntu focal/universe armhf probcons armhf 1.12-12 [97.4 kB] Get:217 http://ftpmaster.internal/ubuntu focal/universe armhf python-all armhf 2.7.17-1 [1088 B] Get:218 http://ftpmaster.internal/ubuntu 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python3-all armhf 3.7.5-1ubuntu1 [1120 B] Get:247 http://ftpmaster.internal/ubuntu focal/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1ubuntu3 [166 kB] Get:248 http://ftpmaster.internal/ubuntu focal-proposed/main armhf python3.7-dev armhf 3.7.5-2 [514 kB] Get:249 http://ftpmaster.internal/ubuntu focal-proposed/main armhf python3-dev armhf 3.7.5-1ubuntu1 [1316 B] Get:250 http://ftpmaster.internal/ubuntu focal/main armhf python3.8-dev armhf 3.8.0-3 [510 kB] Get:251 http://ftpmaster.internal/ubuntu focal-proposed/main armhf python3-all-dev armhf 3.7.5-1ubuntu1 [1128 B] Get:252 http://ftpmaster.internal/ubuntu focal/universe armhf python3-cycler all 0.10.0-1 [7622 B] Get:253 http://ftpmaster.internal/ubuntu focal/main armhf python3-dateutil all 2.7.3-3 [63.3 kB] Get:254 http://ftpmaster.internal/ubuntu focal/main armhf python3-decorator all 4.3.0-1.1 [9600 B] Get:255 http://ftpmaster.internal/ubuntu focal/universe armhf python3-isodate all 0.6.0-1 [23.9 kB] Get:256 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python3-reportlab-accel armhf 3.5.31-1 [21.1 kB] Get:266 http://ftpmaster.internal/ubuntu focal/main armhf python3-reportlab all 3.5.31-1 [531 kB] Get:267 http://ftpmaster.internal/ubuntu focal-proposed/main armhf python3-setuptools all 41.4.0-1 [255 kB] Get:268 http://ftpmaster.internal/ubuntu focal/universe armhf t-coffee armhf 12.00.7fb08c2-4 [1384 kB] Get:269 http://ftpmaster.internal/ubuntu focal-proposed/universe armhf texlive-fonts-recommended all 2019.20191030-1 [5200 kB] Get:270 http://ftpmaster.internal/ubuntu focal-proposed/main armhf texlive-latex-base all 2019.20191030-1 [964 kB] Get:271 http://ftpmaster.internal/ubuntu focal-proposed/main armhf texlive-latex-recommended all 2019.20191030-1 [15.7 MB] Get:272 http://ftpmaster.internal/ubuntu focal-proposed/universe armhf texlive-pictures all 2019.20191030-1 [10.9 MB] Get:273 http://ftpmaster.internal/ubuntu focal-proposed/universe armhf texlive-latex-extra all 2019.20191030-1 [12.3 MB] Get:274 http://ftpmaster.internal/ubuntu focal/universe armhf wise-data all 2.4.1-21 [107 kB] Get:275 http://ftpmaster.internal/ubuntu focal/universe armhf wise armhf 2.4.1-21 [788 kB] Get:276 http://ftpmaster.internal/ubuntu focal/universe armhf fasttree armhf 2.1.11-1 [162 kB] Get:277 http://ftpmaster.internal/ubuntu focal-proposed/universe armhf python-scipy armhf 1.2.2-4ubuntu2 [9885 kB] Get:278 http://ftpmaster.internal/ubuntu focal-proposed/universe armhf python3-scipy armhf 1.3.1-1exp3ubuntu1 [12.0 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 282 MB in 14s (20.3 MB/s) Selecting previously unselected package libpython3.7-minimal:armhf. (Reading database ... 14415 files and directories currently installed.) Preparing to unpack .../libpython3.7-minimal_3.7.5-2_armhf.deb ... Unpacking libpython3.7-minimal:armhf (3.7.5-2) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.2.9-1_armhf.deb ... Unpacking libexpat1:armhf (2.2.9-1) ... Selecting previously unselected package python3.7-minimal. Preparing to unpack .../python3.7-minimal_3.7.5-2_armhf.deb ... Unpacking python3.7-minimal (3.7.5-2) ... Setting up libpython3.7-minimal:armhf (3.7.5-2) ... Setting up libexpat1:armhf (2.2.9-1) ... Setting up python3.7-minimal (3.7.5-2) ... Selecting previously unselected package python3-minimal. (Reading database ... 14664 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.7.5-1ubuntu1_armhf.deb ... Unpacking python3-minimal (3.7.5-1ubuntu1) ... Selecting previously unselected package mime-support. 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Setting up libpixman-1-0:armhf (0.38.4-0ubuntu1) ... Setting up libpciaccess0:armhf (0.16-0ubuntu1) ... Setting up mysql-common (5.8+1.0.5ubuntu2) ... update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode Setting up libmysqlclient21:armhf (8.0.17-0ubuntu3) ... Setting up libxau6:armhf (1:1.0.9-0ubuntu1) ... Setting up libhpdf-2.3.0:armhf (2.3.0+dfsg-1) ... Setting up libkeyutils1:armhf (1.6-6ubuntu1) ... Setting up ttf-bitstream-vera (1.10-8) ... Setting up libpython3.8-minimal:armhf (3.8.0-3) ... Setting up mime-support (3.64ubuntu1) ... Setting up probcons (1.12-12) ... Setting up libmagic-mgc (1:5.37-6) ... Setting up libtexlua53:armhf (2019.20190605.51237-3) ... Setting up mafft (7.429-1) ... Setting up libarchive-zip-perl (1.67-1) ... Setting up libglib2.0-0:armhf (2.62.2-2) ... No schema files found: doing nothing. Setting up fonts-lyx (2.3.3-2) ... Setting up libijs-0.35:armhf (0.35-15) ... Setting up libtexluajit2:armhf (2019.20190605.51237-3) ... Setting up libdebhelper-perl (12.7.1ubuntu1) ... Setting up phylip (1:3.697+dfsg-1) ... Setting up x11-common (1:7.7+19ubuntu12) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libmagic1:armhf (1:5.37-6) ... Setting up gettext-base (0.19.8.1-9) ... Setting up libzzip-0-13:armhf (0.13.62-3.2) ... Setting up file (1:5.37-6) ... Setting up libnetpbm10 (2:10.0-15.3build1) ... Setting up muscle (1:3.8.1551-2) ... Setting up emboss-data (6.6.0+dfsg-7ubuntu2) ... Setting up libldap-common (2.4.48+dfsg-1ubuntu3) ... Setting up libjbig0:armhf (2.1-3.1build1) ... Setting up libicu63:armhf (63.2-2) ... Setting up t-coffee (12.00.7fb08c2-4) ... Setting up poppler-data (0.4.9-2) ... Setting up libkrb5support0:armhf (1.17-6) ... Setting up libsasl2-modules-db:armhf (2.1.27+dfsg-1build3) ... Setting up libpython2.7-stdlib:armhf (2.7.17-1) ... Setting up autotools-dev (20180224.1) ... Setting up libblas3:armhf (3.8.0-8) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up libexpat1-dev:armhf (2.2.9-1) ... Setting up libfreetype6:armhf (2.10.1-2) ... Setting up libx11-data (2:1.6.8-1) ... Setting up libjbig2dec0:armhf (0.17-1) ... Setting up libidn11:armhf (1.33-2.2ubuntu2) ... Setting up libteckit0:armhf (2.5.8+ds2-5ubuntu1) ... Setting up gsfonts (1:8.11+urwcyr1.0.7~pre44-4.4) ... Setting up libavahi-common-data:armhf (0.7-4ubuntu5) ... Setting up libdbus-1-3:armhf (1.12.14-1ubuntu2) ... Setting up libsigsegv2:armhf (2.12-2) ... Setting up t1utils (1.41-3) ... Setting up libimagequant0:armhf (2.12.2-1.1) ... Setting up libevent-core-2.1-7:armhf (2.1.11-stable-1~exp0) ... Setting up libevent-2.1-7:armhf (2.1.11-stable-1~exp0) ... Setting up autopoint (0.19.8.1-9) ... Setting up libwebp6:armhf (0.6.1-2) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up ucf (3.0038+nmu1) ... Setting up wise-data (2.4.1-21) ... Setting up libk5crypto3:armhf (1.17-6) ... Setting up libjpeg-turbo8:armhf (2.0.3-0ubuntu1) ... Setting up libltdl7:armhf (2.4.6-11) ... Setting up libkpathsea6:armhf (2019.20190605.51237-3) ... Setting up libsasl2-2:armhf (2.1.27+dfsg-1build3) ... Setting up libgfortran5:armhf (9.2.1-16ubuntu1) ... Setting up libroken18-heimdal:armhf (7.5.0+dfsg-3build1) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1ubuntu3) ... Setting up python3.8-minimal (3.8.0-3) ... Setting up python-matplotlib2-data (2.2.3-6) ... Setting up ocl-icd-libopencl1:armhf (2.2.11-1ubuntu1) ... Setting up libuchardet0:armhf (0.0.6-3) ... Setting up libnl-3-200:armhf (3.4.0-1) ... Setting up openmpi-common (3.1.3-11build2) ... Setting up clustalw (2.1+lgpl-6) ... Setting up fonts-lmodern (2.004.5-6) ... Setting up libmbedcrypto3:armhf (2.16.3-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libharfbuzz0b:armhf (2.6.2-1) ... Setting up fasttree (2.1.11-1) ... Setting up libkrb5-3:armhf (1.17-6) ... Setting up ocaml-base-nox (4.05.0-12ubuntu3) ... Setting up libmpdec2:armhf (2.4.2-2) ... Setting up libjs-jquery (3.3.1~dfsg-3) ... Setting up libboost-system1.67.0:armhf (1.67.0-13ubuntu2) ... Setting up libpython3.8-stdlib:armhf (3.8.0-3) ... Setting up python3.8 (3.8.0-3) ... Setting up python-matplotlib-data (3.0.2-2ubuntu1) ... Setting up libwebpmux3:armhf (0.6.1-2) ... Setting up libbsd0:armhf (0.10.0-1) ... Setting up libelf1:armhf (0.176-1.1) ... Setting up dialign (2.2.1-10) ... Setting up libxml2:armhf (2.9.4+dfsg1-7ubuntu5) ... Setting up xdg-utils (1.1.3-1ubuntu2) ... Setting up libsynctex2:armhf (2019.20190605.51237-3) ... Setting up prank (0.0.170427+dfsg-2) ... Setting up libheimbase1-heimdal:armhf (7.5.0+dfsg-3build1) ... Setting up libargtable2-0 (13-1) ... Setting up libevent-pthreads-2.1-7:armhf (2.1.11-stable-1~exp0) ... Setting up libjpeg8:armhf (8c-2ubuntu8) ... Setting up libfile-stripnondeterminism-perl (1.6.2-1) ... Setting up libpaper1:armhf (1.1.28) ... Creating config file /etc/papersize with new version Setting up libice6:armhf (2:1.0.10-0ubuntu1) ... Setting up libxdmcp6:armhf (1:1.1.3-0ubuntu1) ... Setting up libpython3.7-stdlib:armhf (3.7.5-2) ... Setting up libpython2.7:armhf (2.7.17-1) ... Setting up liblapack3:armhf (3.8.0-8) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up libpython2.7-dev:armhf (2.7.17-1) ... Setting up libxcb1:armhf (1.13.1-2) ... Setting up libharfbuzz-icu0:armhf (2.6.2-1) ... Setting up python2.7 (2.7.17-1) ... Setting up libboost-thread1.67.0:armhf (1.67.0-13ubuntu2) ... Setting up libpython3.7:armhf (3.7.5-2) ... Setting up libtool (2.4.6-11) ... 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Setting up tex-common (6.12) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libpython-stdlib:armhf (2.7.17-1) ... Setting up python-pyparsing (2.4.2-1) ... Setting up libwind0-heimdal:armhf (7.5.0+dfsg-3build1) ... Setting up libjs-jquery-ui (1.12.1+dfsg-5) ... Setting up libptexenc1:armhf (2019.20190605.51237-3) ... Setting up python-subprocess32 (3.5.4-1) ... Setting up libpython3.8:armhf (3.8.0-3) ... Setting up bsdmainutils (11.1.2ubuntu2) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:armhf (1.17-6) ... Setting up libcroco3:armhf (0.6.13-1) ... Setting up autoconf (2.69-11ubuntu1) ... Setting up dh-strip-nondeterminism (1.6.2-1) ... Setting up python-tz (2019.3-1) ... Setting up dwz (0.13-1) ... Setting up groff-base (1.22.4-3) ... Setting up libx11-6:armhf (2:1.6.8-1) ... Setting up python-reportlab-accel:armhf (3.5.31-1) ... Setting up libpython2-dev:armhf (2.7.17-1) ... Setting up libtiff5:armhf (4.0.10+git191003-1) ... Setting up libfontconfig1:armhf (2.13.1-2ubuntu2) ... Setting up libsm6:armhf (2:1.2.3-1) ... Setting up python (2.7.17-1) ... Setting up libavahi-client3:armhf (0.7-4ubuntu5) ... Setting up libpython3-stdlib:armhf (3.7.5-1ubuntu1) ... Setting up python-mysqldb (1.3.10-2ubuntu2) ... Setting up liblbfgsb0:armhf (3.0+dfsg.3-7) ... Setting up python2.7-dev (2.7.17-1) ... Setting up automake (1:1.16.1-4ubuntu3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up python3.7 (3.7.5-2) ... Setting up libibverbs1:armhf (26.0-2) ... Setting up flex (2.6.4-6.2) ... Setting up gettext (0.19.8.1-9) ... Setting up libpython3-dev:armhf (3.7.5-1ubuntu1) ... Setting up python2-dev (2.7.17-1) ... Setting up libxpm4:armhf (1:3.5.12-1) ... Setting up libxrender1:armhf (1:0.9.10-1) ... Setting up libpmix2:armhf (3.1.4-1build1) ... Setting up python-pkg-resources (41.4.0-1) ... Setting up openssh-client (1:8.1p1-1) ... Setting up libhx509-5-heimdal:armhf (7.5.0+dfsg-3build1) ... Setting up libopenmpi3:armhf (3.1.3-11build2) ... Setting up preview-latex-style (11.91-2ubuntu1) ... Setting up libxext6:armhf (2:1.3.4-0ubuntu1) ... Setting up python3 (3.7.5-1ubuntu1) ... Setting up python-pil:armhf (6.2.1-1) ... Setting up python-all (2.7.17-1) ... Setting up man-db (2.9.0-1) ... 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 python3.7-dev (3.7.5-2) ... Setting up libcairo2:armhf (1.16.0-4) ... Setting up python-decorator (4.3.0-1.1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libpython-dev:armhf (2.7.17-1) ... Setting up python-six (1.12.0-2build1) ... Setting up ncbi-blast+ (2.9.0-2) ... Setting up python3-mysqldb (1.3.10-2ubuntu2) ... Setting up python3-six (1.12.0-2build1) ... Setting up python3-isodate (0.6.0-1) ... Setting up python3-pil:armhf (6.2.1-1) ... Setting up python3-decorator (4.3.0-1.1) ... Setting up python-dateutil (2.7.3-3) ... Setting up python3-pyparsing (2.4.2-1) ... Setting up libpython3.8-dev:armhf (3.8.0-3) ... Setting up libpython3-all-dev:armhf (3.7.5-1ubuntu1) ... Setting up python3-cycler (0.10.0-1) ... Setting up python3-reportlab-accel:armhf (3.5.31-1) ... Setting up libgd3:armhf (2.2.5-5.2) ... Setting up python-isodate (0.6.0-1) ... Setting up python-setuptools (41.4.0-1) ... Setting up python-backports.functools-lru-cache (1.5-3) ... Setting up netpbm (2:10.0-15.3build1) ... Setting up libxt6:armhf (1:1.1.5-1) ... Setting up python3.8-dev (3.8.0-3) ... Setting up python-reportlab (3.5.31-1) ... Setting up python3-reportlab (3.5.31-1) ... Setting up libcups2:armhf (2.3.0-6) ... Setting up python-kiwisolver (1.0.1-2build3) ... Setting up python3-rdflib (4.2.2-2) ... /usr/lib/python3/dist-packages/rdflib/plugins/memory.py:354: SyntaxWarning: "is" with a literal. Did you mean "=="? if triple is None or triple is (None,None,None): Setting up python3-dateutil (2.7.3-3) ... Setting up python3-lib2to3 (3.8.0-1) ... Setting up openmpi-bin (3.1.3-11build2) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up phyml (3:3.3.20190321-2) ... Setting up python-rdflib (4.2.2-2) ... Setting up python-dev (2.7.17-1) ... Setting up libkrb5-26-heimdal:armhf (7.5.0+dfsg-3build1) ... Setting up python3-pkg-resources (41.4.0-1) ... Setting up python3-distutils (3.8.0-1) ... Setting up dh-python (4.20191017ubuntu1) ... Setting up libxmu6:armhf (2:1.1.3-0ubuntu1) ... Setting up python3-renderpm:armhf (3.5.31-1) ... Setting up python3-setuptools (41.4.0-1) ... Setting up libxi6:armhf (2:1.7.10-0ubuntu1) ... Setting up libpython-all-dev:armhf (2.7.17-1) ... Setting up python-numpy (1:1.16.5-1ubuntu2) ... Setting up po-debconf (1.0.21) ... Setting up python-cycler (0.10.0-1) ... Setting up python3-all (3.7.5-1ubuntu1) ... Setting up libxaw7:armhf (2:1.0.13-1) ... Setting up libheimntlm0-heimdal:armhf (7.5.0+dfsg-3build1) ... Setting up libcupsimage2:armhf (2.3.0-6) ... Setting up libgssapi3-heimdal:armhf (7.5.0+dfsg-3build1) ... Setting up python3-dev (3.7.5-1ubuntu1) ... Setting up python3-kiwisolver (1.0.1-2build3) ... Setting up python3-numpy (1:1.17.3-0ubuntu2) ... Setting up texlive-binaries (2019.20190605.51237-3) ... 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 python-all-dev (2.7.17-1) ... Setting up python-scipy (1.2.2-4ubuntu2) ... Setting up texlive-base (2019.20191030-1) ... 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/config/pdftexconfig.tex Setting up python3-all-dev (3.7.5-1ubuntu1) ... Setting up python3-matplotlib (3.0.2-2ubuntu1) ... /usr/lib/python3/dist-packages/matplotlib/backends/qt_editor/figureoptions.py:220: SyntaxWarning: "is not" with a literal. Did you mean "!="? if marker is not 'none': /usr/lib/python3/dist-packages/matplotlib/pyplot.py:2201: SyntaxWarning: "is" with a literal. Did you mean "=="? if fignum is False or fignum is 0: Setting up python3-scipy (1.3.1-1exp3ubuntu1) ... /usr/lib/python3/dist-packages/scipy/optimize/_shgo.py:495: SyntaxWarning: "is" with a literal. Did you mean "=="? if cons['type'] is 'ineq': /usr/lib/python3/dist-packages/scipy/optimize/_shgo.py:743: SyntaxWarning: "is not" with a literal. Did you mean "!="? if len(self.X_min) is not 0: Setting up libgs9:armhf (9.27~dfsg+0-0ubuntu3) ... Setting up python-matplotlib (2.2.3-6) ... Setting up libldap-2.4-2:armhf (2.4.48+dfsg-1ubuntu3) ... Setting up ghostscript (9.27~dfsg+0-0ubuntu3) ... Setting up texlive-latex-base (2019.20191030-1) ... Setting up texlive-latex-recommended (2019.20191030-1) ... Setting up hevea (2.32-2) ... Setting up texlive-pictures (2019.20191030-1) ... Setting up texlive-fonts-recommended (2019.20191030-1) ... Setting up libpq5:armhf (12.0-1) ... Setting up texlive-latex-extra (2019.20191030-1) ... Setting up python-psycopg2 (2.8.3-2ubuntu2) ... Setting up python3-psycopg2 (2.8.3-2ubuntu2) ... Setting up emboss-lib (6.6.0+dfsg-7ubuntu2) ... Setting up emboss (6.6.0+dfsg-7ubuntu2) ... Setting up dh-autoreconf (19) ... Setting up debhelper (12.7.1ubuntu1) ... Setting up sbuild-build-depends-python-biopython-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.30-0ubuntu2) ... Processing triggers for systemd (243-3ubuntu1) ... Processing triggers for tex-common (6.12) ... 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. +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-166-generic arm64 (armv7l) Toolchain package versions: binutils_2.33.1-1ubuntu1 dpkg-dev_1.19.7ubuntu2 g++-9_9.2.1-16ubuntu1 gcc-9_9.2.1-16ubuntu1 libc6-dev_2.30-0ubuntu2 libstdc++-9-dev_9.2.1-16ubuntu1 libstdc++6_9.2.1-16ubuntu1 linux-libc-dev_5.3.0-21.22 Package versions: adduser_3.118ubuntu1 advancecomp_2.1-2.1 apt_1.9.4 autoconf_2.69-11ubuntu1 automake_1:1.16.1-4ubuntu3 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_11ubuntu1 base-passwd_3.5.46 bash_5.0-4ubuntu1 binutils_2.33.1-1ubuntu1 binutils-arm-linux-gnueabihf_2.33.1-1ubuntu1 binutils-common_2.33.1-1ubuntu1 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.34-0.1ubuntu2 build-essential_12.8ubuntu1 bzip2_1.0.8-2 ca-certificates_20190110 clustalo_1.2.4-2 clustalw_2.1+lgpl-6 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sbuild-build-depends-python-biopython-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 systemd_243-3ubuntu1 systemd-sysv_243-3ubuntu1 sysvinit-utils_2.96-1ubuntu1 t-coffee_12.00.7fb08c2-4 t1utils_1.41-3 tar_1.30+dfsg-6 tex-common_6.12 texlive-base_2019.20191030-1 texlive-binaries_2019.20190605.51237-3 texlive-fonts-recommended_2019.20191030-1 texlive-latex-base_2019.20191030-1 texlive-latex-extra_2019.20191030-1 texlive-latex-recommended_2019.20191030-1 texlive-pictures_2019.20191030-1 ttf-bitstream-vera_1.10-8 tzdata_2019c-3 ubuntu-keyring_2018.09.18.1 ucf_3.0038+nmu1 util-linux_2.34-0.1ubuntu2 wise_2.4.1-21 wise-data_2.4.1-21 x11-common_1:7.7+19ubuntu12 xdg-utils_1.1.3-1ubuntu2 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1ubuntu3 zlib1g-dev_1:1.2.11.dfsg-1ubuntu3 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Fri Oct 18 18:51:31 2019 UTC gpgv: using RSA key D56571B88A8BBAF140BF63D6BD7EAA60778FA6F5 gpgv: issuer "doko@ubuntu.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./python-biopython_1.73+dfsg-1ubuntu2.dsc dpkg-source: info: extracting python-biopython in python-biopython-1.73+dfsg dpkg-source: info: unpacking python-biopython_1.73+dfsg.orig.tar.xz dpkg-source: info: unpacking python-biopython_1.73+dfsg-1ubuntu2.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 reportlab3.5.patch dpkg-source: info: applying test_phenotype_fit-ppc64el.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 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-17940165 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-17940165 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-17940165 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package python-biopython dpkg-buildpackage: info: source version 1.73+dfsg-1ubuntu2 dpkg-buildpackage: info: source distribution focal dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean --with python2,python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/python-biopython-1.73+dfsg' dh_auto_clean pybuild --clean -i python{version} -p 2.7 I: pybuild base:217: python2.7 setup.py clean running clean removing '/<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build' (and everything under it) 'build/bdist.linux-armhf' does not exist -- can't clean it 'build/scripts-2.7' does not exist -- can't clean it pybuild --clean -i python{version} -p "3.8 3.7" I: pybuild base:217: python3.8 setup.py clean running clean removing '/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build' (and everything under it) 'build/bdist.linux-armhf' does not exist -- can't clean it 'build/scripts-3.8' does not exist -- can't clean it I: pybuild base:217: python3.7 setup.py clean running clean removing '/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build' (and everything under it) 'build/bdist.linux-armhf' does not exist -- can't clean it 'build/scripts-3.7' does not exist -- can't clean it rm -rf .pybuild/ find . -name \*.pyc -exec rm {} \; cd Doc && make distclean make[2]: Entering directory '/<>/python-biopython-1.73+dfsg/Doc' make -C install make[3]: Entering directory '/<>/python-biopython-1.73+dfsg/Doc/install' pdflatex Installation.tex This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Installation.tex LaTeX2e <2019-10-01> patch level 1 (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2019/08/27 v1.4j 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 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No file Installation.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/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.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/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) LaTeX Warning: Reference `sec:windows_install' on page 1 undefined on input lin e 108. [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [3] [4] [5] [6] LaTeX Warning: Reference `sec:is_working' on page 7 undefined on input line 460 . [7] LaTeX Warning: Reference `sec:unix_install' on page 8 undefined on input line 5 37. Overfull \hbox (9.0224pt too wide) in paragraph at lines 540--541 []\OT1/cmr/m/n/10 For Python 2.6 we cur-rently use Mi-crosoft's free VC++ 2008 Ex-press Edi-tion from [][]$\OT1/cmtt/m/n/10 http : / / www . microsoft . LaTeX Warning: Reference `sec:is_working' on page 8 undefined on input line 558 . Overfull \hbox (27.57379pt too wide) in paragraph at lines 563--565 [][]\OT1/cmtt/m/n/10 PYTHONPATH []\OT1/cmr/m/n/10 with some-thing like [][]\OT1 /cmtt/m/n/10 export PYTHONPATH = $PYTHONPATH':/directory/where/you/put/Biopytho n' [8] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) Overfull \hbox (9.6602pt too wide) in paragraph at lines 600--601 []\OT1/cmr/m/n/10 NCBI Stan-dalone BLAST, which can used with the [][]\OT1/cmtt /m/n/10 Bio.Blast []\OT1/cmr/m/n/10 mod-ule and parsed with the [][]\OT1/cmtt/m /n/10 Bio.SearchIO [9] [10] (./Installation.aux) Package rerunfilecheck Warning: File `Installation.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on Installation.pdf (10 pages, 144622 bytes). Transcript written on Installation.log. pdflatex Installation.tex This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Installation.tex LaTeX2e <2019-10-01> patch level 1 (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2019/08/27 v1.4j 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/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 52. (./Installation.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/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.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/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./Installation.out) (./Installation.out) (./Installation.toc) [1{/var/lib/texm f/fonts/map/pdftex/updmap/pdftex.map}] [2] [3] [4] [5] [6] [7] Overfull \hbox (9.0224pt too wide) in paragraph at lines 540--541 []\OT1/cmr/m/n/10 For Python 2.6 we cur-rently use Mi-crosoft's free VC++ 2008 Ex-press Edi-tion from [][]$\OT1/cmtt/m/n/10 http : / / www . microsoft . [8] Overfull \hbox (27.57379pt too wide) in paragraph at lines 563--565 [][]\OT1/cmtt/m/n/10 PYTHONPATH []\OT1/cmr/m/n/10 with some-thing like [][]\OT1 /cmtt/m/n/10 export PYTHONPATH = $PYTHONPATH':/directory/where/you/put/Biopytho n' (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) Overfull \hbox (9.6602pt too wide) in paragraph at lines 600--601 []\OT1/cmr/m/n/10 NCBI Stan-dalone BLAST, which can used with the [][]\OT1/cmtt /m/n/10 Bio.Blast []\OT1/cmr/m/n/10 mod-ule and parsed with the [][]\OT1/cmtt/m /n/10 Bio.SearchIO [9] [10] (./Installation.aux) LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on Installation.pdf (10 pages, 150357 bytes). Transcript written on Installation.log. pdflatex Installation.tex This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Installation.tex LaTeX2e <2019-10-01> patch level 1 (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2019/08/27 v1.4j 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/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 52. (./Installation.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/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.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/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./Installation.out) (./Installation.out) (./Installation.toc) [1{/var/lib/texm f/fonts/map/pdftex/updmap/pdftex.map}] [2] [3] [4] [5] [6] [7] Overfull \hbox (9.0224pt too wide) in paragraph at lines 540--541 []\OT1/cmr/m/n/10 For Python 2.6 we cur-rently use Mi-crosoft's free VC++ 2008 Ex-press Edi-tion from [][]$\OT1/cmtt/m/n/10 http : / / www . microsoft . [8] Overfull \hbox (27.57379pt too wide) in paragraph at lines 563--565 [][]\OT1/cmtt/m/n/10 PYTHONPATH []\OT1/cmr/m/n/10 with some-thing like [][]\OT1 /cmtt/m/n/10 export PYTHONPATH = $PYTHONPATH':/directory/where/you/put/Biopytho n' (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) Overfull \hbox (9.6602pt too wide) in paragraph at lines 600--601 []\OT1/cmr/m/n/10 NCBI Stan-dalone BLAST, which can used with the [][]\OT1/cmtt /m/n/10 Bio.Blast []\OT1/cmr/m/n/10 mod-ule and parsed with the [][]\OT1/cmtt/m /n/10 Bio.SearchIO [9] [10] (./Installation.aux) ) (see the transcript file for additional information) Output written on Installation.pdf (10 pages, 150502 bytes). Transcript written on Installation.log. hevea -fix Installation.tex Exclude comment 'comment' ./Installation.tex:67: Warning: Suppressing nested a element ./Installation.tex:67: Warning: Suppressing nested a element ./Installation.tex:108: Warning: Undefined label: 'sec:windows_install' ./Installation.tex:114: Warning: Suppressing nested a element ./Installation.tex:114: Warning: Suppressing nested a element ./Installation.tex:140: Warning: Suppressing nested a element ./Installation.tex:140: Warning: Suppressing nested a element ./Installation.tex:218: Warning: Suppressing nested a element ./Installation.tex:218: Warning: Suppressing nested a element ./Installation.tex:230: Warning: Suppressing nested a element ./Installation.tex:230: Warning: Suppressing nested a element ./Installation.tex:255: Warning: Suppressing nested a element ./Installation.tex:255: Warning: Suppressing nested a element ./Installation.tex:314: Warning: Suppressing nested a element ./Installation.tex:314: Warning: Suppressing nested a element ./Installation.tex:317: Warning: Suppressing nested a element ./Installation.tex:317: Warning: Suppressing nested a element ./Installation.tex:387: Warning: Suppressing nested a element ./Installation.tex:387: Warning: Suppressing nested a element ./Installation.tex:400: Warning: Suppressing nested a element ./Installation.tex:400: Warning: Suppressing nested a element ./Installation.tex:406: Warning: Suppressing nested a element ./Installation.tex:406: Warning: Suppressing nested a element ./Installation.tex:413: Warning: Suppressing nested a element ./Installation.tex:413: Warning: Suppressing nested a element ./Installation.tex:419: Warning: Suppressing nested a element ./Installation.tex:419: Warning: Suppressing nested a element ./Installation.tex:421: Warning: Suppressing nested a element ./Installation.tex:421: Warning: Suppressing nested a element ./Installation.tex:430: Warning: '_' occurring outside math mode ./Installation.tex:456: Warning: Suppressing nested a element ./Installation.tex:456: Warning: Suppressing nested a element ./Installation.tex:460: Warning: Undefined label: 'sec:is_working' ./Installation.tex:467: Warning: Suppressing nested a element ./Installation.tex:467: Warning: Suppressing nested a element ./Installation.tex:497: Warning: Suppressing nested a element ./Installation.tex:497: Warning: Suppressing nested a element ./Installation.tex:516: Warning: Suppressing nested a element ./Installation.tex:516: Warning: Suppressing nested a element ./Installation.tex:535: Warning: '_' occurring outside math mode ./Installation.tex:537: Warning: Undefined label: 'sec:unix_install' ./Installation.tex:540: Warning: Suppressing nested a element ./Installation.tex:540: Warning: Suppressing nested a element ./Installation.tex:548: Warning: Suppressing nested a element ./Installation.tex:548: Warning: Suppressing nested a element ./Installation.tex:556: Warning: Suppressing nested a element ./Installation.tex:556: Warning: Suppressing nested a element ./Installation.tex:558: Warning: Undefined label: 'sec:is_working' ./Installation.tex:561: Warning: '_' occurring outside math mode ./Installation.tex:609: Warning: Suppressing nested a element ./Installation.tex:609: Warning: Suppressing nested a element HeVeA Warning: Label(s) may have changed. Rerun me to get cross-references right. Run, run, again... Exclude comment 'comment' ./Installation.tex:67: Warning: Suppressing nested a element ./Installation.tex:67: Warning: Suppressing nested a element ./Installation.tex:114: Warning: Suppressing nested a element ./Installation.tex:114: Warning: Suppressing nested a element ./Installation.tex:140: Warning: Suppressing nested a element ./Installation.tex:140: Warning: Suppressing nested a element ./Installation.tex:218: Warning: Suppressing nested a element ./Installation.tex:218: Warning: Suppressing nested a element ./Installation.tex:230: Warning: Suppressing nested a element ./Installation.tex:230: Warning: Suppressing nested a element ./Installation.tex:255: Warning: Suppressing nested a element ./Installation.tex:255: Warning: Suppressing nested a element ./Installation.tex:314: Warning: Suppressing nested a element ./Installation.tex:314: Warning: Suppressing nested a element ./Installation.tex:317: Warning: Suppressing nested a element ./Installation.tex:317: Warning: Suppressing nested a element ./Installation.tex:387: Warning: Suppressing nested a element ./Installation.tex:387: Warning: Suppressing nested a element ./Installation.tex:400: Warning: Suppressing nested a element ./Installation.tex:400: Warning: Suppressing nested a element ./Installation.tex:406: Warning: Suppressing nested a element ./Installation.tex:406: Warning: Suppressing nested a element ./Installation.tex:413: Warning: Suppressing nested a element ./Installation.tex:413: Warning: Suppressing nested a element ./Installation.tex:419: Warning: Suppressing nested a element ./Installation.tex:419: Warning: Suppressing nested a element ./Installation.tex:421: Warning: Suppressing nested a element ./Installation.tex:421: Warning: Suppressing nested a element ./Installation.tex:430: Warning: '_' occurring outside math mode ./Installation.tex:456: Warning: Suppressing nested a element ./Installation.tex:456: Warning: Suppressing nested a element ./Installation.tex:467: Warning: Suppressing nested a element ./Installation.tex:467: Warning: Suppressing nested a element ./Installation.tex:497: Warning: Suppressing nested a element ./Installation.tex:497: Warning: Suppressing nested a element ./Installation.tex:516: Warning: Suppressing nested a element ./Installation.tex:516: Warning: Suppressing nested a element ./Installation.tex:535: Warning: '_' occurring outside math mode ./Installation.tex:540: Warning: Suppressing nested a element ./Installation.tex:540: Warning: Suppressing nested a element ./Installation.tex:548: Warning: Suppressing nested a element ./Installation.tex:548: Warning: Suppressing nested a element ./Installation.tex:556: Warning: Suppressing nested a element ./Installation.tex:556: Warning: Suppressing nested a element ./Installation.tex:561: Warning: '_' occurring outside math mode ./Installation.tex:609: Warning: Suppressing nested a element ./Installation.tex:609: Warning: Suppressing nested a element Fixpoint reached in 2 step(s) hevea -fix -text Installation.tex Exclude comment 'comment' ./Installation.tex:55: Warning: tt_mode is an empty style ./Installation.tex:61: Warning: No date given ./Installation.tex:430: Warning: '_' occurring outside math mode ./Installation.tex:535: Warning: '_' occurring outside math mode ./Installation.tex:561: Warning: '_' occurring outside math mode HeVeA Warning: Label(s) may have changed. Rerun me to get cross-references right. Run, run, again... Exclude comment 'comment' ./Installation.tex:55: Warning: tt_mode is an empty style ./Installation.tex:61: Warning: No date given ./Installation.tex:430: Warning: '_' occurring outside math mode ./Installation.tex:535: Warning: '_' occurring outside math mode ./Installation.tex:561: Warning: '_' occurring outside math mode Fixpoint reached in 2 step(s) make[3]: Leaving directory '/<>/python-biopython-1.73+dfsg/Doc/install' ( for f in install ; do make clean -C $f ; done ) make[3]: Entering directory '/<>/python-biopython-1.73+dfsg/Doc/install' rm -f Installation.aux rm -f Installation.log rm -f Installation.out rm -f Installation.toc rm -f Installation.haux rm -f Installation.htoc make[3]: Leaving directory '/<>/python-biopython-1.73+dfsg/Doc/install' 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 install ; do make distclean -C $f ; done ) make[3]: Entering directory '/<>/python-biopython-1.73+dfsg/Doc/install' rm -f Installation.aux rm -f Installation.log rm -f Installation.out rm -f Installation.toc rm -f Installation.haux rm -f Installation.htoc rm -f Installation.pdf rm -f Installation.txt rm -f Installation.html make[3]: Leaving directory '/<>/python-biopython-1.73+dfsg/Doc/install' 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 '/<>/python-biopython-1.73+dfsg/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 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 '/<>/python-biopython-1.73+dfsg' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/python-biopython.substvars debian/python3-biopython.substvars debian/python-biopython-doc.substvars debian/python-biopython-sql.substvars debian/python3-biopython-sql.substvars debian/files rm -fr -- debian/python-biopython/ debian/tmp/ debian/python3-biopython/ debian/python-biopython-doc/ debian/python-biopython-sql/ 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 build-arch dh build-arch --with python2,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 2.7 I: pybuild base:217: python2.7 setup.py config running config pybuild --configure -i python{version} -p "3.8 3.7" I: pybuild base:217: python3.8 setup.py config running config I: pybuild base:217: python3.7 setup.py config running config debian/rules override_dh_auto_build make[1]: Entering directory '/<>/python-biopython-1.73+dfsg' dh_auto_build pybuild --build -i python{version} -p 2.7 I: pybuild base:217: /usr/bin/python2 setup.py build running build running build_py creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio copying Bio/File.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio copying Bio/triefind.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio copying Bio/MarkovModel.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio copying Bio/kNN.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio copying Bio/pairwise2.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio copying Bio/SeqRecord.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio copying Bio/MaxEntropy.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio copying Bio/Index.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio copying Bio/NaiveBayes.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio copying Bio/Seq.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio copying Bio/_utils.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio copying Bio/SeqFeature.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio copying Bio/LogisticRegression.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio copying Bio/bgzf.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio copying Bio/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Align copying Bio/Align/AlignInfo.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Align copying Bio/Align/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Align creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Align/Applications copying Bio/Align/Applications/_ClustalOmega.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Align/Applications copying Bio/Align/Applications/_Mafft.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Align/Applications copying Bio/Align/Applications/_Muscle.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Align/Applications copying Bio/Align/Applications/_Clustalw.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Align/Applications copying Bio/Align/Applications/_TCoffee.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Align/Applications copying Bio/Align/Applications/_Dialign.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Align/Applications copying Bio/Align/Applications/_Prank.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Align/Applications copying Bio/Align/Applications/_MSAProbs.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Align/Applications copying Bio/Align/Applications/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Align/Applications copying Bio/Align/Applications/_Probcons.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Align/Applications creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/AlignIO copying Bio/AlignIO/NexusIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/AlignIO copying Bio/AlignIO/MauveIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/AlignIO copying Bio/AlignIO/MafIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/AlignIO copying Bio/AlignIO/StockholmIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/AlignIO copying Bio/AlignIO/ClustalIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/AlignIO copying Bio/AlignIO/FastaIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/AlignIO copying Bio/AlignIO/EmbossIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/AlignIO copying Bio/AlignIO/Interfaces.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/AlignIO copying Bio/AlignIO/PhylipIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/AlignIO copying Bio/AlignIO/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/AlignIO creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Alphabet copying Bio/Alphabet/Reduced.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Alphabet copying Bio/Alphabet/IUPAC.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Alphabet copying Bio/Alphabet/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Alphabet creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Application copying Bio/Application/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Application creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Blast copying Bio/Blast/Applications.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Blast copying Bio/Blast/Record.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Blast copying Bio/Blast/NCBIXML.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Blast copying Bio/Blast/ParseBlastTable.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Blast copying Bio/Blast/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Blast copying Bio/Blast/NCBIWWW.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Blast creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/CAPS copying Bio/CAPS/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/CAPS creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/codonalign copying Bio/codonalign/codonseq.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/codonalign copying Bio/codonalign/chisq.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/codonalign copying Bio/codonalign/codonalphabet.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/codonalign copying Bio/codonalign/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/codonalign copying Bio/codonalign/codonalignment.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/codonalign creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Compass copying Bio/Compass/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Compass creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Crystal copying Bio/Crystal/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Crystal creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Data copying Bio/Data/SCOPData.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Data copying Bio/Data/CodonTable.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Data copying Bio/Data/IUPACData.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Data copying Bio/Data/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Data creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Emboss copying Bio/Emboss/Applications.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Emboss copying Bio/Emboss/PrimerSearch.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Emboss copying Bio/Emboss/Primer3.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Emboss copying Bio/Emboss/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Emboss creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez copying Bio/Entrez/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez copying Bio/Entrez/Parser.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/ExPASy copying Bio/ExPASy/ScanProsite.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/ExPASy copying Bio/ExPASy/cellosaurus.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/ExPASy copying Bio/ExPASy/Enzyme.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/ExPASy copying Bio/ExPASy/Prodoc.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/ExPASy copying Bio/ExPASy/Prosite.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/ExPASy copying Bio/ExPASy/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/ExPASy creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/FSSP copying Bio/FSSP/FSSPTools.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/FSSP copying Bio/FSSP/fssp_rec.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/FSSP copying Bio/FSSP/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/FSSP creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/GenBank copying Bio/GenBank/Scanner.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/GenBank copying Bio/GenBank/Record.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/GenBank copying Bio/GenBank/utils.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/GenBank copying Bio/GenBank/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/GenBank creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Geo copying Bio/Geo/Record.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Geo copying Bio/Geo/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Geo creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Graphics copying Bio/Graphics/ColorSpiral.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Graphics copying Bio/Graphics/Distribution.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Graphics copying Bio/Graphics/KGML_vis.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Graphics copying Bio/Graphics/BasicChromosome.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Graphics copying Bio/Graphics/DisplayRepresentation.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Graphics copying Bio/Graphics/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Graphics copying Bio/Graphics/Comparative.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Graphics creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Graph.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Colors.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Diagram.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Track.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_GraphSet.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CrossLink.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Feature.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Graphics/GenomeDiagram creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/HMM copying Bio/HMM/Trainer.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/HMM copying Bio/HMM/MarkovModel.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/HMM copying Bio/HMM/DynamicProgramming.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/HMM copying Bio/HMM/Utilities.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/HMM copying Bio/HMM/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/HMM creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/KEGG copying Bio/KEGG/REST.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/KEGG copying Bio/KEGG/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/KEGG creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/KEGG/Compound copying Bio/KEGG/Compound/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/KEGG/Compound creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/KEGG/Enzyme copying Bio/KEGG/Enzyme/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/KEGG/Enzyme creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/KEGG/Gene copying Bio/KEGG/Gene/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/KEGG/Gene creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/KEGG/Map copying Bio/KEGG/Map/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/KEGG/Map creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB/mmtf copying Bio/PDB/mmtf/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB/mmtf copying Bio/PDB/mmtf/DefaultParser.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB/mmtf creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_pathway.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/KEGG/KGML copying Bio/KEGG/KGML/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_parser.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/KEGG/KGML creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Medline copying Bio/Medline/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Medline creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/motifs copying Bio/motifs/thresholds.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/motifs copying Bio/motifs/alignace.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/motifs copying Bio/motifs/meme.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/motifs copying Bio/motifs/transfac.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/motifs copying Bio/motifs/minimal.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/motifs copying Bio/motifs/matrix.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/motifs copying Bio/motifs/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/motifs copying Bio/motifs/mast.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/motifs creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/motifs/applications copying Bio/motifs/applications/_xxmotif.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/motifs/applications copying Bio/motifs/applications/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/motifs/applications creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/motifs/jaspar copying Bio/motifs/jaspar/db.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/motifs/jaspar copying Bio/motifs/jaspar/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/motifs/jaspar creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Nexus copying Bio/Nexus/Trees.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Nexus copying Bio/Nexus/StandardData.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Nexus copying Bio/Nexus/Nodes.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Nexus copying Bio/Nexus/Nexus.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Nexus copying Bio/Nexus/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Nexus creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/NMR copying Bio/NMR/xpktools.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/NMR copying Bio/NMR/NOEtools.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/NMR copying Bio/NMR/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/NMR creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Pathway copying Bio/Pathway/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Pathway creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Pathway/Rep copying Bio/Pathway/Rep/MultiGraph.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Pathway/Rep copying Bio/Pathway/Rep/Graph.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Pathway/Rep copying Bio/Pathway/Rep/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Pathway/Rep copying Bio/PDB/FragmentMapper.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB copying Bio/PDB/Vector.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB copying Bio/PDB/parse_pdb_header.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB copying Bio/PDB/StructureAlignment.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB copying Bio/PDB/Entity.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB copying Bio/PDB/PDBParser.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB copying Bio/PDB/AbstractPropertyMap.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB copying Bio/PDB/StructureBuilder.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB copying Bio/PDB/DSSP.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB copying Bio/PDB/PDBExceptions.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB copying Bio/PDB/Atom.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB copying Bio/PDB/Superimposer.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB copying Bio/PDB/Structure.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB copying Bio/PDB/PDBList.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB copying Bio/PDB/Residue.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB copying Bio/PDB/PDBIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB copying Bio/PDB/MMCIFParser.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB copying Bio/PDB/PSEA.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB copying Bio/PDB/vectors.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB copying Bio/PDB/Model.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB copying Bio/PDB/NACCESS.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB copying Bio/PDB/Selection.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB copying Bio/PDB/ResidueDepth.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB copying Bio/PDB/MMCIF2Dict.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB copying Bio/PDB/Polypeptide.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB copying Bio/PDB/mmcifio.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB copying Bio/PDB/Chain.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB copying Bio/PDB/Dice.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB copying Bio/PDB/HSExposure.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB copying Bio/PDB/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB copying Bio/PDB/NeighborSearch.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PopGen copying Bio/PopGen/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PopGen creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/Controller.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/LargeFileParser.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/EasyController.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/Utils.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/FileParser.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PopGen/GenePop creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Restriction copying Bio/Restriction/PrintFormat.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Restriction copying Bio/Restriction/RanaConfig.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Restriction copying Bio/Restriction/Restriction_Dictionary.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Restriction copying Bio/Restriction/Restriction.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Restriction copying Bio/Restriction/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Restriction creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SCOP copying Bio/SCOP/Hie.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SCOP copying Bio/SCOP/Raf.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SCOP copying Bio/SCOP/Residues.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SCOP copying Bio/SCOP/Des.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SCOP copying Bio/SCOP/Cla.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SCOP copying Bio/SCOP/Dom.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SCOP copying Bio/SCOP/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SCOP creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO copying Bio/SearchIO/BlatIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO copying Bio/SearchIO/_index.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO copying Bio/SearchIO/FastaIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO copying Bio/SearchIO/_utils.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO copying Bio/SearchIO/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO/_legacy copying Bio/SearchIO/_legacy/ParserSupport.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO/_legacy copying Bio/SearchIO/_legacy/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO/_legacy copying Bio/SearchIO/_legacy/NCBIStandalone.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO/_legacy creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/hit.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/_base.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/hsp.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/query.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO/_model creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_text.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_tab.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_xml.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO/BlastIO creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/_base.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_tab.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_text.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO/HmmerIO creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/_base.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_text.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO/ExonerateIO creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/interproscan_xml.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SearchIO/InterproscanIO creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SeqIO copying Bio/SeqIO/UniprotIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SeqIO copying Bio/SeqIO/AceIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SeqIO copying Bio/SeqIO/PdbIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SeqIO copying Bio/SeqIO/IgIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SeqIO copying Bio/SeqIO/_convert.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SeqIO copying Bio/SeqIO/QualityIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SeqIO copying Bio/SeqIO/_index.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SeqIO copying Bio/SeqIO/PhdIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SeqIO copying Bio/SeqIO/FastaIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SeqIO copying Bio/SeqIO/InsdcIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SeqIO copying Bio/SeqIO/Interfaces.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SeqIO copying Bio/SeqIO/PirIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SeqIO copying Bio/SeqIO/TabIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SeqIO copying Bio/SeqIO/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SeqIO copying Bio/SeqIO/SwissIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SeqIO copying Bio/SeqIO/SeqXmlIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SeqIO copying Bio/SeqIO/AbiIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SeqIO copying Bio/SeqIO/SffIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SeqIO creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SeqUtils copying Bio/SeqUtils/CheckSum.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SeqUtils copying Bio/SeqUtils/MeltingTemp.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SeqUtils copying Bio/SeqUtils/ProtParam.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SeqUtils copying Bio/SeqUtils/CodonUsage.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SeqUtils copying Bio/SeqUtils/CodonUsageIndices.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SeqUtils copying Bio/SeqUtils/lcc.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SeqUtils copying Bio/SeqUtils/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SeqUtils copying Bio/SeqUtils/IsoelectricPoint.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SeqUtils copying Bio/SeqUtils/ProtParamData.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SeqUtils creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Sequencing copying Bio/Sequencing/Ace.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Sequencing copying Bio/Sequencing/Phd.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Sequencing copying Bio/Sequencing/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Sequencing creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_bwa.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_samtools.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_Novoalign.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Sequencing/Applications creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Statistics copying Bio/Statistics/lowess.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Statistics copying Bio/Statistics/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Statistics creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SubsMat copying Bio/SubsMat/MatrixInfo.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SubsMat copying Bio/SubsMat/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SubsMat copying Bio/SubsMat/FreqTable.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SubsMat creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SVDSuperimposer copying Bio/SVDSuperimposer/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SVDSuperimposer creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB/QCPSuperimposer copying Bio/PDB/QCPSuperimposer/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB/QCPSuperimposer creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SwissProt copying Bio/SwissProt/KeyWList.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SwissProt copying Bio/SwissProt/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/SwissProt creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/TogoWS copying Bio/TogoWS/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/TogoWS creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Phylo copying Bio/Phylo/NewickIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Phylo copying Bio/Phylo/PhyloXMLIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Phylo copying Bio/Phylo/NexusIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Phylo copying Bio/Phylo/_cdao_owl.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Phylo copying Bio/Phylo/BaseTree.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Phylo copying Bio/Phylo/PhyloXML.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Phylo copying Bio/Phylo/CDAO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Phylo copying Bio/Phylo/Consensus.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Phylo copying Bio/Phylo/_utils.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Phylo copying Bio/Phylo/Newick.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Phylo copying Bio/Phylo/_io.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Phylo copying Bio/Phylo/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Phylo copying Bio/Phylo/CDAOIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Phylo copying Bio/Phylo/TreeConstruction.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Phylo copying Bio/Phylo/NeXML.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Phylo copying Bio/Phylo/NeXMLIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Phylo creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Fasttree.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Raxml.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Phyml.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Phylo/Applications creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/chi2.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_yn00.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/yn00.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_codeml.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/codeml.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_paml.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_baseml.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/baseml.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Phylo/PAML creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/UniGene copying Bio/UniGene/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/UniGene creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/UniProt copying Bio/UniProt/GOA.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/UniProt copying Bio/UniProt/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/UniProt creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Wise copying Bio/Wise/dnal.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Wise copying Bio/Wise/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Wise copying Bio/Wise/psw.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Wise creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/_py3k copying Bio/_py3k/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/_py3k creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/BioSQL copying BioSQL/Loader.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/BioSQL copying BioSQL/BioSeq.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/BioSQL copying BioSQL/DBUtils.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/BioSQL copying BioSQL/BioSeqDatabase.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/BioSQL copying BioSQL/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/BioSQL creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Affy copying Bio/Affy/CelFile.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Affy copying Bio/Affy/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Affy creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Cluster copying Bio/Cluster/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Cluster creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/KDTree copying Bio/KDTree/KDTree.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/KDTree copying Bio/KDTree/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/KDTree creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/phenotype copying Bio/phenotype/phen_micro.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/phenotype copying Bio/phenotype/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/phenotype copying Bio/phenotype/pm_fitting.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/phenotype running egg_info creating biopython.egg-info writing requirements to biopython.egg-info/requires.txt writing biopython.egg-info/PKG-INFO writing top-level names to biopython.egg-info/top_level.txt writing dependency_links to biopython.egg-info/dependency_links.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 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 writing manifest file 'biopython.egg-info/SOURCES.txt' copying Bio/cpairwise2module.c -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio copying Bio/trie.c -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio copying Bio/trie.h -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio copying Bio/triemodule.c -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio copying Bio/Align/_aligners.c -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Align creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Gene.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_General.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_General.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medlars.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medline.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mim.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mime.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Organism.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Project.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Protein.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Pub.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PubMed.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_RNA.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Remap.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Rsite.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> 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Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_080101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_100101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/notat.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/para.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/phrase.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pmc-1.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_020114.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_080101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_090101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100301.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_110101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_120101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130501.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_140101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_150101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180601.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_190101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/references.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/section.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/taxon.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xmlspecchars.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/DTDs creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/XSDs copying Bio/Entrez/XSDs/IPGReportSet.xsd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Entrez/XSDs copying Bio/motifs/_pwm.c -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/motifs copying Bio/Nexus/cnexus.c -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Nexus copying Bio/PDB/kdtrees.c -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB copying Bio/PDB/QCPSuperimposer/qcprotmodule.c -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB/QCPSuperimposer copying Bio/Cluster/cluster.c -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Cluster copying Bio/Cluster/cluster.h -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Cluster copying Bio/Cluster/clustermodule.c -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Cluster copying Bio/KDTree/KDTree.c -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/KDTree copying Bio/KDTree/KDTree.h -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/KDTree copying Bio/KDTree/KDTreemodule.c -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/KDTree copying Bio/KDTree/Neighbor.h -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/KDTree running build_ext building 'Bio.Align._aligners' extension creating build creating build/temp.linux-armhf-2.7 creating build/temp.linux-armhf-2.7/Bio creating build/temp.linux-armhf-2.7/Bio/Align arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -c Bio/Align/_aligners.c -o build/temp.linux-armhf-2.7/Bio/Align/_aligners.o arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-i9QlNx/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-armhf-2.7/Bio/Align/_aligners.o -o /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Align/_aligners.so building 'Bio.cpairwise2' extension arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -c Bio/cpairwise2module.c -o build/temp.linux-armhf-2.7/Bio/cpairwise2module.o arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-i9QlNx/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-armhf-2.7/Bio/cpairwise2module.o -o /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/cpairwise2.so building 'Bio.Nexus.cnexus' extension creating build/temp.linux-armhf-2.7/Bio/Nexus arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -c Bio/Nexus/cnexus.c -o build/temp.linux-armhf-2.7/Bio/Nexus/cnexus.o arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-i9QlNx/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-armhf-2.7/Bio/Nexus/cnexus.o -o /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Nexus/cnexus.so building 'Bio.PDB.QCPSuperimposer.qcprotmodule' extension creating build/temp.linux-armhf-2.7/Bio/PDB creating build/temp.linux-armhf-2.7/Bio/PDB/QCPSuperimposer arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -c Bio/PDB/QCPSuperimposer/qcprotmodule.c -o build/temp.linux-armhf-2.7/Bio/PDB/QCPSuperimposer/qcprotmodule.o arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-i9QlNx/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-armhf-2.7/Bio/PDB/QCPSuperimposer/qcprotmodule.o -o /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB/QCPSuperimposer/qcprotmodule.so building 'Bio.motifs._pwm' extension creating build/temp.linux-armhf-2.7/Bio/motifs arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -c Bio/motifs/_pwm.c -o build/temp.linux-armhf-2.7/Bio/motifs/_pwm.o arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-i9QlNx/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-armhf-2.7/Bio/motifs/_pwm.o -o /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/motifs/_pwm.so building 'Bio.Cluster._cluster' extension creating build/temp.linux-armhf-2.7/Bio/Cluster arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -c Bio/Cluster/cluster.c -o build/temp.linux-armhf-2.7/Bio/Cluster/cluster.o arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -c Bio/Cluster/clustermodule.c -o build/temp.linux-armhf-2.7/Bio/Cluster/clustermodule.o arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-i9QlNx/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-armhf-2.7/Bio/Cluster/cluster.o build/temp.linux-armhf-2.7/Bio/Cluster/clustermodule.o -o /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Cluster/_cluster.so building 'Bio.PDB.kdtrees' extension arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -c Bio/PDB/kdtrees.c -o build/temp.linux-armhf-2.7/Bio/PDB/kdtrees.o arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-i9QlNx/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-armhf-2.7/Bio/PDB/kdtrees.o -o /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB/kdtrees.so building 'Bio.KDTree._CKDTree' extension creating build/temp.linux-armhf-2.7/Bio/KDTree arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -c Bio/KDTree/KDTree.c -o build/temp.linux-armhf-2.7/Bio/KDTree/KDTree.o arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -c Bio/KDTree/KDTreemodule.c -o build/temp.linux-armhf-2.7/Bio/KDTree/KDTreemodule.o arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-i9QlNx/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-armhf-2.7/Bio/KDTree/KDTree.o build/temp.linux-armhf-2.7/Bio/KDTree/KDTreemodule.o -o /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/KDTree/_CKDTree.so building 'Bio.trie' extension arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -IBio -I/usr/include/python2.7 -c Bio/triemodule.c -o build/temp.linux-armhf-2.7/Bio/triemodule.o arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -IBio -I/usr/include/python2.7 -c Bio/trie.c -o build/temp.linux-armhf-2.7/Bio/trie.o In file included from /usr/include/string.h:494, from Bio/trie.c:17: In function ‘strncat’, inlined from ‘_with_prefix_helper.constprop’ at Bio/trie.c:595:6: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:136:10: warning: ‘__builtin___strncat_chk’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Bio/trie.c: In function ‘_with_prefix_helper.constprop’: Bio/trie.c:561:14: note: length computed here 561 | suffixlen = strlen(suffix); | ^~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-i9QlNx/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-armhf-2.7/Bio/triemodule.o build/temp.linux-armhf-2.7/Bio/trie.o -o /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/trie.so pybuild --build -i python{version} -p "3.8 3.7" I: pybuild base:217: /usr/bin/python3.8 setup.py build running build running build_py creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/File.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/triefind.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/MarkovModel.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/kNN.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/pairwise2.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/SeqRecord.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/MaxEntropy.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/Index.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/NaiveBayes.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/Seq.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/_utils.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/SeqFeature.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/LogisticRegression.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/bgzf.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Align copying Bio/Align/AlignInfo.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Align copying Bio/Align/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Align creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/Applications copying Bio/Align/Applications/_ClustalOmega.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/Applications copying Bio/Align/Applications/_Mafft.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/Applications copying Bio/Align/Applications/_Muscle.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/Applications copying Bio/Align/Applications/_Clustalw.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/Applications copying Bio/Align/Applications/_TCoffee.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/Applications copying Bio/Align/Applications/_Dialign.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/Applications copying Bio/Align/Applications/_Prank.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/Applications copying Bio/Align/Applications/_MSAProbs.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/Applications copying Bio/Align/Applications/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/Applications copying Bio/Align/Applications/_Probcons.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/Applications creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/AlignIO copying Bio/AlignIO/NexusIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/AlignIO copying Bio/AlignIO/MauveIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/AlignIO copying Bio/AlignIO/MafIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/AlignIO copying Bio/AlignIO/StockholmIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/AlignIO copying Bio/AlignIO/ClustalIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/AlignIO copying Bio/AlignIO/FastaIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/AlignIO copying Bio/AlignIO/EmbossIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/AlignIO copying Bio/AlignIO/Interfaces.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/AlignIO copying Bio/AlignIO/PhylipIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/AlignIO copying Bio/AlignIO/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/AlignIO creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Alphabet copying Bio/Alphabet/Reduced.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Alphabet copying Bio/Alphabet/IUPAC.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Alphabet copying Bio/Alphabet/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Alphabet creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Application copying Bio/Application/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Application creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Blast copying Bio/Blast/Applications.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Blast copying Bio/Blast/Record.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Blast copying Bio/Blast/NCBIXML.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Blast copying Bio/Blast/ParseBlastTable.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Blast copying Bio/Blast/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Blast copying Bio/Blast/NCBIWWW.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Blast creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/CAPS copying Bio/CAPS/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/CAPS creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/codonalign copying Bio/codonalign/codonseq.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/codonalign copying Bio/codonalign/chisq.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/codonalign copying Bio/codonalign/codonalphabet.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/codonalign copying Bio/codonalign/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/codonalign copying Bio/codonalign/codonalignment.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/codonalign creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Compass copying Bio/Compass/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Compass creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Crystal copying Bio/Crystal/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Crystal creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Data copying Bio/Data/SCOPData.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Data copying Bio/Data/CodonTable.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Data copying Bio/Data/IUPACData.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Data copying Bio/Data/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Data creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Emboss copying Bio/Emboss/Applications.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Emboss copying Bio/Emboss/PrimerSearch.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Emboss copying Bio/Emboss/Primer3.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Emboss copying Bio/Emboss/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Emboss creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez copying Bio/Entrez/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez copying Bio/Entrez/Parser.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/ExPASy copying Bio/ExPASy/ScanProsite.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/ExPASy copying Bio/ExPASy/cellosaurus.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/ExPASy copying Bio/ExPASy/Enzyme.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/ExPASy copying Bio/ExPASy/Prodoc.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/ExPASy copying Bio/ExPASy/Prosite.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/ExPASy copying Bio/ExPASy/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/ExPASy creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/FSSP copying Bio/FSSP/FSSPTools.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/FSSP copying Bio/FSSP/fssp_rec.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/FSSP copying Bio/FSSP/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/FSSP creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/GenBank copying Bio/GenBank/Scanner.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/GenBank copying Bio/GenBank/Record.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/GenBank copying Bio/GenBank/utils.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/GenBank copying Bio/GenBank/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/GenBank creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Geo copying Bio/Geo/Record.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Geo copying Bio/Geo/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Geo creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics copying Bio/Graphics/ColorSpiral.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics copying Bio/Graphics/Distribution.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics copying Bio/Graphics/KGML_vis.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics copying Bio/Graphics/BasicChromosome.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics copying Bio/Graphics/DisplayRepresentation.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics copying Bio/Graphics/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics copying Bio/Graphics/Comparative.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Graph.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Colors.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Diagram.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Track.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_GraphSet.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CrossLink.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Feature.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics/GenomeDiagram creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/HMM copying Bio/HMM/Trainer.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/HMM copying Bio/HMM/MarkovModel.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/HMM copying Bio/HMM/DynamicProgramming.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/HMM copying Bio/HMM/Utilities.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/HMM copying Bio/HMM/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/HMM creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/KEGG copying Bio/KEGG/REST.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/KEGG copying Bio/KEGG/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/KEGG creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/KEGG/Compound copying Bio/KEGG/Compound/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/KEGG/Compound creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/KEGG/Enzyme copying Bio/KEGG/Enzyme/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/KEGG/Enzyme creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/KEGG/Gene copying Bio/KEGG/Gene/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/KEGG/Gene creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/KEGG/Map copying Bio/KEGG/Map/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/KEGG/Map creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB/mmtf copying Bio/PDB/mmtf/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB/mmtf copying Bio/PDB/mmtf/DefaultParser.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB/mmtf creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_pathway.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/KEGG/KGML copying Bio/KEGG/KGML/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_parser.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/KEGG/KGML creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Medline copying Bio/Medline/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Medline creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs copying Bio/motifs/thresholds.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs copying Bio/motifs/alignace.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs copying Bio/motifs/meme.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs copying Bio/motifs/transfac.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs copying Bio/motifs/minimal.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs copying Bio/motifs/matrix.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs copying Bio/motifs/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs copying Bio/motifs/mast.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs/applications copying Bio/motifs/applications/_xxmotif.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs/applications copying Bio/motifs/applications/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs/applications creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs/jaspar copying Bio/motifs/jaspar/db.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs/jaspar copying Bio/motifs/jaspar/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs/jaspar creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Nexus copying Bio/Nexus/Trees.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Nexus copying Bio/Nexus/StandardData.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Nexus copying Bio/Nexus/Nodes.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Nexus copying Bio/Nexus/Nexus.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Nexus copying Bio/Nexus/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Nexus creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/NMR copying Bio/NMR/xpktools.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/NMR copying Bio/NMR/NOEtools.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/NMR copying Bio/NMR/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/NMR creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Pathway copying Bio/Pathway/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Pathway creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Pathway/Rep copying Bio/Pathway/Rep/MultiGraph.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Pathway/Rep copying Bio/Pathway/Rep/Graph.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Pathway/Rep copying Bio/Pathway/Rep/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Pathway/Rep copying Bio/PDB/FragmentMapper.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/Vector.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/parse_pdb_header.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/StructureAlignment.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/Entity.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/PDBParser.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/AbstractPropertyMap.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/StructureBuilder.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/DSSP.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/PDBExceptions.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/Atom.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/Superimposer.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/Structure.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/PDBList.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/Residue.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/PDBIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/MMCIFParser.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/PSEA.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/vectors.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/Model.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/NACCESS.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/Selection.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/ResidueDepth.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/MMCIF2Dict.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/Polypeptide.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/mmcifio.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/Chain.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/Dice.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/HSExposure.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/NeighborSearch.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PopGen copying Bio/PopGen/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PopGen creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/Controller.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/LargeFileParser.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/EasyController.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/Utils.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/FileParser.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PopGen/GenePop creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Restriction copying Bio/Restriction/PrintFormat.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Restriction copying Bio/Restriction/RanaConfig.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Restriction copying Bio/Restriction/Restriction_Dictionary.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Restriction copying Bio/Restriction/Restriction.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Restriction copying Bio/Restriction/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Restriction creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SCOP copying Bio/SCOP/Hie.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SCOP copying Bio/SCOP/Raf.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SCOP copying Bio/SCOP/Residues.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SCOP copying Bio/SCOP/Des.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SCOP copying Bio/SCOP/Cla.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SCOP copying Bio/SCOP/Dom.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SCOP copying Bio/SCOP/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SCOP creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO copying Bio/SearchIO/BlatIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO copying Bio/SearchIO/_index.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO copying Bio/SearchIO/FastaIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO copying Bio/SearchIO/_utils.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO copying Bio/SearchIO/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/_legacy copying Bio/SearchIO/_legacy/ParserSupport.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/_legacy copying Bio/SearchIO/_legacy/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/_legacy copying Bio/SearchIO/_legacy/NCBIStandalone.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/_legacy creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/hit.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/_base.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/hsp.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/query.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/_model creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_text.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_tab.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_xml.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/BlastIO creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/_base.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_tab.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_text.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/HmmerIO creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/_base.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_text.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/ExonerateIO creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/interproscan_xml.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/InterproscanIO creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/UniprotIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/AceIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/PdbIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/IgIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/_convert.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/QualityIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/_index.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/PhdIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/FastaIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/InsdcIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/Interfaces.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/PirIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/TabIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/SwissIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/SeqXmlIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/AbiIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/SffIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqUtils copying Bio/SeqUtils/CheckSum.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqUtils copying Bio/SeqUtils/MeltingTemp.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqUtils copying Bio/SeqUtils/ProtParam.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqUtils copying Bio/SeqUtils/CodonUsage.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqUtils copying Bio/SeqUtils/CodonUsageIndices.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqUtils copying Bio/SeqUtils/lcc.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqUtils copying Bio/SeqUtils/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqUtils copying Bio/SeqUtils/IsoelectricPoint.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqUtils copying Bio/SeqUtils/ProtParamData.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqUtils creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Sequencing copying Bio/Sequencing/Ace.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Sequencing copying Bio/Sequencing/Phd.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Sequencing copying Bio/Sequencing/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Sequencing creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_bwa.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_samtools.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_Novoalign.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Sequencing/Applications creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Statistics copying Bio/Statistics/lowess.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Statistics copying Bio/Statistics/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Statistics creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SubsMat copying Bio/SubsMat/MatrixInfo.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SubsMat copying Bio/SubsMat/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SubsMat copying Bio/SubsMat/FreqTable.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SubsMat creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SVDSuperimposer copying Bio/SVDSuperimposer/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SVDSuperimposer creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB/QCPSuperimposer copying Bio/PDB/QCPSuperimposer/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB/QCPSuperimposer creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SwissProt copying Bio/SwissProt/KeyWList.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SwissProt copying Bio/SwissProt/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SwissProt creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/TogoWS copying Bio/TogoWS/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/TogoWS creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo copying Bio/Phylo/NewickIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo copying Bio/Phylo/PhyloXMLIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo copying Bio/Phylo/NexusIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo copying Bio/Phylo/_cdao_owl.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo copying Bio/Phylo/BaseTree.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo copying Bio/Phylo/PhyloXML.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo copying Bio/Phylo/CDAO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo copying Bio/Phylo/Consensus.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo copying Bio/Phylo/_utils.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo copying Bio/Phylo/Newick.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo copying Bio/Phylo/_io.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo copying Bio/Phylo/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo copying Bio/Phylo/CDAOIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo copying Bio/Phylo/TreeConstruction.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo copying Bio/Phylo/NeXML.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo copying Bio/Phylo/NeXMLIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Fasttree.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Raxml.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Phyml.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo/Applications creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/chi2.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_yn00.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/yn00.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_codeml.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/codeml.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_paml.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_baseml.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/baseml.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo/PAML creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/UniGene copying Bio/UniGene/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/UniGene creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/UniProt copying Bio/UniProt/GOA.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/UniProt copying Bio/UniProt/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/UniProt creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Wise copying Bio/Wise/dnal.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Wise copying Bio/Wise/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Wise copying Bio/Wise/psw.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Wise creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/_py3k copying Bio/_py3k/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/_py3k creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL copying BioSQL/Loader.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL copying BioSQL/BioSeq.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL copying BioSQL/DBUtils.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL copying BioSQL/BioSeqDatabase.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL copying BioSQL/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Affy copying Bio/Affy/CelFile.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Affy copying Bio/Affy/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Affy creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Cluster copying Bio/Cluster/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Cluster creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/KDTree copying Bio/KDTree/KDTree.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/KDTree copying Bio/KDTree/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/KDTree creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/phenotype copying Bio/phenotype/phen_micro.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/phenotype copying Bio/phenotype/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/phenotype copying Bio/phenotype/pm_fitting.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/phenotype 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 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 writing manifest file 'biopython.egg-info/SOURCES.txt' copying Bio/cpairwise2module.c -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/trie.c -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/trie.h -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/triemodule.c -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/Align/_aligners.c -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Align creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Gene.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_General.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_General.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medlars.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medline.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mim.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mime.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Organism.dtd -> 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Bio/Entrez/DTDs/isopub.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isotech.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/journalmeta.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/link.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/list.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/math.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml-in-pubmed.mod -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml2.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml3-qname1.mod -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml3.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathmlsetup.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mmlalias.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mmlextra.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/modules.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_011101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_080101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_090101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_011101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_080101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_090101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_080101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_100101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/notat.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/para.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/phrase.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pmc-1.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_020114.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_080101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_090101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100301.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_110101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_120101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130501.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_140101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_150101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180601.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_190101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/references.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/section.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/taxon.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xmlspecchars.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/XSDs copying Bio/Entrez/XSDs/IPGReportSet.xsd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/XSDs copying Bio/motifs/_pwm.c -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs copying Bio/Nexus/cnexus.c -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Nexus copying Bio/PDB/kdtrees.c -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/QCPSuperimposer/qcprotmodule.c -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB/QCPSuperimposer copying Bio/Cluster/cluster.c -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Cluster copying Bio/Cluster/cluster.h -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Cluster copying Bio/Cluster/clustermodule.c -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Cluster copying Bio/KDTree/KDTree.c -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/KDTree copying Bio/KDTree/KDTree.h -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/KDTree copying Bio/KDTree/KDTreemodule.c -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/KDTree copying Bio/KDTree/Neighbor.h -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/KDTree running build_ext building 'Bio.Align._aligners' extension creating build/temp.linux-armhf-3.8 creating build/temp.linux-armhf-3.8/Bio creating build/temp.linux-armhf-3.8/Bio/Align arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.8 -c Bio/Align/_aligners.c -o build/temp.linux-armhf-3.8/Bio/Align/_aligners.o Bio/Align/_aligners.c: In function ‘PathGenerator_length’: Bio/Align/_aligners.c:701:22: warning: ‘count’ may be used uninitialized in this function [-Wmaybe-uninitialized] 701 | self->length = length; | ~~~~~~~~~~~~~^~~~~~~~ arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.8/Bio/Align/_aligners.o -o /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/_aligners.cpython-38-arm-linux-gnueabihf.so building 'Bio.cpairwise2' extension arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.8 -c Bio/cpairwise2module.c -o build/temp.linux-armhf-3.8/Bio/cpairwise2module.o In file included from /usr/include/python3.8/Python.h:106, from Bio/cpairwise2module.c:14: Bio/cpairwise2module.c: In function ‘cpairwise2__make_score_matrix_fast’: /usr/include/python3.8/listobject.h:73:58: warning: ‘py_trace_row’ may be used uninitialized in this function [-Wmaybe-uninitialized] 73 | #define PyList_SET_ITEM(op, i, v) (((PyListObject *)(op))->ob_item[i] = (v)) | ^~ Bio/cpairwise2module.c:343:34: note: ‘py_trace_row’ was declared here 343 | PyObject *py_score_row, *py_trace_row; | ^~~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.8/Bio/cpairwise2module.o -o /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/cpairwise2.cpython-38-arm-linux-gnueabihf.so building 'Bio.Nexus.cnexus' extension creating build/temp.linux-armhf-3.8/Bio/Nexus arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.8 -c Bio/Nexus/cnexus.c -o build/temp.linux-armhf-3.8/Bio/Nexus/cnexus.o arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.8/Bio/Nexus/cnexus.o -o /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Nexus/cnexus.cpython-38-arm-linux-gnueabihf.so building 'Bio.PDB.QCPSuperimposer.qcprotmodule' extension creating build/temp.linux-armhf-3.8/Bio/PDB creating build/temp.linux-armhf-3.8/Bio/PDB/QCPSuperimposer arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.8 -c Bio/PDB/QCPSuperimposer/qcprotmodule.c -o build/temp.linux-armhf-3.8/Bio/PDB/QCPSuperimposer/qcprotmodule.o arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.8/Bio/PDB/QCPSuperimposer/qcprotmodule.o -o /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-38-arm-linux-gnueabihf.so building 'Bio.motifs._pwm' extension creating build/temp.linux-armhf-3.8/Bio/motifs arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.8 -c Bio/motifs/_pwm.c -o build/temp.linux-armhf-3.8/Bio/motifs/_pwm.o arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.8/Bio/motifs/_pwm.o -o /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs/_pwm.cpython-38-arm-linux-gnueabihf.so building 'Bio.Cluster._cluster' extension creating build/temp.linux-armhf-3.8/Bio/Cluster arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.8 -c Bio/Cluster/cluster.c -o build/temp.linux-armhf-3.8/Bio/Cluster/cluster.o arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.8 -c Bio/Cluster/clustermodule.c -o build/temp.linux-armhf-3.8/Bio/Cluster/clustermodule.o arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.8/Bio/Cluster/cluster.o build/temp.linux-armhf-3.8/Bio/Cluster/clustermodule.o -o /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Cluster/_cluster.cpython-38-arm-linux-gnueabihf.so building 'Bio.PDB.kdtrees' extension arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.8 -c Bio/PDB/kdtrees.c -o build/temp.linux-armhf-3.8/Bio/PDB/kdtrees.o arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.8/Bio/PDB/kdtrees.o -o /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB/kdtrees.cpython-38-arm-linux-gnueabihf.so building 'Bio.KDTree._CKDTree' extension creating build/temp.linux-armhf-3.8/Bio/KDTree arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.8 -c Bio/KDTree/KDTree.c -o build/temp.linux-armhf-3.8/Bio/KDTree/KDTree.o arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.8 -c Bio/KDTree/KDTreemodule.c -o build/temp.linux-armhf-3.8/Bio/KDTree/KDTreemodule.o arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.8/Bio/KDTree/KDTree.o build/temp.linux-armhf-3.8/Bio/KDTree/KDTreemodule.o -o /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/KDTree/_CKDTree.cpython-38-arm-linux-gnueabihf.so building 'Bio.trie' extension arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -IBio -I/usr/include/python3.8 -c Bio/triemodule.c -o build/temp.linux-armhf-3.8/Bio/triemodule.o Bio/triemodule.c:585:5: warning: initialization of ‘Py_hash_t (*)(PyObject *)’ {aka ‘int (*)(struct _object *)’} from incompatible pointer type ‘long int (*)(PyObject *)’ {aka ‘long int (*)(struct _object *)’} [-Wincompatible-pointer-types] 585 | trie_nohash, /*tp_hash */ | ^~~~~~~~~~~ Bio/triemodule.c:585:5: note: (near initialization for ‘Trie_Type.tp_hash’) arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -IBio -I/usr/include/python3.8 -c Bio/trie.c -o build/temp.linux-armhf-3.8/Bio/trie.o Bio/trie.c: In function ‘_iterate_helper’: Bio/trie.c:510:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 510 | if(keylen + strlen(suffix) >= max_key) { | ^~ In file included from /usr/include/string.h:494, from Bio/trie.c:17: In function ‘strncat’, inlined from ‘_with_prefix_helper.constprop’ at Bio/trie.c:595:6: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:136:10: warning: ‘__builtin___strncat_chk’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Bio/trie.c: In function ‘_with_prefix_helper.constprop’: Bio/trie.c:561:14: note: length computed here 561 | suffixlen = strlen(suffix); | ^~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.8/Bio/triemodule.o build/temp.linux-armhf-3.8/Bio/trie.o -o /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/trie.cpython-38-arm-linux-gnueabihf.so I: pybuild base:217: /usr/bin/python3 setup.py build running build running build_py creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio copying Bio/File.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio copying Bio/triefind.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio copying Bio/MarkovModel.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio copying Bio/kNN.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio copying Bio/pairwise2.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio copying Bio/SeqRecord.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio copying Bio/MaxEntropy.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio copying Bio/Index.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio copying Bio/NaiveBayes.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio copying Bio/Seq.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio copying Bio/_utils.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio copying Bio/SeqFeature.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio copying Bio/LogisticRegression.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio copying Bio/bgzf.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio copying Bio/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Align copying Bio/Align/AlignInfo.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Align copying Bio/Align/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Align creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Align/Applications copying Bio/Align/Applications/_ClustalOmega.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Align/Applications copying Bio/Align/Applications/_Mafft.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Align/Applications copying Bio/Align/Applications/_Muscle.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Align/Applications copying Bio/Align/Applications/_Clustalw.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Align/Applications copying Bio/Align/Applications/_TCoffee.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Align/Applications copying Bio/Align/Applications/_Dialign.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Align/Applications copying Bio/Align/Applications/_Prank.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Align/Applications copying Bio/Align/Applications/_MSAProbs.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Align/Applications copying Bio/Align/Applications/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Align/Applications copying Bio/Align/Applications/_Probcons.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Align/Applications creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/AlignIO copying Bio/AlignIO/NexusIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/AlignIO copying Bio/AlignIO/MauveIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/AlignIO copying Bio/AlignIO/MafIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/AlignIO copying Bio/AlignIO/StockholmIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/AlignIO copying Bio/AlignIO/ClustalIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/AlignIO copying Bio/AlignIO/FastaIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/AlignIO copying Bio/AlignIO/EmbossIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/AlignIO copying Bio/AlignIO/Interfaces.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/AlignIO copying Bio/AlignIO/PhylipIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/AlignIO copying Bio/AlignIO/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/AlignIO creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Alphabet copying Bio/Alphabet/Reduced.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Alphabet copying Bio/Alphabet/IUPAC.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Alphabet copying Bio/Alphabet/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Alphabet creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Application copying Bio/Application/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Application creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Blast copying Bio/Blast/Applications.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Blast copying Bio/Blast/Record.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Blast copying Bio/Blast/NCBIXML.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Blast copying Bio/Blast/ParseBlastTable.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Blast copying Bio/Blast/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Blast copying Bio/Blast/NCBIWWW.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Blast creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/CAPS copying Bio/CAPS/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/CAPS creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/codonalign copying Bio/codonalign/codonseq.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/codonalign copying Bio/codonalign/chisq.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/codonalign copying Bio/codonalign/codonalphabet.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/codonalign copying Bio/codonalign/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/codonalign copying Bio/codonalign/codonalignment.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/codonalign creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Compass copying Bio/Compass/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Compass creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Crystal copying Bio/Crystal/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Crystal creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Data copying Bio/Data/SCOPData.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Data copying Bio/Data/CodonTable.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Data copying Bio/Data/IUPACData.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Data copying Bio/Data/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Data creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Emboss copying Bio/Emboss/Applications.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Emboss copying Bio/Emboss/PrimerSearch.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Emboss copying Bio/Emboss/Primer3.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Emboss copying Bio/Emboss/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Emboss creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez copying Bio/Entrez/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez copying Bio/Entrez/Parser.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/ExPASy copying Bio/ExPASy/ScanProsite.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/ExPASy copying Bio/ExPASy/cellosaurus.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/ExPASy copying Bio/ExPASy/Enzyme.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/ExPASy copying Bio/ExPASy/Prodoc.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/ExPASy copying Bio/ExPASy/Prosite.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/ExPASy copying Bio/ExPASy/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/ExPASy creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/FSSP copying Bio/FSSP/FSSPTools.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/FSSP copying Bio/FSSP/fssp_rec.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/FSSP copying Bio/FSSP/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/FSSP creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/GenBank copying Bio/GenBank/Scanner.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/GenBank copying Bio/GenBank/Record.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/GenBank copying Bio/GenBank/utils.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/GenBank copying Bio/GenBank/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/GenBank creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Geo copying Bio/Geo/Record.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Geo copying Bio/Geo/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Geo creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Graphics copying Bio/Graphics/ColorSpiral.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Graphics copying Bio/Graphics/Distribution.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Graphics copying Bio/Graphics/KGML_vis.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Graphics copying Bio/Graphics/BasicChromosome.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Graphics copying Bio/Graphics/DisplayRepresentation.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Graphics copying Bio/Graphics/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Graphics copying Bio/Graphics/Comparative.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Graphics creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Graph.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Colors.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Diagram.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Track.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_GraphSet.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CrossLink.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Feature.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Graphics/GenomeDiagram creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/HMM copying Bio/HMM/Trainer.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/HMM copying Bio/HMM/MarkovModel.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/HMM copying Bio/HMM/DynamicProgramming.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/HMM copying Bio/HMM/Utilities.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/HMM copying Bio/HMM/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/HMM creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/KEGG copying Bio/KEGG/REST.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/KEGG copying Bio/KEGG/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/KEGG creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/KEGG/Compound copying Bio/KEGG/Compound/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/KEGG/Compound creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/KEGG/Enzyme copying Bio/KEGG/Enzyme/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/KEGG/Enzyme creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/KEGG/Gene copying Bio/KEGG/Gene/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/KEGG/Gene creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/KEGG/Map copying Bio/KEGG/Map/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/KEGG/Map creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB/mmtf copying Bio/PDB/mmtf/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB/mmtf copying Bio/PDB/mmtf/DefaultParser.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB/mmtf creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_pathway.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/KEGG/KGML copying Bio/KEGG/KGML/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_parser.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/KEGG/KGML creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Medline copying Bio/Medline/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Medline creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/motifs copying Bio/motifs/thresholds.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/motifs copying Bio/motifs/alignace.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/motifs copying Bio/motifs/meme.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/motifs copying Bio/motifs/transfac.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/motifs copying Bio/motifs/minimal.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/motifs copying Bio/motifs/matrix.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/motifs copying Bio/motifs/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/motifs copying Bio/motifs/mast.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/motifs creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/motifs/applications copying Bio/motifs/applications/_xxmotif.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/motifs/applications copying Bio/motifs/applications/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/motifs/applications creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/motifs/jaspar copying Bio/motifs/jaspar/db.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/motifs/jaspar copying Bio/motifs/jaspar/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/motifs/jaspar creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Nexus copying Bio/Nexus/Trees.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Nexus copying Bio/Nexus/StandardData.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Nexus copying Bio/Nexus/Nodes.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Nexus copying Bio/Nexus/Nexus.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Nexus copying Bio/Nexus/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Nexus creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/NMR copying Bio/NMR/xpktools.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/NMR copying Bio/NMR/NOEtools.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/NMR copying Bio/NMR/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/NMR creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Pathway copying Bio/Pathway/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Pathway creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Pathway/Rep copying Bio/Pathway/Rep/MultiGraph.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Pathway/Rep copying Bio/Pathway/Rep/Graph.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Pathway/Rep copying Bio/Pathway/Rep/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Pathway/Rep copying Bio/PDB/FragmentMapper.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB copying Bio/PDB/Vector.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB copying Bio/PDB/parse_pdb_header.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB copying Bio/PDB/StructureAlignment.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB copying Bio/PDB/Entity.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB copying Bio/PDB/PDBParser.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB copying Bio/PDB/AbstractPropertyMap.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB copying Bio/PDB/StructureBuilder.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB copying Bio/PDB/DSSP.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB copying Bio/PDB/PDBExceptions.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB copying Bio/PDB/Atom.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB copying Bio/PDB/Superimposer.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB copying Bio/PDB/Structure.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB copying Bio/PDB/PDBList.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB copying Bio/PDB/Residue.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB copying Bio/PDB/PDBIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB copying Bio/PDB/MMCIFParser.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB copying Bio/PDB/PSEA.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB copying Bio/PDB/vectors.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB copying Bio/PDB/Model.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB copying Bio/PDB/NACCESS.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB copying Bio/PDB/Selection.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB copying Bio/PDB/ResidueDepth.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB copying Bio/PDB/MMCIF2Dict.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB copying Bio/PDB/Polypeptide.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB copying Bio/PDB/mmcifio.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB copying Bio/PDB/Chain.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB copying Bio/PDB/Dice.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB copying Bio/PDB/HSExposure.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB copying Bio/PDB/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB copying Bio/PDB/NeighborSearch.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PopGen copying Bio/PopGen/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PopGen creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/Controller.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/LargeFileParser.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/EasyController.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/Utils.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/FileParser.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PopGen/GenePop creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Restriction copying Bio/Restriction/PrintFormat.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Restriction copying Bio/Restriction/RanaConfig.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Restriction copying Bio/Restriction/Restriction_Dictionary.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Restriction copying Bio/Restriction/Restriction.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Restriction copying Bio/Restriction/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Restriction creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SCOP copying Bio/SCOP/Hie.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SCOP copying Bio/SCOP/Raf.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SCOP copying Bio/SCOP/Residues.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SCOP copying Bio/SCOP/Des.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SCOP copying Bio/SCOP/Cla.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SCOP copying Bio/SCOP/Dom.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SCOP copying Bio/SCOP/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SCOP creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO copying Bio/SearchIO/BlatIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO copying Bio/SearchIO/_index.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO copying Bio/SearchIO/FastaIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO copying Bio/SearchIO/_utils.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO copying Bio/SearchIO/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO/_legacy copying Bio/SearchIO/_legacy/ParserSupport.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO/_legacy copying Bio/SearchIO/_legacy/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO/_legacy copying Bio/SearchIO/_legacy/NCBIStandalone.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO/_legacy creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/hit.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/_base.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/hsp.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/query.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO/_model creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_text.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_tab.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_xml.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO/BlastIO creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/_base.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_tab.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_text.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO/HmmerIO creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/_base.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_text.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO/ExonerateIO creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/interproscan_xml.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SearchIO/InterproscanIO creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SeqIO copying Bio/SeqIO/UniprotIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SeqIO copying Bio/SeqIO/AceIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SeqIO copying Bio/SeqIO/PdbIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SeqIO copying Bio/SeqIO/IgIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SeqIO copying Bio/SeqIO/_convert.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SeqIO copying Bio/SeqIO/QualityIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SeqIO copying Bio/SeqIO/_index.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SeqIO copying Bio/SeqIO/PhdIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SeqIO copying Bio/SeqIO/FastaIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SeqIO copying Bio/SeqIO/InsdcIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SeqIO copying Bio/SeqIO/Interfaces.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SeqIO copying Bio/SeqIO/PirIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SeqIO copying Bio/SeqIO/TabIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SeqIO copying Bio/SeqIO/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SeqIO copying Bio/SeqIO/SwissIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SeqIO copying Bio/SeqIO/SeqXmlIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SeqIO copying Bio/SeqIO/AbiIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SeqIO copying Bio/SeqIO/SffIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SeqIO creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SeqUtils copying Bio/SeqUtils/CheckSum.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SeqUtils copying Bio/SeqUtils/MeltingTemp.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SeqUtils copying Bio/SeqUtils/ProtParam.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SeqUtils copying Bio/SeqUtils/CodonUsage.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SeqUtils copying Bio/SeqUtils/CodonUsageIndices.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SeqUtils copying Bio/SeqUtils/lcc.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SeqUtils copying Bio/SeqUtils/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SeqUtils copying Bio/SeqUtils/IsoelectricPoint.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SeqUtils copying Bio/SeqUtils/ProtParamData.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SeqUtils creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Sequencing copying Bio/Sequencing/Ace.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Sequencing copying Bio/Sequencing/Phd.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Sequencing copying Bio/Sequencing/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Sequencing creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_bwa.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_samtools.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_Novoalign.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Sequencing/Applications creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Statistics copying Bio/Statistics/lowess.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Statistics copying Bio/Statistics/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Statistics creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SubsMat copying Bio/SubsMat/MatrixInfo.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SubsMat copying Bio/SubsMat/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SubsMat copying Bio/SubsMat/FreqTable.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SubsMat creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SVDSuperimposer copying Bio/SVDSuperimposer/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SVDSuperimposer creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB/QCPSuperimposer copying Bio/PDB/QCPSuperimposer/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB/QCPSuperimposer creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SwissProt copying Bio/SwissProt/KeyWList.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SwissProt copying Bio/SwissProt/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/SwissProt creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/TogoWS copying Bio/TogoWS/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/TogoWS creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Phylo copying Bio/Phylo/NewickIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Phylo copying Bio/Phylo/PhyloXMLIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Phylo copying Bio/Phylo/NexusIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Phylo copying Bio/Phylo/_cdao_owl.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Phylo copying Bio/Phylo/BaseTree.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Phylo copying Bio/Phylo/PhyloXML.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Phylo copying Bio/Phylo/CDAO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Phylo copying Bio/Phylo/Consensus.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Phylo copying Bio/Phylo/_utils.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Phylo copying Bio/Phylo/Newick.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Phylo copying Bio/Phylo/_io.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Phylo copying Bio/Phylo/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Phylo copying Bio/Phylo/CDAOIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Phylo copying Bio/Phylo/TreeConstruction.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Phylo copying Bio/Phylo/NeXML.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Phylo copying Bio/Phylo/NeXMLIO.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Phylo creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Fasttree.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Raxml.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Phyml.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Phylo/Applications creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/chi2.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_yn00.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/yn00.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_codeml.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/codeml.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_paml.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_baseml.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/baseml.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Phylo/PAML creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/UniGene copying Bio/UniGene/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/UniGene creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/UniProt copying Bio/UniProt/GOA.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/UniProt copying Bio/UniProt/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/UniProt creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Wise copying Bio/Wise/dnal.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Wise copying Bio/Wise/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Wise copying Bio/Wise/psw.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Wise creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/_py3k copying Bio/_py3k/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/_py3k creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/BioSQL copying BioSQL/Loader.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/BioSQL copying BioSQL/BioSeq.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/BioSQL copying BioSQL/DBUtils.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/BioSQL copying BioSQL/BioSeqDatabase.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/BioSQL copying BioSQL/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/BioSQL creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Affy copying Bio/Affy/CelFile.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Affy copying Bio/Affy/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Affy creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Cluster copying Bio/Cluster/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Cluster creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/KDTree copying Bio/KDTree/KDTree.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/KDTree copying Bio/KDTree/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/KDTree creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/phenotype copying Bio/phenotype/phen_micro.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/phenotype copying Bio/phenotype/__init__.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/phenotype copying Bio/phenotype/pm_fitting.py -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/phenotype 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 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 writing manifest file 'biopython.egg-info/SOURCES.txt' copying Bio/cpairwise2module.c -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio copying Bio/trie.c -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio copying Bio/trie.h -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio copying Bio/triemodule.c -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio copying Bio/Align/_aligners.c -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Align creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> 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copying Bio/Entrez/DTDs/isoamsn.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamso.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsr.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isobox.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isocyr1.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isocyr2.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isodia.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk1.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk2.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk3.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk4.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isolat1.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isolat2.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomfrk.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomopf.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomscr.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isonum.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isopub.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isotech.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/journalmeta.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/link.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/list.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/math.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml-in-pubmed.mod -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml2.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml3-qname1.mod -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml3.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathmlsetup.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mmlalias.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mmlextra.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/modules.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_011101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_080101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_090101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_011101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_080101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_090101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_080101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_100101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/notat.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/para.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/phrase.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pmc-1.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_020114.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_080101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_090101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100301.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_110101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_120101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130501.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_140101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_150101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180601.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_190101.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/references.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/section.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/taxon.dtd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xmlspecchars.ent -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/DTDs creating /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/XSDs copying Bio/Entrez/XSDs/IPGReportSet.xsd -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Entrez/XSDs copying Bio/motifs/_pwm.c -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/motifs copying Bio/Nexus/cnexus.c -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Nexus copying Bio/PDB/kdtrees.c -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB copying Bio/PDB/QCPSuperimposer/qcprotmodule.c -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB/QCPSuperimposer copying Bio/Cluster/cluster.c -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Cluster copying Bio/Cluster/cluster.h -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Cluster copying Bio/Cluster/clustermodule.c -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Cluster copying Bio/KDTree/KDTree.c -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/KDTree copying Bio/KDTree/KDTree.h -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/KDTree copying Bio/KDTree/KDTreemodule.c -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/KDTree copying Bio/KDTree/Neighbor.h -> /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/KDTree running build_ext building 'Bio.Align._aligners' extension creating build/temp.linux-armhf-3.7 creating build/temp.linux-armhf-3.7/Bio creating build/temp.linux-armhf-3.7/Bio/Align arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.7m -c Bio/Align/_aligners.c -o build/temp.linux-armhf-3.7/Bio/Align/_aligners.o Bio/Align/_aligners.c: In function ‘PathGenerator_length’: Bio/Align/_aligners.c:701:22: warning: ‘count’ may be used uninitialized in this function [-Wmaybe-uninitialized] 701 | self->length = length; | ~~~~~~~~~~~~~^~~~~~~~ arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/Bio/Align/_aligners.o -o /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Align/_aligners.cpython-37m-arm-linux-gnueabihf.so building 'Bio.cpairwise2' extension arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.7m -c Bio/cpairwise2module.c -o build/temp.linux-armhf-3.7/Bio/cpairwise2module.o In file included from /usr/include/python3.7m/Python.h:108, from Bio/cpairwise2module.c:14: Bio/cpairwise2module.c: In function ‘cpairwise2__make_score_matrix_fast’: /usr/include/python3.7m/listobject.h:73:58: warning: ‘py_trace_row’ may be used uninitialized in this function [-Wmaybe-uninitialized] 73 | #define PyList_SET_ITEM(op, i, v) (((PyListObject *)(op))->ob_item[i] = (v)) | ^~ Bio/cpairwise2module.c:343:34: note: ‘py_trace_row’ was declared here 343 | PyObject *py_score_row, *py_trace_row; | ^~~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/Bio/cpairwise2module.o -o /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/cpairwise2.cpython-37m-arm-linux-gnueabihf.so building 'Bio.Nexus.cnexus' extension creating build/temp.linux-armhf-3.7/Bio/Nexus arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.7m -c Bio/Nexus/cnexus.c -o build/temp.linux-armhf-3.7/Bio/Nexus/cnexus.o arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/Bio/Nexus/cnexus.o -o /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Nexus/cnexus.cpython-37m-arm-linux-gnueabihf.so building 'Bio.PDB.QCPSuperimposer.qcprotmodule' extension creating build/temp.linux-armhf-3.7/Bio/PDB creating build/temp.linux-armhf-3.7/Bio/PDB/QCPSuperimposer arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.7m -c Bio/PDB/QCPSuperimposer/qcprotmodule.c -o build/temp.linux-armhf-3.7/Bio/PDB/QCPSuperimposer/qcprotmodule.o arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/Bio/PDB/QCPSuperimposer/qcprotmodule.o -o /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-37m-arm-linux-gnueabihf.so building 'Bio.motifs._pwm' extension creating build/temp.linux-armhf-3.7/Bio/motifs arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.7m -c Bio/motifs/_pwm.c -o build/temp.linux-armhf-3.7/Bio/motifs/_pwm.o arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/Bio/motifs/_pwm.o -o /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/motifs/_pwm.cpython-37m-arm-linux-gnueabihf.so building 'Bio.Cluster._cluster' extension creating build/temp.linux-armhf-3.7/Bio/Cluster arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.7m -c Bio/Cluster/cluster.c -o build/temp.linux-armhf-3.7/Bio/Cluster/cluster.o arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.7m -c Bio/Cluster/clustermodule.c -o build/temp.linux-armhf-3.7/Bio/Cluster/clustermodule.o arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/Bio/Cluster/cluster.o build/temp.linux-armhf-3.7/Bio/Cluster/clustermodule.o -o /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/Cluster/_cluster.cpython-37m-arm-linux-gnueabihf.so building 'Bio.PDB.kdtrees' extension arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.7m -c Bio/PDB/kdtrees.c -o build/temp.linux-armhf-3.7/Bio/PDB/kdtrees.o arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/Bio/PDB/kdtrees.o -o /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/PDB/kdtrees.cpython-37m-arm-linux-gnueabihf.so building 'Bio.KDTree._CKDTree' extension creating build/temp.linux-armhf-3.7/Bio/KDTree arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.7m -c Bio/KDTree/KDTree.c -o build/temp.linux-armhf-3.7/Bio/KDTree/KDTree.o arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.7m -c Bio/KDTree/KDTreemodule.c -o build/temp.linux-armhf-3.7/Bio/KDTree/KDTreemodule.o arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/Bio/KDTree/KDTree.o build/temp.linux-armhf-3.7/Bio/KDTree/KDTreemodule.o -o /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/KDTree/_CKDTree.cpython-37m-arm-linux-gnueabihf.so building 'Bio.trie' extension arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -IBio -I/usr/include/python3.7m -c Bio/triemodule.c -o build/temp.linux-armhf-3.7/Bio/triemodule.o Bio/triemodule.c:585:5: warning: initialization of ‘Py_hash_t (*)(PyObject *)’ {aka ‘int (*)(struct _object *)’} from incompatible pointer type ‘long int (*)(PyObject *)’ {aka ‘long int (*)(struct _object *)’} [-Wincompatible-pointer-types] 585 | trie_nohash, /*tp_hash */ | ^~~~~~~~~~~ Bio/triemodule.c:585:5: note: (near initialization for ‘Trie_Type.tp_hash’) arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -IBio -I/usr/include/python3.7m -c Bio/trie.c -o build/temp.linux-armhf-3.7/Bio/trie.o Bio/trie.c: In function ‘_iterate_helper’: Bio/trie.c:510:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 510 | if(keylen + strlen(suffix) >= max_key) { | ^~ In file included from /usr/include/string.h:494, from Bio/trie.c:17: In function ‘strncat’, inlined from ‘_with_prefix_helper.constprop’ at Bio/trie.c:595:6: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:136:10: warning: ‘__builtin___strncat_chk’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Bio/trie.c: In function ‘_with_prefix_helper.constprop’: Bio/trie.c:561:14: note: length computed here 561 | suffixlen = strlen(suffix); | ^~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.73+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/Bio/triemodule.o build/temp.linux-armhf-3.7/Bio/trie.o -o /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.7/build/Bio/trie.cpython-37m-arm-linux-gnueabihf.so cd Doc && make make[2]: Entering directory '/<>/python-biopython-1.73+dfsg/Doc' hevea -fix Tutorial.tex Exclude comment 'comment' ./Tutorial/chapter_introduction.tex:110: Warning: Undefined citation: 'cock2009' ./Tutorial/chapter_introduction.tex:114: Warning: Undefined citation: 'chapman2000' ./Tutorial/chapter_introduction.tex:115: Warning: Undefined citation: 'hamelryck2003a' ./Tutorial/chapter_introduction.tex:116: Warning: Undefined citation: 'dehoon2004' ./Tutorial/chapter_introduction.tex:117: Warning: Undefined citation: 'pritchard2006' ./Tutorial/chapter_introduction.tex:118: Warning: Undefined citation: 'talevich2012' ./Tutorial/chapter_introduction.tex:119: Warning: Undefined citation: 'cock2010' ./Tutorial/chapter_introduction.tex:237: Warning: Undefined label: 'sec:seq-comparison' ./Tutorial/chapter_introduction.tex:250: Warning: Undefined label: 'sec:appendix-handles' ./Tutorial/chapter_introduction.tex:292: Warning: Undefined label: 'sec:SeqIO-conversion' ./Tutorial/chapter_introduction.tex:292: Warning: Undefined label: 'sec:converting-alignments' ./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:Bio.Seq' ./Tutorial/chapter_quick_start.tex:35: Warning: Undefined label: 'chapter:Bio.Seq' ./Tutorial/chapter_quick_start.tex:49: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_quick_start.tex:69: Warning: Undefined label: 'sec:sequence-parsing' ./Tutorial/chapter_quick_start.tex:69: Warning: Undefined label: 'chapter:entrez' ./Tutorial/chapter_quick_start.tex:69: Warning: Undefined label: 'chapter:swiss_prot' ./Tutorial/chapter_quick_start.tex:69: Warning: Undefined label: 'sec:align_clustal' ./Tutorial/chapter_quick_start.tex:76: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_quick_start.tex:83: Warning: Undefined label: 'sec:connecting-with-biological-databases' ./Tutorial/chapter_quick_start.tex:149: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_quick_start.tex:149: Warning: Undefined label: 'chapter:Bio.AlignIO' ./Tutorial/chapter_quick_start.tex:154: Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_quick_start.tex:162: Warning: Undefined label: 'chapter:entrez' ./Tutorial/chapter_quick_start.tex:163: Warning: Undefined label: 'chapter:swiss_prot' ./Tutorial/chapter_quick_start.tex:173: Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined label: 'chapter:SeqRecord' ./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_objects.tex:137: Warning: Undefined label: 'sec:mutable-seq' ./Tutorial/chapter_seq_objects.tex:207: Warning: Undefined label: 'sec:SeqRecord-format' ./Tutorial/chapter_seq_objects.tex:209: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_objects.tex:376: Warning: Undefined label: 'sec:SeqIO-reverse-complement' ./Tutorial/chapter_seq_objects.tex:449: Warning: Undefined label: 'sec:seq-module-functions' ./Tutorial/chapter_seq_objects.tex:564: Warning: Undefined label: 'sec:SeqIO-translate' ./Tutorial/chapter_seq_objects.tex:570: Warning: Undefined label: 'sec:seq-module-functions' ./Tutorial/chapter_seq_objects.tex:719: Warning: Undefined label: 'sec:seq-to-string' ./Tutorial/chapter_seq_objects.tex:810: Warning: Undefined label: 'sec:seq-to-string' ./Tutorial/chapter_seq_objects.tex:871: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined label: 'chapter:Bio.Seq' ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:21: Warning: Undefined label: 'chapter:Bio.Seq' ./Tutorial/chapter_seq_annot.tex:21: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:34: Warning: Undefined label: 'sec:FASTQ-filtering-example' ./Tutorial/chapter_seq_annot.tex:38: Warning: Undefined label: 'sec:seq_features' ./Tutorial/chapter_seq_annot.tex:48: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:131: Warning: Undefined label: 'chapter:quick-start' ./Tutorial/chapter_seq_annot.tex:133: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:158: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:216: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:229: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:279: Warning: Undefined label: 'sec:seq_features' ./Tutorial/chapter_seq_annot.tex:282: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_annot.tex:288: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:296: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:528: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:632: Warning: Undefined label: 'sec:seq-comparison' ./Tutorial/chapter_seq_annot.tex:640: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:676: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:679: Warning: Undefined label: 'sec:Bio.SeqIO-and-StringIO' ./Tutorial/chapter_seq_annot.tex:833: Warning: Undefined label: 'sec:SeqRecord-format' ./Tutorial/chapter_seq_annot.tex:841: Warning: Undefined label: 'sec:FASTQ-slicing-off-primer' ./Tutorial/chapter_seq_annot.tex:842: Warning: Undefined label: 'sec:FASTQ-slicing-off-adaptor' ./Tutorial/chapter_seq_annot.tex:855: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seqio.tex:4: Warning: Undefined label: 'chapter:quick-start' ./Tutorial/chapter_seqio.tex:4: Warning: Undefined label: 'chapter:SeqRecord' ./Tutorial/chapter_seqio.tex:13: Warning: Undefined label: 'chapter:SeqRecord' ./Tutorial/chapter_seqio.tex:13: Warning: Undefined label: 'chapter:Bio.Seq' ./Tutorial/chapter_seqio.tex:15: Warning: Undefined label: 'sec:low-level-fasta-fastq' ./Tutorial/chapter_seqio.tex:23: Warning: Undefined label: 'sec:SeqIO_Online' ./Tutorial/chapter_seqio.tex:23: Warning: Undefined label: 'sec:appendix-handles' ./Tutorial/chapter_seqio.tex:45: Warning: Undefined label: 'sec:sequence-parsing' ./Tutorial/chapter_seqio.tex:69: Warning: Undefined label: 'seq:sequence-parsing-plus-pylab' ./Tutorial/chapter_seqio.tex:148: Warning: Undefined label: 'chapter:SeqRecord' ./Tutorial/chapter_seqio.tex:280: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:283: Warning: Undefined label: 'sec:appendix-handles' ./Tutorial/chapter_seqio.tex:359: Warning: Undefined label: 'sec:SeqIO-index-bgzf' ./Tutorial/chapter_seqio.tex:362: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:374: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:374: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:375: Warning: Undefined label: 'sec:efetch' ./Tutorial/chapter_seqio.tex:451: Warning: Undefined label: 'chapter:entrez' ./Tutorial/chapter_seqio.tex:451: Warning: Undefined label: 'sec:entrez-guidelines' ./Tutorial/chapter_seqio.tex:454: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:454: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:454: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:456: Warning: Undefined label: 'chapter:swiss_prot' ./Tutorial/chapter_seqio.tex:491: Warning: Undefined label: 'SeqIO:to_dict' ./Tutorial/chapter_seqio.tex:497: Warning: Undefined label: 'sec:SeqIO-index' ./Tutorial/chapter_seqio.tex:501: Warning: Undefined label: 'sec:SeqIO-index-db' ./Tutorial/chapter_seqio.tex:504: Warning: Undefined label: 'sec:SeqIO-indexing-discussion' ./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:514: Warning: Undefined label: 'sec:SeqIO-index' ./Tutorial/chapter_seqio.tex:588: Warning: Undefined label: 'sec:fasta-parsing' ./Tutorial/chapter_seqio.tex:704: Warning: Undefined label: 'sec:fastq-indexing' ./Tutorial/chapter_seqio.tex:725: Warning: Undefined label: 'seq:seqio-todict-functionkey' ./Tutorial/chapter_seqio.tex:787: Warning: Undefined label: 'sec:SeqIO-sort' ./Tutorial/chapter_seqio.tex:869: Warning: Undefined label: 'sec:seqio-index-getraw' ./Tutorial/chapter_seqio.tex:1097: Warning: Undefined label: 'sec:seqio-index-getraw' ./Tutorial/chapter_seqio.tex:1139: Warning: Undefined label: 'sec:SeqIO-fastq-conversion' ./Tutorial/chapter_seqio.tex:1139: Warning: Undefined label: 'sec:SeqIO-fasta-qual-conversion' ./Tutorial/chapter_seqio.tex:1154: Warning: Undefined label: 'sec:seq-reverse-complement' ./Tutorial/chapter_seqio.tex:1164: Warning: Undefined label: 'sec:SeqRecord-reverse-complement' ./Tutorial/chapter_seqio.tex:1205: Warning: Undefined label: 'sec:SeqIO-translate' ./Tutorial/chapter_seqio.tex:1224: Warning: Undefined label: 'sec:SeqRecord-format' ./Tutorial/chapter_seqio.tex:1303: 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:115: Warning: Undefined label: 'sec:alignment-format-method' ./Tutorial/chapter_align.tex:445: Warning: Undefined label: 'sec:SeqIO-conversion' ./Tutorial/chapter_align.tex:617: Warning: Undefined label: 'sec:SeqRecord-format' ./Tutorial/chapter_align.tex:792: Warning: Undefined label: 'sec:SeqRecord-addition' ./Tutorial/chapter_align.tex:844: Warning: Undefined label: 'sec:pairwise2' ./Tutorial/chapter_align.tex:849: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_align.tex:876: Warning: Undefined label: 'seq:emboss-needle-water' ./Tutorial/chapter_align.tex:884: Warning: '_' occurring outside math mode ./Tutorial/chapter_align.tex:1023: Warning: Undefined label: 'sec:Phylo' ./Tutorial/chapter_align.tex:1245: Warning: Undefined label: 'sec:appendix-handles' ./Tutorial/chapter_align.tex:1550: Warning: Undefined citation: 'durbin1998' ./Tutorial/chapter_align.tex:1562: Warning: Undefined label: 'sec:pairwise-aligner' ./Tutorial/chapter_align.tex:1644: Warning: Undefined label: 'sec:pairwise-matchscores' ./Tutorial/chapter_align.tex:1644: Warning: Undefined label: 'sec:pairwise-affine-gapscores' ./Tutorial/chapter_align.tex:1644: Warning: Undefined label: 'sec:pairwise-general-gapscores' ./Tutorial/chapter_align.tex:1645: Warning: Undefined label: 'sec:pairwise-basic' ./Tutorial/chapter_align.tex:1648: Warning: Undefined label: 'sec:pairwise-affine-gapscores' ./Tutorial/chapter_align.tex:1649: Warning: Undefined label: 'sec:pairwise-general-gapscores' ./Tutorial/chapter_align.tex:1855: Warning: Undefined label: 'sec:pairwise-examples' ./Tutorial/chapter_align.tex:1982: Warning: Undefined citation: 'kent2002' ./Tutorial/chapter_blast.tex:18: Warning: Undefined label: 'chapter:searchio' ./Tutorial/chapter_blast.tex:58: Warning: Undefined label: 'sec:parsing-blast' ./Tutorial/chapter_blast.tex:119: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_blast.tex:124: Warning: Undefined label: 'sec:parsing-blast' ./Tutorial/chapter_blast.tex:146: Warning: Undefined label: 'sec:parsing-blast' ./Tutorial/chapter_blast.tex:155: Warning: Undefined label: 'sec:parsing-blast' ./Tutorial/chapter_blast.tex:164: Warning: Undefined label: 'sec:running-www-blast' ./Tutorial/chapter_blast.tex:192: Warning: Undefined label: 'sec:alignment-tools' ./Tutorial/chapter_blast.tex:236: Warning: Undefined label: 'sec:parsing-blast' ./Tutorial/chapter_blast.tex:268: Warning: Undefined label: 'sec:parsing-blast-deprecated' ./Tutorial/chapter_blast.tex:282: Warning: Undefined label: 'sec:running-www-blast' ./Tutorial/chapter_blast.tex:284: Warning: Undefined label: 'sec:running-local-blast' ./Tutorial/chapter_blast.tex:335: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_blast.tex:335: Warning: Undefined label: 'chapter:Bio.AlignIO' ./Tutorial/chapter_blast.tex:445: Warning: Undefined label: 'fig:blastrecord' ./Tutorial/chapter_blast.tex:461: Warning: Undefined label: 'fig:psiblastrecord' ./Tutorial/chapter_searchio.tex:734: Warning: Undefined label: 'chapter:SeqRecord' ./Tutorial/chapter_searchio.tex:1082: Warning: Undefined label: 'sec:SeqIO-index' ./Tutorial/chapter_entrez.tex:22: Warning: Undefined label: 'sec:entrez-specialized-parsers' ./Tutorial/chapter_entrez.tex:57: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:60: Warning: Undefined label: 'sec:BioSQL' ./Tutorial/chapter_entrez.tex:209: Warning: Undefined label: 'sec:efetch' ./Tutorial/chapter_entrez.tex:213: Warning: Undefined label: 'sec:entrez-einfo' ./Tutorial/chapter_entrez.tex:227: Warning: Undefined label: 'sec:efetch' ./Tutorial/chapter_entrez.tex:289: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:314: Warning: Undefined label: 'sec:SeqIO_GenBank_Online' ./Tutorial/chapter_entrez.tex:314: Warning: Undefined label: 'sec:efetch' ./Tutorial/chapter_entrez.tex:408: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_entrez.tex:467: Warning: Undefined label: 'sec:entrez-specialized-parsers' ./Tutorial/chapter_entrez.tex:469: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:550: Warning: Undefined label: 'sec:elink-citations' ./Tutorial/chapter_entrez.tex:556: Warning: Undefined label: 'subsec:entrez_example_genbank' ./Tutorial/chapter_entrez.tex:767: Warning: Undefined label: 'sec:SeqIO_GenBank_Online' ./Tutorial/chapter_entrez.tex:767: Warning: Undefined label: 'sec:efetch' ./Tutorial/chapter_entrez.tex:884: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1035: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1038: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1042: Warning: Undefined label: 'sec:orchids' ./Tutorial/chapter_entrez.tex:1083: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1126: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1126: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1128: Warning: Undefined label: 'sec:orchids' ./Tutorial/chapter_entrez.tex:1180: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1215: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1222: Warning: Undefined label: 'sec:SeqIO_GenBank_Online' ./Tutorial/chapter_entrez.tex:1223: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1275: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_entrez.tex:1299: Warning: Undefined label: 'sec:entrez-guidelines' ./Tutorial/chapter_entrez.tex:1300: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1358: Warning: Undefined label: 'sec:entrez-search-fetch-genbank' ./Tutorial/chapter_entrez.tex:1389: Warning: Undefined label: 'subsec:entrez_example_genbank' ./Tutorial/chapter_entrez.tex:1487: Warning: Undefined label: 'subsec:entrez-and-medline' ./Tutorial/chapter_entrez.tex:1492: Warning: Undefined label: 'sec:elink' ./Tutorial/chapter_entrez.tex:1516: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_uniprot.tex:2: Warning: '_' occurring outside math mode 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Undefined label: 'fig:smcra' ./Tutorial/chapter_pdb.tex:769: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:870: Warning: Undefined citation: 'golub1989' ./Tutorial/chapter_pdb.tex:898: Warning: Undefined citation: 'hamelryck2005' ./Tutorial/chapter_pdb.tex:933: Warning: Undefined label: 'cap:DSSP-codes' ./Tutorial/chapter_pdb.tex:972: Warning: Undefined label: 'subsec:residue_depth' ./Tutorial/chapter_pdb.tex:974: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:1022: Warning: Undefined citation: 'hamelryck2003a' ./Tutorial/chapter_pdb.tex:1234: Warning: Undefined citation: 'hamelryck2003b' ./Tutorial/chapter_pdb.tex:1235: 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:192: Warning: Undefined label: 'fig:phylo-color-draw' ./Tutorial/chapter_phylo.tex:376: Warning: 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./Tutorial/chapter_learning.tex:272: Warning: Undefined label: 'eq:NOP' ./Tutorial/chapter_learning.tex:274: Warning: Undefined label: 'eq:OP' ./Tutorial/chapter_learning.tex:274: Warning: Undefined label: 'eq:NOP' ./Tutorial/chapter_learning.tex:284: Warning: Undefined label: 'sec:LogisticRegression' ./Tutorial/chapter_learning.tex:288: Warning: Undefined label: 'table:training' ./Tutorial/chapter_learning.tex:296: Warning: Undefined label: 'subsec: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:SeqRecord' ./Tutorial/chapter_graphics.tex:36: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:61: 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./Tutorial/chapter_graphics.tex:384: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:464: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:464: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:467: Warning: Undefined label: 'sec:gd_top_down' ./Tutorial/chapter_graphics.tex:557: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:557: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:562: Warning: Undefined citation: 'proux2002' ./Tutorial/chapter_graphics.tex:571: Warning: Undefined label: 'sec:efetch' ./Tutorial/chapter_graphics.tex:574: Warning: Undefined label: 'sec:SeqRecord-slicing' ./Tutorial/chapter_graphics.tex:576: Warning: Undefined label: 'sec:SeqRecord-reverse-complement' ./Tutorial/chapter_graphics.tex:671: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:671: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:678: Warning: Undefined citation: 'proux2002' ./Tutorial/chapter_graphics.tex:919: Warning: Undefined citation: 'jupe2012' ./Tutorial/chapter_phenotype.tex:229: Warning: Optional argument to \item in itemize environment ./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_cookbook.tex:22: Warning: Undefined label: 'chapter:Bio.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:192: Warning: Undefined label: 'sec:translation' ./Tutorial/chapter_cookbook.tex:197: Warning: Undefined label: 'sec:SeqIO-reverse-complement' ./Tutorial/chapter_cookbook.tex:317: Warning: Undefined label: 'sec:seqio-index-getraw' ./Tutorial/chapter_cookbook.tex:415: Warning: Undefined label: 'sec:low-level-fasta-fastq' ./Tutorial/chapter_cookbook.tex:429: Warning: Undefined label: 'sec:low-level-fasta-fastq' ./Tutorial/chapter_cookbook.tex:449: Warning: Undefined label: 'sec:SeqRecord-slicing' ./Tutorial/chapter_cookbook.tex:597: Warning: Undefined label: 'sec:SeqIO-conversion' ./Tutorial/chapter_cookbook.tex:600: Warning: Undefined citation: 'cock2010' ./Tutorial/chapter_cookbook.tex:750: Warning: Undefined label: 'sec:SeqIO-index' ./Tutorial/chapter_cookbook.tex:772: Warning: Undefined label: 'sec:SeqIO-index' ./Tutorial/chapter_cookbook.tex:774: Warning: Undefined label: 'sec:SeqIO-sort' ./Tutorial/chapter_cookbook.tex:788: Warning: Undefined label: 'sec:SeqIO-conversion' ./Tutorial/chapter_cookbook.tex:855: Warning: Undefined label: 'sec:translation' ./Tutorial/chapter_cookbook.tex:967: Warning: Undefined label: 'sec:gd_nice_example' ./Tutorial/chapter_cookbook.tex:984: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_cookbook.tex:1343: Warning: Undefined label: 'chapter:Bio.AlignIO' ./Tutorial/chapter_cookbook.tex:1346: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1350: Warning: Undefined label: 'chapter:Bio.AlignIO' ./Tutorial/chapter_cookbook.tex:1360: Warning: Undefined label: 'sec:consensus' ./Tutorial/chapter_cookbook.tex:1361: Warning: Undefined label: 'sec:pssm' ./Tutorial/chapter_cookbook.tex:1362: Warning: Undefined label: 'sec:getting_info_content' ./Tutorial/chapter_cookbook.tex:1363: Warning: Undefined label: 'sec:sub_matrix' ./Tutorial/chapter_cookbook.tex:1369: Warning: Undefined label: 'sec:summary_info' ./Tutorial/chapter_cookbook.tex:1470: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1470: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1497: Warning: Undefined label: 'sec:summary_info' ./Tutorial/chapter_cookbook.tex:1516: Warning: Undefined label: 'sec:freq_table' ./Tutorial/chapter_cookbook.tex:1570: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1579: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1579: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1603: Warning: Undefined label: 'sec:align_clustal' ./Tutorial/chapter_cookbook.tex:1603: Warning: Undefined label: 'sec:summary_info' ./Tutorial/chapter_cookbook.tex:1701: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_testing.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_testing.tex:49: Warning: Undefined label: 'section:doctest' ./Tutorial/chapter_testing.tex:409: Warning: Undefined label: 'section:doctest' ./Tutorial/chapter_advanced.tex:163: Warning: Undefined label: 'sec:freq_table' ./Tutorial/chapter_advanced.tex:223: Warning: '_' occurring outside math mode ./Tutorial/chapter_contributing.tex:31: Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_contributing.tex:37: Warning: '_' occurring outside math mode ./Tutorial/chapter_contributing.tex:84: Warning: Undefined label: 'sec:regr_test' ./Tutorial/chapter_contributing.tex:100: Warning: Undefined label: 'sec:regr_test' ./Tutorial/chapter_appendix.tex:88: 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_seq_annot.tex:282: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:280: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:362: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:374: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:374: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:454: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:454: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:454: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode ./Tutorial/chapter_align.tex:884: Warning: '_' occurring outside math mode ./Tutorial/chapter_blast.tex:268: Warning: Undefined label: 'sec:parsing-blast-deprecated' ./Tutorial/chapter_entrez.tex:1035: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1038: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1126: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1126: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:345: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:769: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:974: 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:203: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:203: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:203: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:254: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:254: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:301: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:301: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:327: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:384: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:384: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:464: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:464: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:557: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:557: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:671: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:671: Warning: '_' occurring outside math mode ./Tutorial/chapter_phenotype.tex:229: Warning: Optional argument to \item in itemize environment ./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_cookbook.tex:1346: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1470: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1470: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1570: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1579: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1579: Warning: '_' occurring outside math mode ./Tutorial/chapter_testing.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_advanced.tex:223: Warning: '_' occurring outside math mode ./Tutorial/chapter_contributing.tex:37: Warning: '_' occurring outside math mode HeVeA Warning: Label(s) may have changed. Rerun me to get cross-references right. Run, run, again... 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occurring outside math mode ./Tutorial/chapter_graphics.tex:301: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:301: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:327: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:384: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:384: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:464: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:464: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:557: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:557: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:671: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:671: Warning: '_' occurring outside math mode ./Tutorial/chapter_phenotype.tex:229: Warning: Optional argument to \item in itemize environment 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math mode ./Tutorial/chapter_contributing.tex:10: Warning: '_' occurring outside math mode ./Tutorial/chapter_contributing.tex:37: Warning: '_' occurring outside math mode ./Tutorial/chapter_contributing.tex:79: Warning: '_' occurring outside math mode ./Tutorial.tex:122: Warning: line too long ./Tutorial.tex:133: Warning: Application of '\'' on 'e' failed ./Tutorial.tex:133: Warning: Application of '\'' on 'o' failed ./Tutorial.tex:137: Warning: Application of '\"' on 'u' failed ./Tutorial.tex:202: Warning: Application of '\"' on 'o' failed ./Tutorial.tex:202: 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:68: Warning: tt_mode is an empty style ./Tutorial.haux:527: Giving up command: \@hevea@cbrace ./Tutorial.tex:68: Giving up command: \input ./Tutorial.tex:68: Warning: Failure while reading .haux ./Tutorial.tex:95: Warning: Application of '\'' on 'n' failed ./Tutorial/chapter_introduction.tex:110: Warning: Undefined citation: 'cock2009' ./Tutorial/chapter_introduction.tex:114: Warning: Undefined citation: 'chapman2000' ./Tutorial/chapter_introduction.tex:115: Warning: Undefined citation: 'hamelryck2003a' ./Tutorial/chapter_introduction.tex:116: Warning: Undefined citation: 'dehoon2004' ./Tutorial/chapter_introduction.tex:117: Warning: Undefined citation: 'pritchard2006' ./Tutorial/chapter_introduction.tex:118: Warning: Undefined citation: 'talevich2012' ./Tutorial/chapter_introduction.tex:119: Warning: Undefined citation: 'cock2010' ./Tutorial/chapter_introduction.tex:237: Warning: Undefined label: 'sec:seq-comparison' ./Tutorial/chapter_introduction.tex:250: Warning: Undefined label: 'sec:appendix-handles' ./Tutorial/chapter_introduction.tex:292: Warning: Undefined label: 'sec:SeqIO-conversion' ./Tutorial/chapter_introduction.tex:292: Warning: Undefined label: 'sec:converting-alignments' ./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:Bio.Seq' ./Tutorial/chapter_quick_start.tex:35: Warning: Undefined label: 'chapter:Bio.Seq' ./Tutorial/chapter_quick_start.tex:49: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_quick_start.tex:69: Warning: Undefined label: 'sec:sequence-parsing' ./Tutorial/chapter_quick_start.tex:69: Warning: Undefined label: 'chapter:entrez' ./Tutorial/chapter_quick_start.tex:69: Warning: Undefined label: 'chapter:swiss_prot' ./Tutorial/chapter_quick_start.tex:69: Warning: Undefined label: 'sec:align_clustal' ./Tutorial/chapter_quick_start.tex:76: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_quick_start.tex:78: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:78: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:83: Warning: Undefined label: 'sec:connecting-with-biological-databases' ./Tutorial/chapter_quick_start.tex:88: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:123: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:149: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_quick_start.tex:149: Warning: Undefined label: 'chapter:Bio.AlignIO' ./Tutorial/chapter_quick_start.tex:154: Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_quick_start.tex:162: Warning: Undefined label: 'chapter:entrez' ./Tutorial/chapter_quick_start.tex:163: Warning: Undefined label: 'chapter:swiss_prot' ./Tutorial/chapter_quick_start.tex:173: 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:5: Warning: Undefined label: 'chapter:SeqRecord' ./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_objects.tex:137: Warning: Undefined label: 'sec:mutable-seq' ./Tutorial/chapter_seq_objects.tex:207: Warning: Undefined label: 'sec:SeqRecord-format' ./Tutorial/chapter_seq_objects.tex:209: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_objects.tex:376: Warning: Undefined label: 'sec:SeqIO-reverse-complement' ./Tutorial/chapter_seq_objects.tex:394: Warning: Command not found: \downarrow ./Tutorial/chapter_seq_objects.tex:449: Warning: Undefined label: 'sec:seq-module-functions' ./Tutorial/chapter_seq_objects.tex:564: Warning: Undefined label: 'sec:SeqIO-translate' ./Tutorial/chapter_seq_objects.tex:570: Warning: Undefined label: 'sec:seq-module-functions' ./Tutorial/chapter_seq_objects.tex:719: Warning: Undefined label: 'sec:seq-to-string' ./Tutorial/chapter_seq_objects.tex:810: Warning: Undefined label: 'sec:seq-to-string' ./Tutorial/chapter_seq_objects.tex:871: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined label: 'chapter:Bio.Seq' ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:21: Warning: Undefined label: 'chapter:Bio.Seq' ./Tutorial/chapter_seq_annot.tex:21: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:34: Warning: Undefined label: 'sec:FASTQ-filtering-example' ./Tutorial/chapter_seq_annot.tex:38: Warning: Undefined label: 'sec:seq_features' ./Tutorial/chapter_seq_annot.tex:48: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:121: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_annot.tex:131: Warning: Undefined label: 'chapter:quick-start' ./Tutorial/chapter_seq_annot.tex:133: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:140: Warning: line too long ./Tutorial/chapter_seq_annot.tex:158: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:203: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_annot.tex:216: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:222: Warning: line too long ./Tutorial/chapter_seq_annot.tex:229: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:279: Warning: Undefined label: 'sec:seq_features' ./Tutorial/chapter_seq_annot.tex:282: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_annot.tex:288: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:296: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:528: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:534: Warning: line too long ./Tutorial/chapter_seq_annot.tex:543: Warning: line too long ./Tutorial/chapter_seq_annot.tex:632: Warning: Undefined label: 'sec:seq-comparison' ./Tutorial/chapter_seq_annot.tex:640: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:657: Warning: line too long ./Tutorial/chapter_seq_annot.tex:676: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:679: Warning: Undefined label: 'sec:Bio.SeqIO-and-StringIO' ./Tutorial/chapter_seq_annot.tex:699: Warning: line too long ./Tutorial/chapter_seq_annot.tex:758: Warning: line too long ./Tutorial/chapter_seq_annot.tex:833: Warning: Undefined label: 'sec:SeqRecord-format' ./Tutorial/chapter_seq_annot.tex:841: Warning: Undefined label: 'sec:FASTQ-slicing-off-primer' ./Tutorial/chapter_seq_annot.tex:842: Warning: Undefined label: 'sec:FASTQ-slicing-off-adaptor' ./Tutorial/chapter_seq_annot.tex:855: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:926: Warning: line too long ./Tutorial/chapter_seq_annot.tex:956: Warning: line too long ./Tutorial/chapter_seqio.tex:1: Warning: line too long ./Tutorial/chapter_seqio.tex:1: Warning: line too long ./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 label: 'chapter:quick-start' ./Tutorial/chapter_seqio.tex:4: Warning: Undefined label: 'chapter:SeqRecord' ./Tutorial/chapter_seqio.tex:13: Warning: Undefined label: 'chapter:SeqRecord' ./Tutorial/chapter_seqio.tex:13: Warning: Undefined label: 'chapter:Bio.Seq' ./Tutorial/chapter_seqio.tex:15: Warning: Undefined label: 'sec:low-level-fasta-fastq' ./Tutorial/chapter_seqio.tex:23: Warning: 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./Tutorial/chapter_seqio.tex:362: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:374: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:374: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:375: Warning: Undefined label: 'sec:efetch' ./Tutorial/chapter_seqio.tex:451: Warning: Undefined label: 'chapter:entrez' ./Tutorial/chapter_seqio.tex:451: Warning: Undefined label: 'sec:entrez-guidelines' ./Tutorial/chapter_seqio.tex:454: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:454: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:454: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:456: Warning: Undefined label: 'chapter:swiss_prot' ./Tutorial/chapter_seqio.tex:491: Warning: Undefined label: 'SeqIO:to_dict' ./Tutorial/chapter_seqio.tex:497: Warning: Undefined label: 'sec:SeqIO-index' ./Tutorial/chapter_seqio.tex:501: Warning: Undefined label: 'sec:SeqIO-index-db' 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./Tutorial/chapter_blast.tex:124: Warning: Undefined label: 'sec:parsing-blast' ./Tutorial/chapter_blast.tex:146: Warning: Undefined label: 'sec:parsing-blast' ./Tutorial/chapter_blast.tex:155: Warning: Undefined label: 'sec:parsing-blast' ./Tutorial/chapter_blast.tex:164: Warning: Undefined label: 'sec:running-www-blast' ./Tutorial/chapter_blast.tex:188: Warning: '_' occurring outside math mode ./Tutorial/chapter_blast.tex:188: Warning: '_' occurring outside math mode ./Tutorial/chapter_blast.tex:192: Warning: Undefined label: 'sec:alignment-tools' ./Tutorial/chapter_blast.tex:236: Warning: Undefined label: 'sec:parsing-blast' ./Tutorial/chapter_blast.tex:268: Warning: Undefined label: 'sec:parsing-blast-deprecated' ./Tutorial/chapter_blast.tex:282: Warning: Undefined label: 'sec:running-www-blast' ./Tutorial/chapter_blast.tex:284: Warning: Undefined label: 'sec:running-local-blast' ./Tutorial/chapter_blast.tex:335: Warning: Undefined label: 'chapter:Bio.SeqIO' 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outside math mode ./Tutorial/chapter_entrez.tex:1042: Warning: Undefined label: 'sec:orchids' ./Tutorial/chapter_entrez.tex:1083: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1126: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1126: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1128: Warning: Undefined label: 'sec:orchids' ./Tutorial/chapter_entrez.tex:1180: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1215: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1222: Warning: Undefined label: 'sec:SeqIO_GenBank_Online' ./Tutorial/chapter_entrez.tex:1223: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1275: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_entrez.tex:1299: Warning: Undefined label: 'sec:entrez-guidelines' ./Tutorial/chapter_entrez.tex:1300: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1358: Warning: Undefined label: 'sec:entrez-search-fetch-genbank' ./Tutorial/chapter_entrez.tex:1389: Warning: Undefined label: 'subsec:entrez_example_genbank' ./Tutorial/chapter_entrez.tex:1487: Warning: Undefined label: 'subsec:entrez-and-medline' ./Tutorial/chapter_entrez.tex:1492: Warning: Undefined label: 'sec:elink' ./Tutorial/chapter_entrez.tex:1516: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_uniprot.tex:1: Warning: line too long ./Tutorial/chapter_uniprot.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:10: Warning: Undefined label: 'sec:SeqIO_ExPASy_and_SwissProt' ./Tutorial/chapter_uniprot.tex:29: Warning: line too long ./Tutorial/chapter_uniprot.tex:38: Warning: line too long ./Tutorial/chapter_uniprot.tex:41: Warning: Undefined label: 'subsec:expasy_swissprot' ./Tutorial/chapter_uniprot.tex:49: Warning: Undefined label: 'sec:SeqIO_ExPASy_and_SwissProt' ./Tutorial/chapter_uniprot.tex:84: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:84: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:345: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:347: Warning: Undefined label: 'sec:orchids' ./Tutorial/chapter_uniprot.tex:446: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:446: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:495: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:1: Warning: line too long ./Tutorial/chapter_pdb.tex:18: Warning: Undefined label: 'problem structures' ./Tutorial/chapter_pdb.tex:207: Warning: Undefined label: 'fig:smcra' ./Tutorial/chapter_pdb.tex:216: Warning: Undefined label: 'problem structures' ./Tutorial/chapter_pdb.tex:220: Warning: Image in text ./Tutorial/chapter_pdb.tex:353: Warning: Undefined label: 'hetero problems' ./Tutorial/chapter_pdb.tex:398: Warning: Undefined label: 'point mutations' ./Tutorial/chapter_pdb.tex:415: Warning: Undefined label: 'disordered atoms' ./Tutorial/chapter_pdb.tex:540: Warning: Undefined label: 'fig:smcra' ./Tutorial/chapter_pdb.tex:586: Warning: Undefined label: 'fig:smcra' ./Tutorial/chapter_pdb.tex:769: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:870: Warning: Undefined citation: 'golub1989' ./Tutorial/chapter_pdb.tex:898: Warning: Undefined citation: 'hamelryck2005' ./Tutorial/chapter_pdb.tex:933: Warning: Undefined label: 'cap:DSSP-codes' ./Tutorial/chapter_pdb.tex:972: Warning: Undefined label: 'subsec:residue_depth' ./Tutorial/chapter_pdb.tex:974: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:1022: Warning: Undefined citation: 'hamelryck2003a' ./Tutorial/chapter_pdb.tex:1234: Warning: Undefined citation: 'hamelryck2003b' ./Tutorial/chapter_pdb.tex:1235: 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:104: Warning: Image in text ./Tutorial/chapter_phylo.tex:192: Warning: Undefined label: 'fig:phylo-color-draw' ./Tutorial/chapter_phylo.tex:199: Warning: Image in text ./Tutorial/chapter_phylo.tex:345: Warning: line too long ./Tutorial/chapter_phylo.tex:359: Warning: Image in text ./Tutorial/chapter_phylo.tex:376: Warning: Undefined label: 'fig:phylo-dot' ./Tutorial/chapter_phylo.tex:387: Warning: Image in text ./Tutorial/chapter_phylo.tex:412: Warning: Undefined label: 'fig:phylo-rooted' ./Tutorial/chapter_phylo.tex:421: Warning: Image in text ./Tutorial/chapter_phylo.tex:428: Warning: Undefined label: 'fig:phylo-color' ./Tutorial/chapter_phylo.tex:454: Warning: Image in text ./Tutorial/chapter_phylo.tex:471: Warning: Image in text ./Tutorial/chapter_phylo.tex:473: Warning: Image in text ./Tutorial/chapter_phylo.tex:832: Warning: Undefined label: 'sec:alignment-tools' ./Tutorial/chapter_phylo.tex:903: Warning: Undefined label: 'sec:PhyloXML' ./Tutorial/chapter_motifs.tex:1: Warning: line too long ./Tutorial/chapter_motifs.tex:7: Warning: Undefined label: 'sec:links' ./Tutorial/chapter_motifs.tex:152: Warning: Undefined citation: 'cornish1985' ./Tutorial/chapter_motifs.tex:153: Warning: Undefined citation: 'cavener1987' ./Tutorial/chapter_motifs.tex:522: Warning: Undefined citation: 'bailey1994' ./Tutorial/chapter_motifs.tex:530: Warning: line too long ./Tutorial/chapter_motifs.tex:532: Warning: line too long ./Tutorial/chapter_motifs.tex:538: Warning: line too long ./Tutorial/chapter_motifs.tex:540: Warning: line too long ./Tutorial/chapter_motifs.tex:549: Warning: line too long ./Tutorial/chapter_motifs.tex:553: Warning: line too long ./Tutorial/chapter_motifs.tex:555: Warning: line too long ./Tutorial/chapter_motifs.tex:564: Warning: line too long ./Tutorial/chapter_motifs.tex:566: Warning: line too long ./Tutorial/chapter_motifs.tex:567: Warning: 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on 'x' failed ./Tutorial/chapter_cluster.tex:85: Warning: Application of '\=' on 'y' failed ./Tutorial/chapter_cluster.tex:116: Warning: Application of '\=' on 'x' failed ./Tutorial/chapter_cluster.tex:116: Warning: Application of '\=' on 'y' failed ./Tutorial/chapter_cluster.tex:153: Warning: Undefined citation: 'snedecor1989' ./Tutorial/chapter_cluster.tex:182: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:263: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:331: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:546: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:594: Warning: Undefined citation: 'kohonen1997' ./Tutorial/chapter_cluster.tex:594: Warning: Undefined citation: 'tamayo1999' ./Tutorial/chapter_cluster.tex:601: Warning: Cannot output that numerical entity: U+00B7 ./Tutorial/chapter_cluster.tex:605: Warning: Cannot output that numerical entity: U+00B7 ./Tutorial/chapter_cluster.tex:610: Warning: Cannot output that numerical entity: U+00B7 ./Tutorial/chapter_cluster.tex:641: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:654: Warning: Undefined citation: 'yeung2001' ./Tutorial/chapter_cluster.tex:662: Warning: Undefined citation: 'golub1971' ./Tutorial/chapter_cluster.tex:706: Warning: line too long ./Tutorial/chapter_cluster.tex:714: Warning: line too long ./Tutorial/chapter_cluster.tex:750: Warning: overfull line in array : array too wide ./Tutorial/chapter_cluster.tex:750: Warning: line too long ./Tutorial/chapter_cluster.tex:750: Warning: line too long ./Tutorial/chapter_cluster.tex:803: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:806: Warning: Undefined label: 'subsec:distancematrix' ./Tutorial/chapter_cluster.tex:824: Warning: Undefined label: 'subsec:clustercentroids' ./Tutorial/chapter_cluster.tex:847: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:872: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:901: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:923: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:955: Warning: Undefined citation: 'hihara2001' ./Tutorial/chapter_learning.tex:38: Warning: overfull line in array : array too wide ./Tutorial/chapter_learning.tex:38: Warning: overfull line in array : array too wide ./Tutorial/chapter_learning.tex:39: Warning: Undefined label: 'eq:OP' ./Tutorial/chapter_learning.tex:39: Warning: Undefined label: 'eq:NOP' ./Tutorial/chapter_learning.tex:69: Warning: overfull line in array : array too wide ./Tutorial/chapter_learning.tex:69: Warning: line too long ./Tutorial/chapter_learning.tex:69: Warning: line too long ./Tutorial/chapter_learning.tex:69: Warning: line too long ./Tutorial/chapter_learning.tex:74: Warning: Undefined label: 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occurring outside math mode ./Tutorial/chapter_graphics.tex:206: Warning: Undefined label: 'sec:seq_features' ./Tutorial/chapter_graphics.tex:254: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:254: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:300: Warning: Image in text ./Tutorial/chapter_graphics.tex:300: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:300: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:301: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:301: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:320: Warning: Undefined label: 'sec:gd_nice_example' ./Tutorial/chapter_graphics.tex:327: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:371: Warning: Image in text ./Tutorial/chapter_graphics.tex:371: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:384: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:384: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:406: Warning: Image in text ./Tutorial/chapter_graphics.tex:406: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:406: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:406: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:438: Warning: Image in text ./Tutorial/chapter_graphics.tex:438: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:438: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:438: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:464: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:464: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:467: Warning: Undefined label: 'sec:gd_top_down' ./Tutorial/chapter_graphics.tex:530: Warning: Image in text ./Tutorial/chapter_graphics.tex:530: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:530: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:532: Warning: Image in text ./Tutorial/chapter_graphics.tex:532: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:532: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:557: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:557: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:562: Warning: Undefined citation: 'proux2002' ./Tutorial/chapter_graphics.tex:571: Warning: Undefined label: 'sec:efetch' ./Tutorial/chapter_graphics.tex:574: Warning: Undefined label: 'sec:SeqRecord-slicing' ./Tutorial/chapter_graphics.tex:576: Warning: Undefined label: 'sec:SeqRecord-reverse-complement' ./Tutorial/chapter_graphics.tex:647: Warning: Image in text ./Tutorial/chapter_graphics.tex:647: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:647: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:671: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:671: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:678: Warning: Undefined citation: 'proux2002' ./Tutorial/chapter_graphics.tex:762: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:762: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:762: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:762: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:762: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:801: Warning: Image in text ./Tutorial/chapter_graphics.tex:801: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:801: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:828: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:828: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:828: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:828: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:828: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:834: Warning: Image in text ./Tutorial/chapter_graphics.tex:834: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:834: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:919: Warning: Undefined citation: 'jupe2012' ./Tutorial/chapter_graphics.tex:942: Warning: line too long ./Tutorial/chapter_graphics.tex:1012: Warning: Image in text ./Tutorial/chapter_graphics.tex:1012: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:1027: Warning: line too long ./Tutorial/chapter_graphics.tex:1089: Warning: Image in text ./Tutorial/chapter_graphics.tex:1089: 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_phenotype.tex:10: Warning: '_' occurring outside math mode ./Tutorial/chapter_phenotype.tex:16: Warning: '_' occurring outside math mode ./Tutorial/chapter_phenotype.tex:32: Warning: '_' occurring outside math mode ./Tutorial/chapter_phenotype.tex:229: Warning: Optional argument to \item in itemize environment ./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_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 label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_cookbook.tex:58: Warning: Undefined label: 'sec:low-level-fasta-fastq' ./Tutorial/chapter_cookbook.tex:103: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:146: Warning: Undefined label: 'sec:Bio.SeqIO-and-StringIO' ./Tutorial/chapter_cookbook.tex:192: Warning: Undefined label: 'sec:translation' ./Tutorial/chapter_cookbook.tex:197: Warning: Undefined label: 'sec:SeqIO-reverse-complement' ./Tutorial/chapter_cookbook.tex:317: Warning: Undefined label: 'sec:seqio-index-getraw' ./Tutorial/chapter_cookbook.tex:415: Warning: Undefined label: 'sec:low-level-fasta-fastq' ./Tutorial/chapter_cookbook.tex:424: Warning: line too long ./Tutorial/chapter_cookbook.tex:429: Warning: Undefined label: 'sec:low-level-fasta-fastq' ./Tutorial/chapter_cookbook.tex:449: Warning: Undefined label: 'sec:SeqRecord-slicing' ./Tutorial/chapter_cookbook.tex:519: Warning: line too long ./Tutorial/chapter_cookbook.tex:597: Warning: Undefined label: 'sec:SeqIO-conversion' ./Tutorial/chapter_cookbook.tex:600: Warning: Undefined citation: 'cock2010' ./Tutorial/chapter_cookbook.tex:750: Warning: Undefined label: 'sec:SeqIO-index' ./Tutorial/chapter_cookbook.tex:753: Warning: line too long ./Tutorial/chapter_cookbook.tex:772: Warning: Undefined label: 'sec:SeqIO-index' ./Tutorial/chapter_cookbook.tex:774: Warning: Undefined label: 'sec:SeqIO-sort' ./Tutorial/chapter_cookbook.tex:788: Warning: Undefined label: 'sec:SeqIO-conversion' ./Tutorial/chapter_cookbook.tex:854: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:855: Warning: Undefined label: 'sec:translation' ./Tutorial/chapter_cookbook.tex:967: Warning: Undefined label: 'sec:gd_nice_example' ./Tutorial/chapter_cookbook.tex:984: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_cookbook.tex:996: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1034: Warning: Image in text ./Tutorial/chapter_cookbook.tex:1034: Warning: '_' occurring outside math mode 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mode ./Tutorial/chapter_cookbook.tex:1350: Warning: Undefined label: 'chapter:Bio.AlignIO' ./Tutorial/chapter_cookbook.tex:1360: Warning: Undefined label: 'sec:consensus' ./Tutorial/chapter_cookbook.tex:1361: Warning: Undefined label: 'sec:pssm' ./Tutorial/chapter_cookbook.tex:1362: Warning: Undefined label: 'sec:getting_info_content' ./Tutorial/chapter_cookbook.tex:1363: Warning: Undefined label: 'sec:sub_matrix' ./Tutorial/chapter_cookbook.tex:1369: Warning: Undefined label: 'sec:summary_info' ./Tutorial/chapter_cookbook.tex:1470: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1470: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1497: Warning: Undefined label: 'sec:summary_info' ./Tutorial/chapter_cookbook.tex:1516: Warning: Undefined label: 'sec:freq_table' ./Tutorial/chapter_cookbook.tex:1570: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1579: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1579: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1603: Warning: Undefined label: 'sec:align_clustal' ./Tutorial/chapter_cookbook.tex:1603: Warning: Undefined label: 'sec:summary_info' ./Tutorial/chapter_cookbook.tex:1696: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1701: Warning: Undefined label: 'chapter:Bio.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:1: Warning: line too long ./Tutorial/chapter_testing.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_testing.tex:49: Warning: Undefined label: 'section:doctest' ./Tutorial/chapter_testing.tex:349: 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./Tutorial/chapter_contributing.tex:79: Warning: '_' occurring outside math mode ./Tutorial/chapter_contributing.tex:84: Warning: Undefined label: 'sec:regr_test' ./Tutorial/chapter_contributing.tex:100: Warning: Undefined label: 'sec:regr_test' ./Tutorial/chapter_appendix.tex:88: Warning: Undefined label: 'sec:SeqIO_compressed' ./Tutorial.tex:122: Warning: line too long ./Tutorial.tex:133: Warning: Application of '\'' on 'e' failed ./Tutorial.tex:133: Warning: Application of '\'' on 'o' failed ./Tutorial.tex:137: Warning: Application of '\"' on 'u' failed ./Tutorial.tex:202: Warning: Application of '\"' on 'o' failed ./Tutorial.tex:202: 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:68: Warning: tt_mode is an empty style ./Tutorial.haux:527: Giving up command: \@hevea@cbrace ./Tutorial.tex:68: Giving up command: \input ./Tutorial.tex:68: Warning: Failure while reading .haux ./Tutorial.tex:95: Warning: Application of '\'' on 'n' failed ./Tutorial/chapter_introduction.tex:110: Warning: Undefined citation: 'cock2009' ./Tutorial/chapter_introduction.tex:114: Warning: Undefined citation: 'chapman2000' ./Tutorial/chapter_introduction.tex:115: Warning: Undefined citation: 'hamelryck2003a' ./Tutorial/chapter_introduction.tex:116: Warning: Undefined citation: 'dehoon2004' ./Tutorial/chapter_introduction.tex:117: Warning: Undefined citation: 'pritchard2006' ./Tutorial/chapter_introduction.tex:118: Warning: Undefined citation: 'talevich2012' ./Tutorial/chapter_introduction.tex:119: Warning: Undefined citation: 'cock2010' ./Tutorial/chapter_introduction.tex:237: Warning: Undefined label: 'sec:seq-comparison' ./Tutorial/chapter_introduction.tex:250: Warning: Undefined label: 'sec:appendix-handles' ./Tutorial/chapter_introduction.tex:292: Warning: Undefined label: 'sec:SeqIO-conversion' ./Tutorial/chapter_introduction.tex:292: Warning: Undefined label: 'sec:converting-alignments' ./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:Bio.Seq' ./Tutorial/chapter_quick_start.tex:35: Warning: Undefined label: 'chapter:Bio.Seq' ./Tutorial/chapter_quick_start.tex:49: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_quick_start.tex:69: Warning: Undefined label: 'sec:sequence-parsing' ./Tutorial/chapter_quick_start.tex:69: Warning: Undefined label: 'chapter:entrez' ./Tutorial/chapter_quick_start.tex:69: Warning: Undefined label: 'chapter:swiss_prot' ./Tutorial/chapter_quick_start.tex:69: Warning: Undefined label: 'sec:align_clustal' ./Tutorial/chapter_quick_start.tex:76: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_quick_start.tex:78: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:78: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:83: Warning: Undefined label: 'sec:connecting-with-biological-databases' ./Tutorial/chapter_quick_start.tex:88: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:123: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:149: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_quick_start.tex:149: Warning: Undefined label: 'chapter:Bio.AlignIO' ./Tutorial/chapter_quick_start.tex:154: Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_quick_start.tex:162: Warning: Undefined label: 'chapter:entrez' ./Tutorial/chapter_quick_start.tex:163: Warning: Undefined label: 'chapter:swiss_prot' ./Tutorial/chapter_quick_start.tex:173: 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:5: Warning: Undefined label: 'chapter:SeqRecord' ./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_objects.tex:137: Warning: Undefined label: 'sec:mutable-seq' ./Tutorial/chapter_seq_objects.tex:207: Warning: Undefined label: 'sec:SeqRecord-format' ./Tutorial/chapter_seq_objects.tex:209: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_objects.tex:376: Warning: Undefined label: 'sec:SeqIO-reverse-complement' ./Tutorial/chapter_seq_objects.tex:394: Warning: Command not found: \downarrow ./Tutorial/chapter_seq_objects.tex:449: Warning: Undefined label: 'sec:seq-module-functions' ./Tutorial/chapter_seq_objects.tex:564: Warning: Undefined label: 'sec:SeqIO-translate' ./Tutorial/chapter_seq_objects.tex:570: Warning: Undefined label: 'sec:seq-module-functions' ./Tutorial/chapter_seq_objects.tex:719: Warning: Undefined label: 'sec:seq-to-string' ./Tutorial/chapter_seq_objects.tex:810: Warning: Undefined label: 'sec:seq-to-string' ./Tutorial/chapter_seq_objects.tex:871: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined label: 'chapter:Bio.Seq' ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:21: Warning: Undefined label: 'chapter:Bio.Seq' ./Tutorial/chapter_seq_annot.tex:21: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:34: Warning: Undefined label: 'sec:FASTQ-filtering-example' ./Tutorial/chapter_seq_annot.tex:38: Warning: Undefined label: 'sec:seq_features' ./Tutorial/chapter_seq_annot.tex:48: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:121: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_annot.tex:131: Warning: Undefined label: 'chapter:quick-start' ./Tutorial/chapter_seq_annot.tex:133: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:140: Warning: line too long ./Tutorial/chapter_seq_annot.tex:158: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:203: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_annot.tex:216: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:222: Warning: line too long ./Tutorial/chapter_seq_annot.tex:229: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:279: Warning: Undefined label: 'sec:seq_features' ./Tutorial/chapter_seq_annot.tex:282: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_annot.tex:288: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:296: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:528: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:534: Warning: line too long ./Tutorial/chapter_seq_annot.tex:543: Warning: line too long ./Tutorial/chapter_seq_annot.tex:632: Warning: Undefined label: 'sec:seq-comparison' ./Tutorial/chapter_seq_annot.tex:640: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:657: Warning: line too long ./Tutorial/chapter_seq_annot.tex:676: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:679: Warning: Undefined label: 'sec:Bio.SeqIO-and-StringIO' ./Tutorial/chapter_seq_annot.tex:699: Warning: line too long ./Tutorial/chapter_seq_annot.tex:758: Warning: line too long ./Tutorial/chapter_seq_annot.tex:833: Warning: Undefined label: 'sec:SeqRecord-format' ./Tutorial/chapter_seq_annot.tex:841: Warning: Undefined label: 'sec:FASTQ-slicing-off-primer' ./Tutorial/chapter_seq_annot.tex:842: Warning: Undefined label: 'sec:FASTQ-slicing-off-adaptor' ./Tutorial/chapter_seq_annot.tex:855: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:926: Warning: line too long ./Tutorial/chapter_seq_annot.tex:956: Warning: line too long ./Tutorial/chapter_seqio.tex:1: Warning: line too long ./Tutorial/chapter_seqio.tex:1: Warning: line too long ./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 label: 'chapter:quick-start' ./Tutorial/chapter_seqio.tex:4: Warning: Undefined label: 'chapter:SeqRecord' ./Tutorial/chapter_seqio.tex:13: Warning: Undefined label: 'chapter:SeqRecord' ./Tutorial/chapter_seqio.tex:13: Warning: Undefined label: 'chapter:Bio.Seq' ./Tutorial/chapter_seqio.tex:15: Warning: Undefined label: 'sec:low-level-fasta-fastq' ./Tutorial/chapter_seqio.tex:23: Warning: Undefined label: 'sec:SeqIO_Online' ./Tutorial/chapter_seqio.tex:23: Warning: Undefined label: 'sec:appendix-handles' ./Tutorial/chapter_seqio.tex:45: Warning: Undefined label: 'sec:sequence-parsing' ./Tutorial/chapter_seqio.tex:45: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:45: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:69: Warning: Undefined label: 'seq:sequence-parsing-plus-pylab' ./Tutorial/chapter_seqio.tex:148: Warning: Undefined label: 'chapter:SeqRecord' ./Tutorial/chapter_seqio.tex:148: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:195: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:241: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:280: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:283: Warning: Undefined label: 'sec:appendix-handles' ./Tutorial/chapter_seqio.tex:359: Warning: Undefined label: 'sec:SeqIO-index-bgzf' ./Tutorial/chapter_seqio.tex:362: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:374: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:374: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:375: Warning: Undefined label: 'sec:efetch' ./Tutorial/chapter_seqio.tex:451: Warning: Undefined label: 'chapter:entrez' ./Tutorial/chapter_seqio.tex:451: Warning: Undefined label: 'sec:entrez-guidelines' ./Tutorial/chapter_seqio.tex:454: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:454: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:454: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:456: Warning: Undefined label: 'chapter:swiss_prot' ./Tutorial/chapter_seqio.tex:491: Warning: Undefined label: 'SeqIO:to_dict' ./Tutorial/chapter_seqio.tex:497: Warning: Undefined label: 'sec:SeqIO-index' ./Tutorial/chapter_seqio.tex:501: Warning: Undefined label: 'sec:SeqIO-index-db' ./Tutorial/chapter_seqio.tex:504: Warning: Undefined label: 'sec:SeqIO-indexing-discussion' ./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:514: Warning: Undefined label: 'sec:SeqIO-index' ./Tutorial/chapter_seqio.tex:588: Warning: Undefined label: 'sec:fasta-parsing' ./Tutorial/chapter_seqio.tex:704: Warning: Undefined label: 'sec:fastq-indexing' ./Tutorial/chapter_seqio.tex:725: Warning: Undefined label: 'seq:seqio-todict-functionkey' ./Tutorial/chapter_seqio.tex:771: Warning: line too long ./Tutorial/chapter_seqio.tex:787: Warning: Undefined label: 'sec:SeqIO-sort' ./Tutorial/chapter_seqio.tex:869: Warning: Undefined label: 'sec:seqio-index-getraw' ./Tutorial/chapter_seqio.tex:1009: Warning: line too long ./Tutorial/chapter_seqio.tex:1016: Warning: line too long ./Tutorial/chapter_seqio.tex:1021: Warning: line too long ./Tutorial/chapter_seqio.tex:1097: Warning: Undefined label: 'sec:seqio-index-getraw' ./Tutorial/chapter_seqio.tex:1106: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:1139: Warning: Undefined label: 'sec:SeqIO-fastq-conversion' ./Tutorial/chapter_seqio.tex:1139: Warning: Undefined label: 'sec:SeqIO-fasta-qual-conversion' ./Tutorial/chapter_seqio.tex:1154: Warning: Undefined label: 'sec:seq-reverse-complement' ./Tutorial/chapter_seqio.tex:1164: Warning: Undefined label: 'sec:SeqRecord-reverse-complement' ./Tutorial/chapter_seqio.tex:1205: Warning: Undefined label: 'sec:SeqIO-translate' ./Tutorial/chapter_seqio.tex:1224: Warning: Undefined label: 'sec:SeqRecord-format' ./Tutorial/chapter_seqio.tex:1303: 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:31: Warning: Undefined label: 'sec:appendix-handles' ./Tutorial/chapter_align.tex:35: Warning: Undefined label: 'sec:AlignIO-count-argument' ./Tutorial/chapter_align.tex:115: Warning: Undefined label: 'sec:alignment-format-method' ./Tutorial/chapter_align.tex:445: Warning: Undefined label: 'sec:SeqIO-conversion' ./Tutorial/chapter_align.tex:617: Warning: Undefined label: 'sec:SeqRecord-format' ./Tutorial/chapter_align.tex:792: Warning: Undefined label: 'sec:SeqRecord-addition' ./Tutorial/chapter_align.tex:844: Warning: Undefined label: 'sec:pairwise2' ./Tutorial/chapter_align.tex:849: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_align.tex:876: Warning: Undefined label: 'seq:emboss-needle-water' ./Tutorial/chapter_align.tex:884: Warning: '_' occurring outside math mode ./Tutorial/chapter_align.tex:1023: Warning: Undefined label: 'sec:Phylo' ./Tutorial/chapter_align.tex:1245: Warning: Undefined label: 'sec:appendix-handles' ./Tutorial/chapter_align.tex:1458: Warning: line too long ./Tutorial/chapter_align.tex:1459: Warning: line too long ./Tutorial/chapter_align.tex:1460: Warning: line too long ./Tutorial/chapter_align.tex:1550: Warning: Undefined citation: 'durbin1998' ./Tutorial/chapter_align.tex:1562: Warning: Undefined label: 'sec:pairwise-aligner' ./Tutorial/chapter_align.tex:1644: Warning: Undefined label: 'sec:pairwise-matchscores' ./Tutorial/chapter_align.tex:1644: Warning: Undefined label: 'sec:pairwise-affine-gapscores' ./Tutorial/chapter_align.tex:1644: Warning: Undefined label: 'sec:pairwise-general-gapscores' ./Tutorial/chapter_align.tex:1645: Warning: Undefined label: 'sec:pairwise-basic' ./Tutorial/chapter_align.tex:1648: Warning: Undefined label: 'sec:pairwise-affine-gapscores' ./Tutorial/chapter_align.tex:1649: Warning: Undefined label: 'sec:pairwise-general-gapscores' ./Tutorial/chapter_align.tex:1812: Warning: overfull line in array : array too wide ./Tutorial/chapter_align.tex:1812: Warning: line too long ./Tutorial/chapter_align.tex:1812: Warning: line too long ./Tutorial/chapter_align.tex:1855: Warning: Undefined label: 'sec:pairwise-examples' ./Tutorial/chapter_align.tex:1982: Warning: Undefined citation: 'kent2002' ./Tutorial/chapter_align.tex:1986: Warning: line too long ./Tutorial/chapter_align.tex:2035: Warning: line too long ./Tutorial/chapter_align.tex:2036: Warning: line too long ./Tutorial/chapter_align.tex:2037: Warning: line too long ./Tutorial/chapter_align.tex:2070: Warning: line too long ./Tutorial/chapter_align.tex:2072: Warning: line too long ./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:58: Warning: Undefined label: 'sec:parsing-blast' ./Tutorial/chapter_blast.tex:119: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_blast.tex:124: Warning: Undefined label: 'sec:parsing-blast' ./Tutorial/chapter_blast.tex:146: Warning: Undefined label: 'sec:parsing-blast' ./Tutorial/chapter_blast.tex:155: Warning: Undefined label: 'sec:parsing-blast' ./Tutorial/chapter_blast.tex:164: Warning: Undefined label: 'sec:running-www-blast' ./Tutorial/chapter_blast.tex:188: Warning: '_' occurring outside math mode ./Tutorial/chapter_blast.tex:188: Warning: '_' occurring outside math mode ./Tutorial/chapter_blast.tex:192: Warning: Undefined label: 'sec:alignment-tools' ./Tutorial/chapter_blast.tex:236: Warning: Undefined label: 'sec:parsing-blast' ./Tutorial/chapter_blast.tex:268: Warning: Undefined label: 'sec:parsing-blast-deprecated' ./Tutorial/chapter_blast.tex:282: Warning: Undefined label: 'sec:running-www-blast' ./Tutorial/chapter_blast.tex:284: Warning: Undefined label: 'sec:running-local-blast' ./Tutorial/chapter_blast.tex:335: Warning: Undefined label: 'chapter:Bio.SeqIO' 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./Tutorial/chapter_entrez.tex:1358: Warning: Undefined label: 'sec:entrez-search-fetch-genbank' ./Tutorial/chapter_entrez.tex:1389: Warning: Undefined label: 'subsec:entrez_example_genbank' ./Tutorial/chapter_entrez.tex:1487: Warning: Undefined label: 'subsec:entrez-and-medline' ./Tutorial/chapter_entrez.tex:1492: Warning: Undefined label: 'sec:elink' ./Tutorial/chapter_entrez.tex:1516: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_uniprot.tex:1: Warning: line too long ./Tutorial/chapter_uniprot.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:10: Warning: Undefined label: 'sec:SeqIO_ExPASy_and_SwissProt' ./Tutorial/chapter_uniprot.tex:29: Warning: line too long ./Tutorial/chapter_uniprot.tex:38: Warning: line too long ./Tutorial/chapter_uniprot.tex:41: Warning: Undefined label: 'subsec:expasy_swissprot' ./Tutorial/chapter_uniprot.tex:49: Warning: Undefined label: 'sec:SeqIO_ExPASy_and_SwissProt' ./Tutorial/chapter_uniprot.tex:84: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:84: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:345: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:347: Warning: Undefined label: 'sec:orchids' ./Tutorial/chapter_uniprot.tex:446: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:446: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:495: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:1: Warning: line too long ./Tutorial/chapter_pdb.tex:18: Warning: Undefined label: 'problem structures' ./Tutorial/chapter_pdb.tex:207: Warning: Undefined label: 'fig:smcra' ./Tutorial/chapter_pdb.tex:216: Warning: Undefined label: 'problem structures' ./Tutorial/chapter_pdb.tex:220: Warning: Image in text ./Tutorial/chapter_pdb.tex:353: Warning: Undefined label: 'hetero problems' ./Tutorial/chapter_pdb.tex:398: Warning: Undefined label: 'point mutations' ./Tutorial/chapter_pdb.tex:415: Warning: Undefined label: 'disordered atoms' ./Tutorial/chapter_pdb.tex:540: Warning: Undefined label: 'fig:smcra' ./Tutorial/chapter_pdb.tex:586: Warning: Undefined label: 'fig:smcra' ./Tutorial/chapter_pdb.tex:769: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:870: Warning: Undefined citation: 'golub1989' ./Tutorial/chapter_pdb.tex:898: Warning: Undefined citation: 'hamelryck2005' ./Tutorial/chapter_pdb.tex:933: Warning: Undefined label: 'cap:DSSP-codes' ./Tutorial/chapter_pdb.tex:972: Warning: Undefined label: 'subsec:residue_depth' ./Tutorial/chapter_pdb.tex:974: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:1022: Warning: Undefined citation: 'hamelryck2003a' ./Tutorial/chapter_pdb.tex:1234: Warning: Undefined citation: 'hamelryck2003b' ./Tutorial/chapter_pdb.tex:1235: 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:104: Warning: Image in text ./Tutorial/chapter_phylo.tex:192: Warning: Undefined label: 'fig:phylo-color-draw' ./Tutorial/chapter_phylo.tex:199: Warning: Image in text ./Tutorial/chapter_phylo.tex:345: Warning: line too long ./Tutorial/chapter_phylo.tex:359: Warning: Image in text ./Tutorial/chapter_phylo.tex:376: Warning: Undefined label: 'fig:phylo-dot' ./Tutorial/chapter_phylo.tex:387: Warning: Image in text ./Tutorial/chapter_phylo.tex:412: Warning: Undefined label: 'fig:phylo-rooted' ./Tutorial/chapter_phylo.tex:421: Warning: Image in text ./Tutorial/chapter_phylo.tex:428: Warning: Undefined label: 'fig:phylo-color' ./Tutorial/chapter_phylo.tex:454: Warning: Image in text ./Tutorial/chapter_phylo.tex:471: Warning: Image in text ./Tutorial/chapter_phylo.tex:473: Warning: Image in text ./Tutorial/chapter_phylo.tex:832: Warning: Undefined label: 'sec:alignment-tools' ./Tutorial/chapter_phylo.tex:903: Warning: Undefined label: 'sec:PhyloXML' ./Tutorial/chapter_motifs.tex:1: Warning: line too long ./Tutorial/chapter_motifs.tex:7: Warning: Undefined label: 'sec:links' ./Tutorial/chapter_motifs.tex:152: Warning: Undefined citation: 'cornish1985' ./Tutorial/chapter_motifs.tex:153: Warning: Undefined citation: 'cavener1987' ./Tutorial/chapter_motifs.tex:522: Warning: Undefined citation: 'bailey1994' ./Tutorial/chapter_motifs.tex:530: Warning: line too long ./Tutorial/chapter_motifs.tex:532: Warning: line too long ./Tutorial/chapter_motifs.tex:538: Warning: line too long ./Tutorial/chapter_motifs.tex:540: Warning: line too long ./Tutorial/chapter_motifs.tex:549: Warning: line too long ./Tutorial/chapter_motifs.tex:553: Warning: line too long ./Tutorial/chapter_motifs.tex:555: Warning: line too long ./Tutorial/chapter_motifs.tex:564: Warning: line too long ./Tutorial/chapter_motifs.tex:566: Warning: line too long ./Tutorial/chapter_motifs.tex:567: Warning: line too long ./Tutorial/chapter_motifs.tex:569: Warning: line too long ./Tutorial/chapter_motifs.tex:658: Warning: Undefined citation: 'matys2003' ./Tutorial/chapter_motifs.tex:733: Warning: Undefined label: 'table:transfaccodes' ./Tutorial/chapter_motifs.tex:1496: Warning: '_' occurring outside math mode ./Tutorial/chapter_motifs.tex:1497: Warning: '_' occurring outside math mode ./Tutorial/chapter_motifs.tex:1497: Warning: '_' occurring outside math mode ./Tutorial/chapter_motifs.tex:1498: Warning: '_' occurring outside math mode ./Tutorial/chapter_cluster.tex:5: Warning: Undefined citation: 'dehoon2004' ./Tutorial/chapter_cluster.tex:29: Warning: Undefined citation: 'lecuyer1988' ./Tutorial/chapter_cluster.tex:29: Warning: Undefined citation: 'kachitvichyanukul1988' ./Tutorial/chapter_cluster.tex:83: Warning: Application of '\=' on 'x' failed ./Tutorial/chapter_cluster.tex:83: Warning: Application of '\=' on 'y' failed ./Tutorial/chapter_cluster.tex:85: Warning: Application of '\=' on 'x' failed ./Tutorial/chapter_cluster.tex:85: Warning: Application of '\=' on 'y' failed ./Tutorial/chapter_cluster.tex:116: Warning: Application of '\=' on 'x' failed ./Tutorial/chapter_cluster.tex:116: Warning: Application of '\=' on 'y' failed ./Tutorial/chapter_cluster.tex:153: Warning: Undefined citation: 'snedecor1989' ./Tutorial/chapter_cluster.tex:182: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:263: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:331: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:546: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:594: Warning: Undefined citation: 'kohonen1997' ./Tutorial/chapter_cluster.tex:594: Warning: Undefined citation: 'tamayo1999' ./Tutorial/chapter_cluster.tex:601: Warning: Cannot output that numerical entity: U+00B7 ./Tutorial/chapter_cluster.tex:605: Warning: Cannot output that numerical entity: U+00B7 ./Tutorial/chapter_cluster.tex:610: Warning: Cannot output that numerical entity: U+00B7 ./Tutorial/chapter_cluster.tex:641: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:654: Warning: Undefined citation: 'yeung2001' ./Tutorial/chapter_cluster.tex:662: Warning: Undefined citation: 'golub1971' ./Tutorial/chapter_cluster.tex:706: Warning: line too long ./Tutorial/chapter_cluster.tex:714: Warning: line too long ./Tutorial/chapter_cluster.tex:750: Warning: overfull line in array : array too wide ./Tutorial/chapter_cluster.tex:750: Warning: line too long ./Tutorial/chapter_cluster.tex:750: Warning: line too long ./Tutorial/chapter_cluster.tex:803: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:806: Warning: Undefined label: 'subsec:distancematrix' ./Tutorial/chapter_cluster.tex:824: Warning: Undefined label: 'subsec:clustercentroids' ./Tutorial/chapter_cluster.tex:847: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:872: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:901: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:923: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:955: Warning: Undefined citation: 'hihara2001' ./Tutorial/chapter_learning.tex:38: Warning: overfull line in array : array too wide ./Tutorial/chapter_learning.tex:38: Warning: overfull line in array : array too wide ./Tutorial/chapter_learning.tex:39: Warning: Undefined label: 'eq:OP' ./Tutorial/chapter_learning.tex:39: Warning: Undefined label: 'eq:NOP' ./Tutorial/chapter_learning.tex:69: Warning: overfull line in array : array too wide ./Tutorial/chapter_learning.tex:69: Warning: line too long ./Tutorial/chapter_learning.tex:69: Warning: line too long ./Tutorial/chapter_learning.tex:69: Warning: line too long ./Tutorial/chapter_learning.tex:74: Warning: Undefined label: 'table:training' ./Tutorial/chapter_learning.tex:210: Warning: Undefined label: 'eq:OP' ./Tutorial/chapter_learning.tex:210: Warning: Undefined label: 'eq:NOP' ./Tutorial/chapter_learning.tex:272: Warning: Undefined label: 'eq:OP' ./Tutorial/chapter_learning.tex:272: Warning: Undefined label: 'eq:NOP' ./Tutorial/chapter_learning.tex:274: Warning: Undefined label: 'eq:OP' ./Tutorial/chapter_learning.tex:274: Warning: Undefined label: 'eq:NOP' ./Tutorial/chapter_learning.tex:284: Warning: Undefined label: 'sec:LogisticRegression' ./Tutorial/chapter_learning.tex:288: Warning: Undefined label: 'table:training' ./Tutorial/chapter_learning.tex:296: Warning: Undefined label: 'subsec:LogisticRegressionTraining' ./Tutorial/chapter_learning.tex:406: Warning: Application of '\"' on 'i' failed ./Tutorial/chapter_graphics.tex:18: Warning: Undefined citation: 'pritchard2006' ./Tutorial/chapter_graphics.tex:28: Warning: Undefined citation: 'toth2006' ./Tutorial/chapter_graphics.tex:31: Warning: 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occurring outside math mode ./Tutorial/chapter_graphics.tex:206: Warning: Undefined label: 'sec:seq_features' ./Tutorial/chapter_graphics.tex:254: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:254: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:300: Warning: Image in text ./Tutorial/chapter_graphics.tex:300: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:300: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:301: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:301: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:320: Warning: Undefined label: 'sec:gd_nice_example' ./Tutorial/chapter_graphics.tex:327: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:371: Warning: Image in text ./Tutorial/chapter_graphics.tex:371: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:384: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:384: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:406: Warning: Image in text ./Tutorial/chapter_graphics.tex:406: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:406: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:406: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:438: Warning: Image in text ./Tutorial/chapter_graphics.tex:438: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:438: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:438: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:464: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:464: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:467: Warning: Undefined label: 'sec:gd_top_down' ./Tutorial/chapter_graphics.tex:530: Warning: Image in text 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mode ./Tutorial/chapter_graphics.tex:647: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:671: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:671: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:678: Warning: Undefined citation: 'proux2002' ./Tutorial/chapter_graphics.tex:762: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:762: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:762: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:762: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:762: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:801: Warning: Image in text ./Tutorial/chapter_graphics.tex:801: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:801: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:828: Warning: '_' occurring outside math mode 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mode ./Tutorial/chapter_cookbook.tex:1350: Warning: Undefined label: 'chapter:Bio.AlignIO' ./Tutorial/chapter_cookbook.tex:1360: Warning: Undefined label: 'sec:consensus' ./Tutorial/chapter_cookbook.tex:1361: Warning: Undefined label: 'sec:pssm' ./Tutorial/chapter_cookbook.tex:1362: Warning: Undefined label: 'sec:getting_info_content' ./Tutorial/chapter_cookbook.tex:1363: Warning: Undefined label: 'sec:sub_matrix' ./Tutorial/chapter_cookbook.tex:1369: Warning: Undefined label: 'sec:summary_info' ./Tutorial/chapter_cookbook.tex:1470: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1470: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1497: Warning: Undefined label: 'sec:summary_info' ./Tutorial/chapter_cookbook.tex:1516: Warning: Undefined label: 'sec:freq_table' ./Tutorial/chapter_cookbook.tex:1570: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1579: Warning: '_' occurring outside math mode 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./Tutorial/chapter_contributing.tex:79: Warning: '_' occurring outside math mode ./Tutorial/chapter_contributing.tex:84: Warning: Undefined label: 'sec:regr_test' ./Tutorial/chapter_contributing.tex:100: Warning: Undefined label: 'sec:regr_test' ./Tutorial/chapter_appendix.tex:88: Warning: Undefined label: 'sec:SeqIO_compressed' ./Tutorial.tex:122: Warning: line too long ./Tutorial.tex:133: Warning: Application of '\'' on 'e' failed ./Tutorial.tex:133: Warning: Application of '\'' on 'o' failed ./Tutorial.tex:137: Warning: Application of '\"' on 'u' failed ./Tutorial.tex:202: Warning: Application of '\"' on 'o' failed ./Tutorial.tex:202: Warning: Application of '\"' on 'u' failed Fixpoint reached in 3 step(s) pdflatex Tutorial.tex This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Tutorial.tex LaTeX2e <2019-10-01> patch level 1 (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls 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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/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.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/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) Excluding 'htmlonly' comment. Excluding 'rawhtml' comment. [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map} <./images/biopython_logo.pdf>]pdfTeX warning (ext4): destination with the same identifier (name{page.1}) has been already us ed, duplicate ignored \relax l.97 \include{Tutorial/chapter_introduction} [1] (./Tutorial/chapter_introduction.tex Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [2] LaTeX Warning: Citation `cock2009' on page 3 undefined on input line 110. [3] LaTeX Warning: Citation `chapman2000' on page 4 undefined on input line 114. LaTeX Warning: Citation `hamelryck2003a' on page 4 undefined on input line 115. LaTeX Warning: Citation `dehoon2004' on page 4 undefined on input line 116. LaTeX Warning: Citation `pritchard2006' on page 4 undefined on input line 117. LaTeX Warning: Citation `talevich2012' on page 4 undefined on input line 118. LaTeX Warning: Citation `cock2010' on page 4 undefined on input line 119. Excluding 'rawhtml' comment. Underfull \hbox (badness 10000) in paragraph at lines 141--147 Underfull \hbox (badness 10000) in paragraph at lines 153--155 [4 <./images/biopython_logo_old.jpg>] LaTeX Warning: Reference `sec:seq-comparison' on page 5 undefined on input line 237. [5] Overfull \hbox (2.99303pt too wide) in paragraph at lines 246--248 \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 6 undefined on input li ne 250. [6] LaTeX Warning: Reference `sec:SeqIO-conversion' on page 7 undefined on input li ne 292. LaTeX Warning: Reference `sec:converting-alignments' on page 7 undefined on inp ut line 292. ) [7] (./Tutorial/chapter_quick_start.tex Chapter 2. LaTeX Warning: Reference `chapter:cookbook' on page 8 undefined on input line 1 4. LaTeX Warning: Reference `chapter:advanced' on page 8 undefined on input line 1 4. LaTeX Warning: Reference `chapter:Bio.Seq' on page 8 undefined on input line 19 . [8] LaTeX Warning: Reference `chapter:Bio.Seq' on page 9 undefined on input line 35 . LaTeX Warning: Reference `chapter:Bio.SeqIO' on page 9 undefined on input line 49. LaTeX Warning: Reference `sec:sequence-parsing' on page 9 undefined on input li ne 69. LaTeX Warning: Reference `chapter:entrez' on page 9 undefined on input line 69. LaTeX Warning: Reference `chapter:swiss_prot' on page 9 undefined on input line 69. LaTeX Warning: Reference `sec:align_clustal' on page 9 undefined on input line 69. [9] LaTeX Warning: Reference `chapter:Bio.SeqIO' on page 10 undefined on input line 76. LaTeX Warning: Reference `sec:connecting-with-biological-databases' on page 10 undefined on input line 83. Overfull \hbox (7.99081pt too wide) in paragraph at lines 117--117 []\OT1/cmtt/m/n/10 Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGATGAGACCGTGG. ..CGC', SingleLetterAlphabet())[] Overfull \hbox (7.99081pt too wide) in paragraph at lines 117--117 []\OT1/cmtt/m/n/10 Seq('CATTGTTGAGATCACATAATAATTGATCGAGTTAATCTGGAGGATCTGTTTACT. ..GCC', SingleLetterAlphabet())[] [10] LaTeX Warning: Reference `chapter:Bio.SeqIO' on page 11 undefined on input line 149. LaTeX Warning: Reference `chapter:Bio.AlignIO' on page 11 undefined on input li ne 149. LaTeX Warning: Reference `chapter:cookbook' on page 11 undefined on input line 154. LaTeX Warning: Reference `chapter:entrez' on page 11 undefined on input line 16 2. LaTeX Warning: Reference `chapter:swiss_prot' on page 11 undefined on input lin e 163. [11] LaTeX Warning: Reference `chapter:cookbook' on page 12 undefined on input line 173. ) [12] (./Tutorial/chapter_seq_objects.tex Chapter 3. LaTeX Warning: Reference `chapter:SeqRecord' on page 13 undefined on input line 5. LaTeX Warning: Reference `chapter:Bio.SeqIO' on page 13 undefined on input line 5. [13] [14] LaTeX Warning: Reference `sec:mutable-seq' on page 15 undefined on input line 1 37. [15] LaTeX Warning: Reference `sec:SeqRecord-format' on page 16 undefined on input l ine 207. LaTeX Warning: Reference `chapter:Bio.SeqIO' on page 16 undefined on input line 209. [16] Overfull \hbox (39.49054pt too wide) in paragraph at lines 274--274 []\OT1/cmtt/m/n/10 >>> list_of_seqs = [Seq("ACGT", generic_dna), Seq("AACC", ge neric_dna), Seq("GGTT", generic_dna)][] Overfull \hbox (39.49054pt too wide) in paragraph at lines 285--285 []\OT1/cmtt/m/n/10 >>> list_of_seqs = [Seq("ACGT", generic_dna), Seq("AACC", ge neric_dna), Seq("GGTT", generic_dna)][] [17] [18] LaTeX Warning: Reference `sec:SeqIO-reverse-complement' on page 19 undefined on input line 376. [19] LaTeX Warning: Reference `sec:seq-module-functions' on page 20 undefined on inp ut line 449. [20] [21] LaTeX Warning: Reference `sec:SeqIO-translate' on page 22 undefined on input li ne 564. LaTeX Warning: Reference `sec:seq-module-functions' on page 22 undefined on inp ut line 570. [22] [23] LaTeX Warning: Reference `sec:seq-to-string' on page 24 undefined on input line 719. [24] LaTeX Warning: Reference `sec:seq-to-string' on page 25 undefined on input line 810. [25] LaTeX Warning: Reference `chapter:Bio.SeqIO' on page 26 undefined on input line 871. [26]) [27] (./Tutorial/chapter_seq_annot.tex Chapter 4. LaTeX Warning: Reference `chapter:Bio.Seq' on page 28 undefined on input line 4 . LaTeX Warning: Reference `chapter:Bio.SeqIO' on page 28 undefined on input line 4. LaTeX Warning: Reference `chapter:Bio.Seq' on page 28 undefined on input line 2 1. LaTeX Warning: Reference `chapter:Bio.SeqIO' on page 28 undefined on input line 21. LaTeX Warning: Reference `sec:FASTQ-filtering-example' on page 28 undefined on input line 34. [28] LaTeX Warning: Reference `sec:seq_features' on page 29 undefined on input line 38. LaTeX Warning: Reference `chapter:Bio.SeqIO' on page 29 undefined on input line 48. [29] Overfull \hbox (2.74086pt too wide) in paragraph at lines 129--129 []\OT1/cmtt/m/n/10 >gi|45478711|ref|NC_005816.1| Yersinia pestis biovar Microtu s ... pPCP1, complete sequence[] LaTeX Warning: Reference `chapter:quick-start' on page 30 undefined on input li ne 131. LaTeX Warning: Reference `chapter:Bio.SeqIO' on page 30 undefined on input line 133. Overfull \hbox (34.24059pt too wide) in paragraph at lines 144--144 []\OT1/cmtt/m/n/10 SingleLetterAlphabet()), id='gi|45478711|ref|NC_005816.1|', name='gi|45478711|ref|NC_005816.1|',[] Overfull \hbox (7.99081pt too wide) in paragraph at lines 153--153 []\OT1/cmtt/m/n/10 Seq('TGTAACGAACGGTGCAATAGTGATCCACACCCAACGCCTGAAATCAGATCCAGG. ..CTG', SingleLetterAlphabet())[] LaTeX Warning: Reference `chapter:Bio.SeqIO' on page 30 undefined on input line 158. Overfull \hbox (7.99081pt too wide) in paragraph at lines 169--169 []\OT1/cmtt/m/n/10 'gi|45478711|ref|NC_005816.1| Yersinia pestis biovar Microtu s ... pPCP1, complete sequence'[] [30] LaTeX Warning: Reference `chapter:Bio.SeqIO' on page 31 undefined on input line 216. Overfull \hbox (7.99081pt too wide) in paragraph at lines 226--226 []\OT1/cmtt/m/n/10 description='Yersinia pestis biovar Microtus str. 91001 plas mid pPCP1, complete sequence.',[] LaTeX Warning: Reference `chapter:Bio.SeqIO' on page 31 undefined on input line 229. [31] LaTeX Warning: Reference `sec:seq_features' on page 32 undefined on input line 279. LaTeX Warning: Reference `sec:locations' on page 32 undefined on input line 288 . LaTeX Warning: Reference `sec:locations' on page 32 undefined on input line 296 . [32] [33] [34] [35] LaTeX Warning: Reference `sec:locations' on page 36 undefined on input line 528 . Overfull \hbox (44.7405pt too wide) in paragraph at lines 536--536 []\OT1/cmtt/m/n/10 >>> example_parent = Seq("ACCGAGACGGCAAAGGCTAGCATAGGTATGAGAC TTCCTTCCTGCCAGTGCTGAGGAACTGGGAGCCTAC")[] Overfull \hbox (128.73976pt too wide) in paragraph at lines 546--546 []\OT1/cmtt/m/n/10 >>> feature_seq = example_parent[example_feature.location.st art:example_feature.location.end].reverse_complement()[] [36] Overfull \hbox (165.48944pt too wide) in paragraph at lines 618--618 []\OT1/cmtt/m/n/10 NotImplementedError: SeqRecord comparison is deliberately no t implemented. Explicitly compare the attributes of interest.[] LaTeX Warning: Reference `sec:seq-comparison' on page 37 undefined on input lin e 632. LaTeX Warning: Reference `sec:locations' on page 37 undefined on input line 640 . [37] LaTeX Warning: Reference `chapter:Bio.SeqIO' on page 38 undefined on input line 676. LaTeX Warning: Reference `sec:Bio.SeqIO-and-StringIO' on page 38 undefined on i nput line 679. Overfull \hbox (2.74086pt too wide) in paragraph at lines 703--703 []\OT1/cmtt/m/n/10 description='Yersinia pestis biovar Microtus str. 91001 plas mid pPCP1, complete sequence',[] [38] Overfull \hbox (7.99081pt too wide) in paragraph at lines 762--762 []\OT1/cmtt/m/n/10 description='Yersinia pestis biovar Microtus str. 91001 plas mid pPCP1, complete sequence.',[] [39] LaTeX Warning: Reference `sec:SeqRecord-format' on page 40 undefined on input l ine 833. Overfull \hbox (39.49054pt too wide) in paragraph at lines 839--839 []\OT1/cmtt/m/n/10 >>> sub_record.description = "Yersinia pestis biovar Microtu s str. 91001 plasmid pPCP1, partial."[] LaTeX Warning: Reference `sec:FASTQ-slicing-off-primer' on page 40 undefined on input line 841. LaTeX Warning: Reference `sec:FASTQ-slicing-off-adaptor' on page 40 undefined o n input line 842. LaTeX Warning: Reference `chapter:Bio.SeqIO' on page 40 undefined on input line 855. [40] Overfull \hbox (7.99081pt too wide) in paragraph at lines 930--930 []\OT1/cmtt/m/n/10 description='Yersinia pestis biovar Microtus str. 91001 plas mid pPCP1, complete sequence.',[] [41] Overfull \hbox (7.99081pt too wide) in paragraph at lines 960--960 []\OT1/cmtt/m/n/10 description='Yersinia pestis biovar Microtus str. 91001 plas mid pPCP1, complete sequence.',[] [42] Overfull \hbox (170.7394pt too wide) in paragraph at lines 1032--1032 []\OT1/cmtt/m/n/10 >>> print("%s %i %i %i %i" % (record.id, len(record), len(re cord.features), len(record.dbxrefs), len(record.annotations)))[] Overfull \hbox (65.74031pt too wide) in paragraph at lines 1042--1042 []\OT1/cmtt/m/n/10 >>> print("%s %i %i %i %i" % (rc.id, len(rc), len(rc.feature s), len(rc.dbxrefs), len(rc.annotations)))[] ) [43] (./Tutorial/chapter_seqio.tex Chapter 5. LaTeX Warning: Reference `chapter:quick-start' on page 44 undefined on input li ne 4. LaTeX Warning: Reference `chapter:SeqRecord' on page 44 undefined on input line 4. LaTeX Warning: Reference `chapter:SeqRecord' on page 44 undefined on input line 13. LaTeX Warning: Reference `chapter:Bio.Seq' on page 44 undefined on input line 1 3. LaTeX Warning: Reference `sec:low-level-fasta-fastq' on page 44 undefined on in put line 15. LaTeX Warning: Reference `sec:SeqIO_Online' on page 44 undefined on input line 23. LaTeX Warning: Reference `sec:appendix-handles' on page 44 undefined on input l ine 23. [44] LaTeX Warning: Reference `sec:sequence-parsing' on page 45 undefined on input l ine 45. Overfull \hbox (7.99081pt too wide) in paragraph at lines 66--66 []\OT1/cmtt/m/n/10 >>> identifiers = [seq_record.id for seq_record in SeqIO.par se("ls_orchid.gbk", "genbank")][] LaTeX Warning: Reference `seq:sequence-parsing-plus-pylab' on page 45 undefined on input line 69. [45] [46] LaTeX Warning: Reference `chapter:SeqRecord' on page 47 undefined on input line 148. [47] [48] LaTeX Warning: Reference `sec:appendix-handles' on page 49 undefined on input l ine 283. [49] LaTeX Warning: Reference `sec:SeqIO-index-bgzf' on page 50 undefined on input l ine 359. LaTeX Warning: Reference `sec:efetch' on page 50 undefined on input line 375. Overfull \hbox (18.49072pt too wide) in paragraph at lines 391--391 []\OT1/cmtt/m/n/10 with Entrez.efetch(db="nucleotide", rettype="fasta", retmode ="text", id="6273291") as handle:[] [50] Overfull \hbox (23.74068pt too wide) in paragraph at lines 438--438 [] \OT1/cmtt/m/n/10 % (len(seq_record), len(seq_record.features), seq_record.annotations["source"]))[] LaTeX Warning: Reference `chapter:entrez' on page 51 undefined on input line 45 1. LaTeX Warning: Reference `sec:entrez-guidelines' on page 51 undefined on input line 451. LaTeX Warning: Reference `chapter:swiss_prot' on page 51 undefined on input lin e 456. Overfull \hbox (18.49072pt too wide) in paragraph at lines 482--482 []\OT1/cmtt/m/n/10 RecName: Full=Chalcone synthase 3; EC=2.3.1.74; AltName: Ful l=Naringenin-chalcone synthase 3;[] [51] LaTeX Warning: Reference `SeqIO:to_dict' on page 52 undefined on input line 491 . LaTeX Warning: Reference `sec:SeqIO-index' on page 52 undefined on input line 4 97. LaTeX Warning: Reference `sec:SeqIO-index-db' on page 52 undefined on input lin e 501. LaTeX Warning: Reference `sec:SeqIO-indexing-discussion' on page 52 undefined o n input line 504. LaTeX Warning: Reference `sec:SeqIO-index' on page 52 undefined on input line 5 14. [52] LaTeX Warning: Reference `sec:fasta-parsing' on page 53 undefined on input line 588. Overfull \hbox (34.24059pt too wide) in paragraph at lines 609--609 []\OT1/cmtt/m/n/10 orchid_dict = SeqIO.to_dict(SeqIO.parse("ls_orchid.fasta", " fasta"), key_function=get_accession)[] [53] [54] LaTeX Warning: Reference `sec:fastq-indexing' on page 55 undefined on input lin e 704. LaTeX Warning: Reference `seq:seqio-todict-functionkey' on page 55 undefined on input line 725. Overfull \hbox (9.93459pt too wide) in paragraph at lines 769--774 \OT1/cmr/m/n/10 FTP site ([][]$\OT1/cmtt/m/n/10 ftp : / / ftp . uniprot . org / pub / databases / uniprot / current _ release / knowledgebase / complete / [55] LaTeX Warning: Reference `sec:SeqIO-sort' on page 56 undefined on input line 78 7. Overfull \hbox (4.48064pt too wide) in paragraph at lines 812--815 []\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 , [56] LaTeX Warning: Reference `sec:seqio-index-getraw' on page 57 undefined on input line 869. [57] [58] [59] LaTeX Warning: Reference `sec:seqio-index-getraw' on page 60 undefined on input line 1097. [60] LaTeX Warning: Reference `sec:SeqIO-fastq-conversion' on page 61 undefined on i nput line 1139. LaTeX Warning: Reference `sec:SeqIO-fasta-qual-conversion' on page 61 undefined on input line 1139. LaTeX Warning: Reference `sec:seq-reverse-complement' on page 61 undefined on i nput line 1154. LaTeX Warning: Reference `sec:SeqRecord-reverse-complement' on page 61 undefine d on input line 1164. Overfull \hbox (13.24077pt too wide) in paragraph at lines 1174--1174 []\OT1/cmtt/m/n/10 >>> records = [rec.reverse_complement(id="rc_"+rec.id, descr iption = "reverse complement") \[] Overfull \hbox (13.24077pt too wide) in paragraph at lines 1184--1184 []\OT1/cmtt/m/n/10 >>> records = [rec.reverse_complement(id="rc_"+rec.id, descr iption = "reverse complement") \[] Overfull \hbox (13.24077pt too wide) in paragraph at lines 1192--1192 []\OT1/cmtt/m/n/10 >>> records = (rec.reverse_complement(id="rc_"+rec.id, descr iption = "reverse complement") \[] [61] Overfull \hbox (13.24077pt too wide) in paragraph at lines 1203--1203 []\OT1/cmtt/m/n/10 >>> records = (rec.reverse_complement(id="rc_"+rec.id, descr iption = "reverse complement") \[] LaTeX Warning: Reference `sec:SeqIO-translate' on page 62 undefined on input li ne 1205. LaTeX Warning: Reference `sec:SeqRecord-format' on page 62 undefined on input l ine 1224. Overfull \hbox (19.46596pt too wide) in paragraph at lines 1240--1242 \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(...) [62] Overfull \hbox (21.32593pt too wide) in paragraph at lines 1284--1288 []\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 LaTeX Warning: Reference `chapter:cookbook' on page 63 undefined on input line 1303. ) [63] (./Tutorial/chapter_align.tex Chapter 6. LaTeX Warning: Reference `sec:appendix-handles' on page 64 undefined on input l ine 31. LaTeX Warning: Reference `sec:AlignIO-count-argument' on page 64 undefined on i nput line 35. [64] [65] LaTeX Warning: Reference `sec:alignment-format-method' on page 66 undefined on input line 115. [66] [67] [68] [69] [70] [71] Overfull \hbox (5.54102pt too wide) in paragraph at lines 435--436 \OT1/cmr/m/n/10 ever you can't do that when your records come from a gen-er-a-t or/it-er-a-tor. There-fore the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write() LaTeX Warning: Reference `sec:SeqIO-conversion' on page 72 undefined on input l ine 445. Overfull \hbox (39.68698pt too wide) in paragraph at lines 443--448 [][]\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() [72] [73] [74] LaTeX Warning: Reference `sec:SeqRecord-format' on page 75 undefined on input l ine 617. Overfull \hbox (16.49278pt too wide) in paragraph at lines 619--622 []\OT1/cmr/m/n/10 Internally the [][]\OT1/cmtt/m/n/10 format() []\OT1/cmr/m/n/1 0 method is us-ing the [][]\OT1/cmtt/m/n/10 StringIO []\OT1/cmr/m/n/10 string b ased han-dle and call-ing [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write()[]\OT1/cmr/m/ n/10 . [75] [76] LaTeX Warning: Reference `sec:SeqRecord-addition' on page 77 undefined on input line 792. [77] LaTeX Warning: Reference `sec:pairwise2' on page 78 undefined on input line 844 . LaTeX Warning: Reference `chapter:Bio.SeqIO' on page 78 undefined on input line 849. LaTeX Warning: Reference `seq:emboss-needle-water' on page 78 undefined on inpu t line 876. [78] [79] LaTeX Warning: Reference `sec:Phylo' on page 80 undefined on input line 1023. [80] Overfull \hbox (8.40039pt too wide) in paragraph at lines 1057--1061 []\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 [81] [82] LaTeX Warning: Reference `sec:appendix-handles' on page 83 undefined on input l ine 1245. [83] Overfull \hbox (23.74068pt too wide) in paragraph at lines 1316--1316 []\OT1/cmtt/m/n/10 needle -outfile=needle.txt -asequence=alpha.faa -bsequence=b eta.faa -gapopen=10 -gapextend=0.5[] [84] Overfull \hbox (23.74068pt too wide) in paragraph at lines 1364--1364 []\OT1/cmtt/m/n/10 needle -outfile=needle.txt -asequence=alpha.faa -bsequence=b eta.faa -gapopen=10 -gapextend=0.5[] [85] [86] LaTeX Warning: Citation `durbin1998' on page 87 undefined on input line 1550. [87] LaTeX Warning: Reference `sec:pairwise-aligner' on page 88 undefined on input l ine 1562. [88] LaTeX Warning: Reference `sec:pairwise-matchscores' on page 89 undefined on inp ut line 1644. LaTeX Warning: Reference `sec:pairwise-affine-gapscores' on page 89 undefined o n input line 1644. LaTeX Warning: Reference `sec:pairwise-general-gapscores' on page 89 undefined on input line 1644. LaTeX Warning: Reference `sec:pairwise-basic' on page 89 undefined on input lin e 1645. LaTeX Warning: Reference `sec:pairwise-affine-gapscores' on page 89 undefined o n input line 1648. LaTeX Warning: Reference `sec:pairwise-general-gapscores' on page 89 undefined on input line 1649. [89] Overfull \hbox (175.46193pt too wide) in paragraph at lines 1776--1813 [][] [90] [91] [92] LaTeX Warning: Reference `sec:pairwise-examples' on page 93 undefined on input line 1855. [93] [94] LaTeX Warning: Citation `kent2002' on page 95 undefined on input line 1982. Overfull \hbox (19.80069pt too wide) in paragraph at lines 2013--2014 \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) [95] [96]) [97] (./Tutorial/chapter_blast.tex Chapter 7. LaTeX Warning: Reference `chapter:searchio' on page 98 undefined on input line 18. [98] LaTeX Warning: Reference `sec:parsing-blast' on page 99 undefined on input line 58. LaTeX Warning: Reference `chapter:Bio.SeqIO' on page 99 undefined on input line 119. LaTeX Warning: Reference `sec:parsing-blast' on page 99 undefined on input line 124. [99] LaTeX Warning: Reference `sec:parsing-blast' on page 100 undefined on input lin e 146. LaTeX Warning: Reference `sec:parsing-blast' on page 100 undefined on input lin e 155. LaTeX Warning: Reference `sec:running-www-blast' on page 100 undefined on input line 164. LaTeX Warning: Reference `sec:alignment-tools' on page 100 undefined on input l ine 192. [100] LaTeX Warning: Reference `sec:parsing-blast' on page 101 undefined on input lin e 236. LaTeX Warning: Reference `sec:parsing-blast-deprecated' on page 101 undefined o n input line 268. LaTeX Warning: Reference `sec:running-www-blast' on page 101 undefined on input line 282. LaTeX Warning: Reference `sec:running-local-blast' on page 101 undefined on inp ut line 284. [101] LaTeX Warning: Reference `chapter:Bio.SeqIO' on page 102 undefined on input lin e 335. LaTeX Warning: Reference `chapter:Bio.AlignIO' on page 102 undefined on input l ine 335. [102] Overfull \hbox (55.2404pt too wide) in paragraph at lines 436--436 []\OT1/cmtt/m/n/10 sequence: >gb|AF283004.1|AF283004 Arabidopsis thaliana cold acclimation protein WCOR413-like protein[] [103] LaTeX Warning: Reference `fig:blastrecord' on page 104 undefined on input line 445. Excluding 'htmlonly' comment. LaTeX Warning: Reference `fig:psiblastrecord' on page 104 undefined on input li ne 461. Excluding 'htmlonly' comment.) [104] [105 <./images/BlastRecord.png>] [106 <./i mages/PSIBlastRecord.png>] (./Tutorial/chapter_searchio.tex Chapter 8. [107] 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 [108] [109] [110] [111] [112] Overfull \hbox (44.7405pt too wide) in paragraph at lines 462--462 []\OT1/cmtt/m/n/10 ... hit.id = hit.id.split("|")[3] # renames "gi|301171 322|ref|NR_035857.1|" to "NR_035857.1"[] [113] [114] [115] [116] Overfull \hbox (469.98679pt too wide) in paragraph at lines 731--731 []\OT1/cmtt/m/n/10 SeqRecord(seq=Seq('CCCTCTACAGGGAAGCGCTTTCTGTTGTCTGAAAGAAAAGA AAGTGCTTCCTTT...GGG', DNAAlphabet()), id='42291', name='aligned query sequence' , description='mystery_seq', dbxrefs=[])[] Overfull \hbox (769.23418pt too wide) in paragraph at lines 731--731 []\OT1/cmtt/m/n/10 SeqRecord(seq=Seq('CCCTCTACAGGGAAGCGCTTTCTGTTGTCTGAAAGAAAAGA AAGTGCTTCCTTT...GGG', DNAAlphabet()), id='gi|262205317|ref|NR_030195.1|', name= 'aligned hit sequence', description='Homo sapiens microRNA 520b (MIR520B), micr oRNA', dbxrefs=[])[] LaTeX Warning: Reference `chapter:SeqRecord' on page 117 undefined on input lin e 734. Overfull \hbox (27.24287pt too wide) in paragraph at lines 738--740 []\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 [117] [118] Overfull \hbox (65.74031pt too wide) in paragraph at lines 870--870 []\OT1/cmtt/m/n/10 >>> blat_hsp2.hit_inter_ranges # start and end coordinates of intervening regions in the hit sequence[] [119] Overfull \hbox (769.23418pt too wide) in paragraph at lines 962--962 []\OT1/cmtt/m/n/10 SeqRecord(seq=Seq('CCCTCTACAGGGAAGCGCTTTCTGTTGTCTGAAAGAAAAGA AAGTGCTTCCTTT...GGG', DNAAlphabet()), id='gi|262205317|ref|NR_030195.1|', name= 'aligned hit sequence', description='Homo sapiens microRNA 520b (MIR520B), micr oRNA', dbxrefs=[])[] [120] Overfull \hbox (14.20721pt too wide) in paragraph at lines 1050--1054 \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 , LaTeX Warning: Reference `sec:SeqIO-index' on page 121 undefined on input line 1082. Overfull \hbox (20.13245pt too wide) in paragraph at lines 1080--1085 []\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 . [121] Overfull \hbox (13.24077pt too wide) in paragraph at lines 1123--1123 []\OT1/cmtt/m/n/10 >>> idx = SearchIO.index("tab_2226_tblastn_001.txt", "blast- tab", key_function=key_function)[] Overfull \hbox (11.82602pt too wide) in paragraph at lines 1160--1163 []\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 [122]) [123] (./Tutorial/chapter_entrez.tex Chapter 9. LaTeX Warning: Reference `sec:entrez-specialized-parsers' on page 124 undefined on input line 22. [124] LaTeX Warning: Reference `sec:entrez-webenv' on page 125 undefined on input lin e 57. LaTeX Warning: Reference `sec:BioSQL' on page 125 undefined on input line 60. [125] [126] [127] LaTeX Warning: Reference `sec:efetch' on page 128 undefined on input line 209. LaTeX Warning: Reference `sec:entrez-einfo' on page 128 undefined on input line 213. Overfull \hbox (70.99026pt too wide) in paragraph at lines 224--224 []\OT1/cmtt/m/n/10 >>> handle = Entrez.esearch(db="nucleotide", term="Cypripedi oideae[Orgn] AND matK[Gene]", idtype="acc")[] LaTeX Warning: Reference `sec:efetch' on page 128 undefined on input line 227. [128] LaTeX Warning: Reference `sec:entrez-webenv' on page 129 undefined on input lin e 289. [129] LaTeX Warning: Reference `sec:SeqIO_GenBank_Online' on page 130 undefined on in put line 314. LaTeX Warning: Reference `sec:efetch' on page 130 undefined on input line 314. [130] [131] LaTeX Warning: Reference `chapter:Bio.SeqIO' on page 132 undefined on input lin e 408. Overfull \hbox (13.24077pt too wide) in paragraph at lines 450--450 [] \OT1/cmtt/m/n/10 net_handle = Entrez.efetch(db="nucleotide", id="EU490707 ", rettype="gb", retmode="text")[] [132] LaTeX Warning: Reference `sec:entrez-specialized-parsers' on page 133 undefined on input line 467. LaTeX Warning: Reference `sec:entrez-webenv' on page 133 undefined on input lin e 469. [133] LaTeX Warning: Reference `sec:elink-citations' on page 134 undefined on input l ine 550. LaTeX Warning: Reference `subsec:entrez_example_genbank' on page 134 undefined on input line 556. [134] [135] Overfull \hbox (312.48816pt too wide) in paragraph at lines 677--677 []\OT1/cmtt/m/n/10 Bio.Entrez.Parser.NotXMLError: Failed to parse the XML data (syntax error: line 1, column 0). Please make sure that the input data are in X ML format.[] [136] Overfull \hbox (249.48871pt too wide) in paragraph at lines 698--698 []\OT1/cmtt/m/n/10 [] Overfull \hbox (370.23766pt too wide) in paragraph at lines 705--705 []\OT1/cmtt/m/n/10 Bio.Entrez.Parser.CorruptedXMLError: Failed to parse the XML data (no element found: line 16, column 0). Please make sure that the input da ta are not corrupted.[] Overfull \hbox (249.48871pt too wide) in paragraph at lines 736--736 []\OT1/cmtt/m/n/10 [] [137] Overfull \hbox (585.48578pt too wide) in paragraph at lines 748--748 []\OT1/cmtt/m/n/10 Bio.Entrez.Parser.ValidationError: Failed to find tag 'Docsu mList' in the DTD. To skip all tags that are not represented in the DTD, please call Bio.Entrez.read or Bio.Entrez.parse with validate=False.[] LaTeX Warning: Reference `sec:SeqIO_GenBank_Online' on page 138 undefined on in put line 767. LaTeX Warning: Reference `sec:efetch' on page 138 undefined on input line 767. [138] [139] LaTeX Warning: Reference `sec:entrez-webenv' on page 140 undefined on input lin e 884. [140] Overfull \hbox (133.98972pt too wide) in paragraph at lines 970--970 []\OT1/cmtt/m/n/10 EXPRESS bone| connective tissue| intestine| liver| live r tumor| normal| soft tissue/muscle tissue tumor| adult[] Overfull \hbox (102.48999pt too wide) in paragraph at lines 970--970 []\OT1/cmtt/m/n/10 SEQUENCE ACC=BG569293.1; NID=g13576946; CLONE=IMAGE:47225 96; END=5'; LID=6989; SEQTYPE=EST; TRACE=44157214[] [141] Overfull \hbox (160.23949pt too wide) in paragraph at lines 992--992 []\OT1/cmtt/m/n/10 ['bone', 'connective tissue', 'intestine', 'liver', 'liver t umor', 'normal', 'soft tissue/muscle tissue tumor', 'adult'][] [142] LaTeX Warning: Reference `sec:orchids' on page 143 undefined on input line 1042 . LaTeX Warning: Reference `sec:entrez-webenv' on page 143 undefined on input lin e 1083. [143] LaTeX Warning: Reference `sec:orchids' on page 144 undefined on input line 1128 . Overfull \hbox (23.74068pt too wide) in paragraph at lines 1152--1152 []\OT1/cmtt/m/n/10 >>> handle = Entrez.esearch(db="nucleotide", term="Cypripedi oideae", retmax=814, idtype="acc")[] [144] LaTeX Warning: Reference `sec:entrez-webenv' on page 145 undefined on input lin e 1180. [145] LaTeX Warning: Reference `sec:entrez-webenv' on page 146 undefined on input lin e 1215. LaTeX Warning: Reference `sec:SeqIO_GenBank_Online' on page 146 undefined on in put line 1222. LaTeX Warning: Reference `sec:entrez-webenv' on page 146 undefined on input lin e 1223. [146] LaTeX Warning: Reference `chapter:Bio.SeqIO' on page 147 undefined on input lin e 1275. LaTeX Warning: Reference `sec:entrez-guidelines' on page 147 undefined on input line 1299. LaTeX Warning: Reference `sec:entrez-webenv' on page 147 undefined on input lin e 1300. [147] LaTeX Warning: Reference `sec:entrez-search-fetch-genbank' on page 148 undefine d on input line 1358. [148] LaTeX Warning: Reference `subsec:entrez_example_genbank' on page 149 undefined on input line 1389. [149] LaTeX Warning: Reference `subsec:entrez-and-medline' on page 150 undefined on i nput line 1487. LaTeX Warning: Reference `sec:elink' on page 150 undefined on input line 1492. [150] LaTeX Warning: Reference `sec:entrez-webenv' on page 151 undefined on input lin e 1516. ) [151] (./Tutorial/chapter_uniprot.tex Chapter 10. LaTeX Warning: Reference `sec:SeqIO_ExPASy_and_SwissProt' on page 152 undefined on input line 10. Overfull \hbox (216.73924pt too wide) in paragraph at lines 30--30 []\OT1/cmtt/m/n/10 >>> handle = TextIOWrapper(urlopen("https://raw.githubuserc ontent.com/biopython/biopython/master/Tests/SwissProt/F2CXE6.txt"))[] Overfull \hbox (137.98993pt too wide) in paragraph at lines 39--39 []\OT1/cmtt/m/n/10 >>> handle = urlopen("https://raw.githubusercontent.com/bio python/biopython/master/Tests/SwissProt/F2CXE6.txt")[] LaTeX Warning: Reference `subsec:expasy_swissprot' on page 152 undefined on inp ut line 41. [152] LaTeX Warning: Reference `sec:SeqIO_ExPASy_and_SwissProt' on page 153 undefined on input line 49. Overfull \hbox (270.48853pt too wide) in paragraph at lines 79--79 []\OT1/cmtt/m/n/10 SubName: Full=Plasma membrane intrinsic protein {ECO:0000313 |EMBL:BAN04711.1}; SubName: Full=Predicted protein {ECO:0000313|EMBL:BAJ87517.1 };[] Overfull \hbox (359.73775pt too wide) in paragraph at lines 79--79 []\OT1/cmtt/m/n/10 authors: Matsumoto T., Tanaka T., Sakai H., Amano N., Kanamo ri H., Kurita K., Kikuta A., Kamiya K., Yamamoto M., Ikawa H., Fujii N., Hori K ., Itoh T., Sato K.[] Overfull \hbox (86.74013pt too wide) in paragraph at lines 79--79 []\OT1/cmtt/m/n/10 title: Comprehensive sequence analysis of 24,783 barley full -length cDNAs derived from 12 clone libraries.[] Overfull \hbox (553.98605pt too wide) in paragraph at lines 79--79 []\OT1/cmtt/m/n/10 ['Eukaryota', 'Viridiplantae', 'Streptophyta', 'Embryophyta' , 'Tracheophyta', 'Spermatophyta', 'Magnoliophyta', 'Liliopsida', 'Poales', 'Po aceae', 'BEP clade', 'Pooideae', 'Triticeae', 'Hordeum'][] Overfull \hbox (7.99081pt too wide) in paragraph at lines 79--79 []\OT1/cmtt/m/n/10 title: Functional characterization of a novel plasma membran e intrinsic protein2 in barley.[] Overfull \hbox (553.98605pt too wide) in paragraph at lines 79--79 []\OT1/cmtt/m/n/10 ['Eukaryota', 'Viridiplantae', 'Streptophyta', 'Embryophyta' , 'Tracheophyta', 'Spermatophyta', 'Magnoliophyta', 'Liliopsida', 'Poales', 'Po aceae', 'BEP clade', 'Pooideae', 'Triticeae', 'Hordeum'][] Overfull \hbox (553.98605pt too wide) in paragraph at lines 79--79 []\OT1/cmtt/m/n/10 ['Eukaryota', 'Viridiplantae', 'Streptophyta', 'Embryophyta' , 'Tracheophyta', 'Spermatophyta', 'Magnoliophyta', 'Liliopsida', 'Poales', 'Po aceae', 'BEP clade', 'Pooideae', 'Triticeae', 'Hordeum'][] [153] [154] [155] [156] [157] LaTeX Warning: Reference `sec:orchids' on page 158 undefined on input line 347. [158] Overfull \hbox (24.29903pt too wide) in paragraph at lines 366--367 []\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) 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 [159] Overfull \hbox (133.98972pt too wide) in paragraph at lines 493--493 []\OT1/cmtt/m/n/10 {'signature_ac': u'PS50948', 'level': u'0', 'stop': 98, 'seq uence_ac': u'USERSEQ1', 'start': 16, 'score': u'8.873'}[] [160]) [161] (./Tutorial/chapter_pdb.tex Chapter 11. LaTeX Warning: Reference `problem structures' on page 162 undefined on input li ne 18. [162] [163] Overfull \hbox (13.022pt too wide) in paragraph at lines 194--196 \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/-Mod-el/Chain/Residue/A tom) [164] LaTeX Warning: Reference `fig:smcra' on page 165 undefined on input line 207. LaTeX Warning: Reference `problem structures' on page 165 undefined on input li ne 216. Excluding 'htmlonly' comment. [165] [166 <./images/smcra.png (PNG copy)>] [167] LaTeX Warning: Reference `hetero problems' on page 168 undefined on input line 353. LaTeX Warning: Reference `point mutations' on page 168 undefined on input line 398. LaTeX Warning: Reference `disordered atoms' on page 168 undefined on input line 415. [168] [169] LaTeX Warning: Reference `fig:smcra' on page 170 undefined on input line 540. [170] LaTeX Warning: Reference `fig:smcra' on page 171 undefined on input line 586. [171] [172] [173] [174] LaTeX Warning: Citation `golub1989' on page 175 undefined on input line 870. [175] LaTeX Warning: Citation `hamelryck2005' on page 176 undefined on input line 898 . LaTeX Warning: Command \r invalid in math mode on input line 901. LaTeX Warning: Reference `cap:DSSP-codes' on page 176 undefined on input line 9 33. LaTeX Warning: Reference `subsec:residue_depth' on page 176 undefined on input line 972. [176] LaTeX Warning: Citation `hamelryck2003a' on page 177 undefined on input line 10 22. [177] [178] [179] LaTeX Warning: Citation `hamelryck2003b' on page 180 undefined on input line 12 34. LaTeX Warning: Citation `majumdar2005' on page 180 undefined on input line 1235 . [180]) [181] (./Tutorial/chapter_popgen.tex Chapter 12. [182]) [183] (./Tutorial/chapter_phylo.tex Chapter 13. LaTeX Warning: Citation `talevich2012' on page 184 undefined on input line 9. [184] LaTeX Warning: Reference `fig:phylo-simple-draw' on page 185 undefined on input line 96. Excluding 'htmlonly' comment. [185] Overfull \hbox (25.13162pt too wide) in paragraph at lines 175--178 []\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 LaTeX Warning: Reference `fig:phylo-color-draw' on page 186 undefined on input line 192. [186 <./images/phylo-simple-draw.png>] Excluding 'htmlonly' comment. [187 <./im ages/phylo-color-draw.png>] [188] Overfull \hbox (406.98734pt too wide) in paragraph at lines 328--328 []\OT1/cmtt/m/n/10 Phylogeny(description='phyloXML allows to use either a "bran ch_length" attribute...', name='example from Prof. Joe Felsenstein's book "Infe rring Phyl...', rooted=True)[] Excluding 'htmlonly' comment. LaTeX Warning: Reference `fig:phylo-dot' on page 189 undefined on input line 37 6. Excluding 'htmlonly' comment. LaTeX Warning: Reference `fig:phylo-rooted' on page 189 undefined on input line 412. Excluding 'htmlonly' comment. LaTeX Warning: Reference `fig:phylo-color' on page 189 undefined on input line 428. [189] [190 <./images/phylo-draw-example.png> <./images/phylo-dot.png>] Excluding 'htmlonly' comment. LaTeX Warning: Reference `fig:phylo-apaf' on page 191 undefined on input line 4 62. LaTeX Warning: Reference `fig:phylo-apaf-zoom' on page 191 undefined on input l ine 462. Excluding 'htmlonly' comment. LaTeX Warning: Reference `fig:phylo-apaf' on page 191 undefined on input line 4 87. [191 <./images/phylo-rooted.png> <./images/phylo-color.png>] [192 <./images/phy lo-apaf.png> <./images/phylo-apaf-zoom.png>] Overfull \hbox (19.85507pt too wide) in paragraph at lines 559--566 \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"}) [193] Overfull \hbox (13.48741pt too wide) in paragraph at lines 614--617 []\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 , [194] [195] Overfull \hbox (4.04672pt too wide) in paragraph at lines 825--828 []\OT1/cmr/m/n/10 A sim-i-lar wrap-per for RAxML ([][]$\OT1/cmtt/m/n/10 https : / / sco . h-[]its . org / exelixis / software . html$[][]\OT1/cmr/m/n/10 ) was added in Biopy- LaTeX Warning: Reference `sec:alignment-tools' on page 196 undefined on input l ine 832. [196] LaTeX Warning: Reference `sec:PhyloXML' on page 197 undefined on input line 903 . [197]) [198] (./Tutorial/chapter_motifs.tex Chapter 14. LaTeX Warning: Reference `sec:links' on page 199 undefined on input line 7. [199] [200] LaTeX Warning: Citation `cornish1985' on page 201 undefined on input line 152. LaTeX Warning: Citation `cavener1987' on page 201 undefined on input line 153. [201] [202] Overfull \hbox (128.73976pt too wide) in paragraph at lines 270--270 []\OT1/cmtt/m/n/10 [Seq('CACGTG', IUPACUnambiguousDNA()), Seq('CACGTG', IUPACUn ambiguousDNA()), Seq('CACGTG', IUPACUnambiguousDNA())][] [203] [204] [205] [206] [207] LaTeX Warning: Citation `bailey1994' on page 208 undefined on input line 522. [208] Overfull \hbox (13.10551pt too wide) in paragraph at lines 582--586 \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 . [209] [210] LaTeX Warning: Citation `matys2003' on page 211 undefined on input line 658. [211] LaTeX Warning: Reference `table:transfaccodes' on page 212 undefined on input l ine 733. LaTeX Warning: `h' float specifier changed to `ht'. [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) [224] (./Tutorial/chapter_cluster.tex Chapter 15. LaTeX Warning: Citation `dehoon2004' on page 225 undefined on input line 5. LaTeX Warning: Citation `lecuyer1988' on page 225 undefined on input line 29. LaTeX Warning: Citation `kachitvichyanukul1988' on page 225 undefined on input line 29. [225] [226] [227] LaTeX Warning: Citation `snedecor1989' on page 228 undefined on input line 153. [228] LaTeX Warning: Reference `sec:distancefunctions' on page 229 undefined on input line 182. [229] Overfull \hbox (78.60634pt too wide) in paragraph at lines 230--231 \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 $[]$ [230] LaTeX Warning: Reference `sec:distancefunctions' on page 231 undefined on input line 263. [231] [232] LaTeX Warning: Reference `sec:distancefunctions' on page 233 undefined on input line 331. [233] [234] Overfull \hbox (16.73593pt too wide) in paragraph at lines 413--414 [][]\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 $[]$, [235] [236] LaTeX Warning: Reference `sec:distancefunctions' on page 237 undefined on input line 546. [237] LaTeX Warning: Citation `kohonen1997' on page 238 undefined on input line 594. LaTeX Warning: Citation `tamayo1999' on page 238 undefined on input line 594. [238] [239] LaTeX Warning: Reference `sec:distancefunctions' on page 240 undefined on input line 641. Overfull \hbox (106.77225pt too wide) in paragraph at lines 648--650 \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 240 undefined on input line 654. LaTeX Warning: Citation `golub1971' on page 240 undefined on input line 662. 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[309 <./images/SRR001666.png>] [310] Overfull \hbox (49.0755pt too wide) in paragraph at lines 1460--1461 []\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 . [311] LaTeX Warning: Reference `sec:summary_info' on page 312 undefined on input line 1497. LaTeX Warning: Reference `sec:freq_table' on page 312 undefined on input line 1 516. [312] LaTeX Warning: Reference `sec:align_clustal' on page 313 undefined on input lin e 1603. LaTeX Warning: Reference `sec:summary_info' on page 313 undefined on input line 1603. [313] LaTeX Warning: Reference `chapter:Bio.SeqIO' on page 314 undefined on input lin e 1701. [314]) [315] (./Tutorial/chapter_testing.tex Chapter 21. LaTeX Warning: Reference `section:doctest' on page 316 undefined on input line 49. [316] [317] [318] [319] [320] [321] LaTeX Warning: Reference `section:doctest' on page 322 undefined on input line 409. 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(rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information)< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pfb> Output written on Tutorial.pdf (337 pages, 2429273 bytes). Transcript written on Tutorial.log. pdflatex Tutorial.tex This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Tutorial.tex LaTeX2e <2019-10-01> patch level 1 (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2019/08/27 v1.4j 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/listings/listings.sty (/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty) (/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 65. 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Excluding 'rawhtml' comment. [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.m ap} <./images/biopython_logo.pdf>] (./Tutorial.tocpdfTeX warning (ext4): destin ation with the same identifier (name{page.1}) has been already used, duplicate ignored \relax l.39 ...tions and locations}{33}{subsection.4.3.2} % [1] [2] [3] [4] [5] [6] [7]) [8] (./Tutorial/chapter_introduction.tex Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [9] [10] Excluding 'rawhtml' comment. Underfull \hbox (badness 10000) in paragraph at lines 141--147 Underfull \hbox (badness 10000) in paragraph at lines 153--155 [11 <./images/biopython_logo_old.jpg>] [12] Overfull \hbox (2.99303pt too wide) in paragraph at lines 246--248 \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 . [13]) [14] (./Tutorial/chapter_quick_start.tex Chapter 2. [15] [16] Overfull \hbox (7.99081pt too wide) in paragraph at lines 117--117 []\OT1/cmtt/m/n/10 Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGATGAGACCGTGG. ..CGC', SingleLetterAlphabet())[] Overfull \hbox (7.99081pt too wide) in paragraph at lines 117--117 []\OT1/cmtt/m/n/10 Seq('CATTGTTGAGATCACATAATAATTGATCGAGTTAATCTGGAGGATCTGTTTACT. ..GCC', SingleLetterAlphabet())[] [17] [18]) [19] (./Tutorial/chapter_seq_objects.tex Chapter 3. [20] [21] [22] [23] Overfull \hbox (39.49054pt too wide) in paragraph at lines 274--274 []\OT1/cmtt/m/n/10 >>> list_of_seqs = [Seq("ACGT", generic_dna), Seq("AACC", ge neric_dna), Seq("GGTT", generic_dna)][] Overfull \hbox (39.49054pt too wide) in paragraph at lines 285--285 []\OT1/cmtt/m/n/10 >>> list_of_seqs = [Seq("ACGT", generic_dna), Seq("AACC", ge neric_dna), Seq("GGTT", generic_dna)][] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33]) [34] (./Tutorial/chapter_seq_annot.tex Chapter 4. [35] [36] Overfull \hbox (2.74086pt too wide) in paragraph at lines 129--129 []\OT1/cmtt/m/n/10 >gi|45478711|ref|NC_005816.1| Yersinia pestis biovar Microtu s ... pPCP1, complete sequence[] Overfull \hbox (34.24059pt too wide) in paragraph at lines 144--144 []\OT1/cmtt/m/n/10 SingleLetterAlphabet()), id='gi|45478711|ref|NC_005816.1|', name='gi|45478711|ref|NC_005816.1|',[] Overfull \hbox (7.99081pt too wide) in paragraph at lines 153--153 []\OT1/cmtt/m/n/10 Seq('TGTAACGAACGGTGCAATAGTGATCCACACCCAACGCCTGAAATCAGATCCAGG. ..CTG', SingleLetterAlphabet())[] Overfull \hbox (7.99081pt too wide) in paragraph at lines 169--169 []\OT1/cmtt/m/n/10 'gi|45478711|ref|NC_005816.1| Yersinia pestis biovar Microtu s ... pPCP1, complete sequence'[] [37] Overfull \hbox (7.99081pt too wide) in paragraph at lines 226--226 []\OT1/cmtt/m/n/10 description='Yersinia pestis biovar Microtus str. 91001 plas mid pPCP1, complete sequence.',[] [38] [39] [40] [41] [42] Overfull \hbox (44.7405pt too wide) in paragraph at lines 536--536 []\OT1/cmtt/m/n/10 >>> example_parent = Seq("ACCGAGACGGCAAAGGCTAGCATAGGTATGAGAC TTCCTTCCTGCCAGTGCTGAGGAACTGGGAGCCTAC")[] Overfull \hbox (128.73976pt too wide) in paragraph at lines 546--546 []\OT1/cmtt/m/n/10 >>> feature_seq = example_parent[example_feature.location.st art:example_feature.location.end].reverse_complement()[] [43] Overfull \hbox (165.48944pt too wide) in paragraph at lines 618--618 []\OT1/cmtt/m/n/10 NotImplementedError: SeqRecord comparison is deliberately no t implemented. Explicitly compare the attributes of interest.[] [44] Overfull \hbox (2.74086pt too wide) in paragraph at lines 703--703 []\OT1/cmtt/m/n/10 description='Yersinia pestis biovar Microtus str. 91001 plas mid pPCP1, complete sequence',[] [45] Overfull \hbox (7.99081pt too wide) in paragraph at lines 762--762 []\OT1/cmtt/m/n/10 description='Yersinia pestis biovar Microtus str. 91001 plas mid pPCP1, complete sequence.',[] [46] Overfull \hbox (39.49054pt too wide) in paragraph at lines 839--839 []\OT1/cmtt/m/n/10 >>> sub_record.description = "Yersinia pestis biovar Microtu s str. 91001 plasmid pPCP1, partial."[] [47] Overfull \hbox (7.99081pt too wide) in paragraph at lines 930--930 []\OT1/cmtt/m/n/10 description='Yersinia pestis biovar Microtus str. 91001 plas mid pPCP1, complete sequence.',[] [48] Overfull \hbox (7.99081pt too wide) in paragraph at lines 960--960 []\OT1/cmtt/m/n/10 description='Yersinia pestis biovar Microtus str. 91001 plas mid pPCP1, complete sequence.',[] [49] Overfull \hbox (170.7394pt too wide) in paragraph at lines 1032--1032 []\OT1/cmtt/m/n/10 >>> print("%s %i %i %i %i" % (record.id, len(record), len(re cord.features), len(record.dbxrefs), len(record.annotations)))[] Overfull \hbox (65.74031pt too wide) in paragraph at lines 1042--1042 []\OT1/cmtt/m/n/10 >>> print("%s %i %i %i %i" % (rc.id, len(rc), len(rc.feature s), len(rc.dbxrefs), len(rc.annotations)))[] ) [50] (./Tutorial/chapter_seqio.tex Chapter 5. [51] Overfull \hbox (7.99081pt too wide) in paragraph at lines 66--66 []\OT1/cmtt/m/n/10 >>> identifiers = [seq_record.id for seq_record in SeqIO.par se("ls_orchid.gbk", "genbank")][] [52] [53] [54] [55] [56] Overfull \hbox (18.49072pt too wide) in paragraph at lines 391--391 []\OT1/cmtt/m/n/10 with Entrez.efetch(db="nucleotide", rettype="fasta", retmode ="text", id="6273291") as handle:[] [57] Overfull \hbox (23.74068pt too wide) in paragraph at lines 438--438 [] \OT1/cmtt/m/n/10 % (len(seq_record), len(seq_record.features), seq_record.annotations["source"]))[] Overfull \hbox (18.49072pt too wide) in paragraph at lines 482--482 []\OT1/cmtt/m/n/10 RecName: Full=Chalcone synthase 3; EC=2.3.1.74; AltName: Ful l=Naringenin-chalcone synthase 3;[] [58] [59] Overfull \hbox (34.24059pt too wide) in paragraph at lines 609--609 []\OT1/cmtt/m/n/10 orchid_dict = SeqIO.to_dict(SeqIO.parse("ls_orchid.fasta", " fasta"), key_function=get_accession)[] [60] [61] Overfull \hbox (9.93459pt too wide) in paragraph at lines 769--774 \OT1/cmr/m/n/10 FTP site ([][]$\OT1/cmtt/m/n/10 ftp : / / ftp . uniprot . org / pub / databases / uniprot / current _ release / knowledgebase / complete / [62] Overfull \hbox (4.48064pt too wide) in paragraph at lines 812--815 []\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 , [63] [64] [65] [66] [67] Overfull \hbox (13.24077pt too wide) in paragraph at lines 1174--1174 []\OT1/cmtt/m/n/10 >>> records = [rec.reverse_complement(id="rc_"+rec.id, descr iption = "reverse complement") \[] Overfull \hbox (13.24077pt too wide) in paragraph at lines 1184--1184 []\OT1/cmtt/m/n/10 >>> records = [rec.reverse_complement(id="rc_"+rec.id, descr iption = "reverse complement") \[] Overfull \hbox (13.24077pt too wide) in paragraph at lines 1192--1192 []\OT1/cmtt/m/n/10 >>> records = (rec.reverse_complement(id="rc_"+rec.id, descr iption = "reverse complement") \[] [68] Overfull \hbox (13.24077pt too wide) in paragraph at lines 1203--1203 []\OT1/cmtt/m/n/10 >>> records = (rec.reverse_complement(id="rc_"+rec.id, descr iption = "reverse complement") \[] Overfull \hbox (19.46596pt too wide) in paragraph at lines 1240--1242 \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(...) [69] Overfull \hbox (21.32593pt too wide) in paragraph at lines 1284--1288 []\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 ) [70] (./Tutorial/chapter_align.tex Chapter 6. [71] [72] [73] [74] [75] [76] [77] [78] Overfull \hbox (5.54102pt too wide) in paragraph at lines 435--436 \OT1/cmr/m/n/10 ever you can't do that when your records come from a gen-er-a-t or/it-er-a-tor. There-fore the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write() Overfull \hbox (39.68698pt too wide) in paragraph at lines 443--448 [][]\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() [79] [80] [81] Overfull \hbox (16.49278pt too wide) in paragraph at lines 619--622 []\OT1/cmr/m/n/10 Internally the [][]\OT1/cmtt/m/n/10 format() []\OT1/cmr/m/n/1 0 method is us-ing the [][]\OT1/cmtt/m/n/10 StringIO []\OT1/cmr/m/n/10 string b ased han-dle and call-ing [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write()[]\OT1/cmr/m/ n/10 . [82] [83] [84] [85] [86] [87] Overfull \hbox (8.40039pt too wide) in paragraph at lines 1057--1061 []\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 [88] [89] [90] Overfull \hbox (23.74068pt too wide) in paragraph at lines 1316--1316 []\OT1/cmtt/m/n/10 needle -outfile=needle.txt -asequence=alpha.faa -bsequence=b eta.faa -gapopen=10 -gapextend=0.5[] [91] Overfull \hbox (23.74068pt too wide) in paragraph at lines 1364--1364 []\OT1/cmtt/m/n/10 needle -outfile=needle.txt -asequence=alpha.faa -bsequence=b eta.faa -gapopen=10 -gapextend=0.5[] [92] [93] [94] [95] [96] Overfull \hbox (175.46193pt too wide) in paragraph at lines 1776--1813 [][] [97] [98] [99] [100] [101] Overfull \hbox (19.80069pt too wide) in paragraph at lines 2013--2014 \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) [102] [103]) [104] (./Tutorial/chapter_blast.tex Chapter 7. [105] [106] [107] LaTeX Warning: Reference `sec:parsing-blast-deprecated' on page 108 undefined o n input line 268. [108] [109] Overfull \hbox (55.2404pt too wide) in paragraph at lines 436--436 []\OT1/cmtt/m/n/10 sequence: >gb|AF283004.1|AF283004 Arabidopsis thaliana cold acclimation protein WCOR413-like protein[] [110] Excluding 'htmlonly' comment. Excluding 'htmlonly' comment.) [111] [112 <./images/BlastRecord.png>] [113 <./images/PSIBlastRecord.png>] (./Tutorial/chapter_searchio.tex Chapter 8. [114] 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 [115] [116] [117] [118] [119] Overfull \hbox (44.7405pt too wide) in paragraph at lines 462--462 []\OT1/cmtt/m/n/10 ... hit.id = hit.id.split("|")[3] # renames "gi|301171 322|ref|NR_035857.1|" to "NR_035857.1"[] [120] [121] [122] [123] Overfull \hbox (469.98679pt too wide) in paragraph at lines 731--731 []\OT1/cmtt/m/n/10 SeqRecord(seq=Seq('CCCTCTACAGGGAAGCGCTTTCTGTTGTCTGAAAGAAAAGA AAGTGCTTCCTTT...GGG', DNAAlphabet()), id='42291', name='aligned query sequence' , description='mystery_seq', dbxrefs=[])[] Overfull \hbox (769.23418pt too wide) in paragraph at lines 731--731 []\OT1/cmtt/m/n/10 SeqRecord(seq=Seq('CCCTCTACAGGGAAGCGCTTTCTGTTGTCTGAAAGAAAAGA AAGTGCTTCCTTT...GGG', DNAAlphabet()), id='gi|262205317|ref|NR_030195.1|', name= 'aligned hit sequence', description='Homo sapiens microRNA 520b (MIR520B), micr oRNA', dbxrefs=[])[] Overfull \hbox (27.24287pt too wide) in paragraph at lines 738--740 []\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 [124] [125] Overfull \hbox (65.74031pt too wide) in paragraph at lines 870--870 []\OT1/cmtt/m/n/10 >>> blat_hsp2.hit_inter_ranges # start and end coordinates of intervening regions in the hit sequence[] [126] Overfull \hbox (769.23418pt too wide) in paragraph at lines 962--962 []\OT1/cmtt/m/n/10 SeqRecord(seq=Seq('CCCTCTACAGGGAAGCGCTTTCTGTTGTCTGAAAGAAAAGA AAGTGCTTCCTTT...GGG', DNAAlphabet()), id='gi|262205317|ref|NR_030195.1|', name= 'aligned hit sequence', description='Homo sapiens microRNA 520b (MIR520B), micr oRNA', dbxrefs=[])[] [127] Overfull \hbox (14.20721pt too wide) in paragraph at lines 1050--1054 \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 , Overfull \hbox (20.13245pt too wide) in paragraph at lines 1080--1085 []\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 . [128] Overfull \hbox (13.24077pt too wide) in paragraph at lines 1123--1123 []\OT1/cmtt/m/n/10 >>> idx = SearchIO.index("tab_2226_tblastn_001.txt", "blast- tab", key_function=key_function)[] Overfull \hbox (11.82602pt too wide) in paragraph at lines 1160--1163 []\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 [129]) [130] (./Tutorial/chapter_entrez.tex Chapter 9. [131] [132] [133] [134] Overfull \hbox (70.99026pt too wide) in paragraph at lines 224--224 []\OT1/cmtt/m/n/10 >>> handle = Entrez.esearch(db="nucleotide", term="Cypripedi oideae[Orgn] AND matK[Gene]", idtype="acc")[] [135] [136] [137] [138] Overfull \hbox (13.24077pt too wide) in paragraph at lines 450--450 [] \OT1/cmtt/m/n/10 net_handle = Entrez.efetch(db="nucleotide", id="EU490707 ", rettype="gb", retmode="text")[] [139] [140] [141] [142] Overfull \hbox (312.48816pt too wide) in paragraph at lines 677--677 []\OT1/cmtt/m/n/10 Bio.Entrez.Parser.NotXMLError: Failed to parse the XML data (syntax error: line 1, column 0). Please make sure that the input data are in X ML format.[] [143] Overfull \hbox (249.48871pt too wide) in paragraph at lines 698--698 []\OT1/cmtt/m/n/10 [] Overfull \hbox (370.23766pt too wide) in paragraph at lines 705--705 []\OT1/cmtt/m/n/10 Bio.Entrez.Parser.CorruptedXMLError: Failed to parse the XML data (no element found: line 16, column 0). Please make sure that the input da ta are not corrupted.[] Overfull \hbox (249.48871pt too wide) in paragraph at lines 736--736 []\OT1/cmtt/m/n/10 [] [144] Overfull \hbox (585.48578pt too wide) in paragraph at lines 748--748 []\OT1/cmtt/m/n/10 Bio.Entrez.Parser.ValidationError: Failed to find tag 'Docsu mList' in the DTD. To skip all tags that are not represented in the DTD, please call Bio.Entrez.read or Bio.Entrez.parse with validate=False.[] [145] [146] [147] Overfull \hbox (133.98972pt too wide) in paragraph at lines 970--970 []\OT1/cmtt/m/n/10 EXPRESS bone| connective tissue| intestine| liver| live r tumor| normal| soft tissue/muscle tissue tumor| adult[] Overfull \hbox (102.48999pt too wide) in paragraph at lines 970--970 []\OT1/cmtt/m/n/10 SEQUENCE ACC=BG569293.1; NID=g13576946; CLONE=IMAGE:47225 96; END=5'; LID=6989; SEQTYPE=EST; TRACE=44157214[] [148] Overfull \hbox (160.23949pt too wide) in paragraph at lines 992--992 []\OT1/cmtt/m/n/10 ['bone', 'connective tissue', 'intestine', 'liver', 'liver t umor', 'normal', 'soft tissue/muscle tissue tumor', 'adult'][] [149] [150] Overfull \hbox (23.74068pt too wide) in paragraph at lines 1152--1152 []\OT1/cmtt/m/n/10 >>> handle = Entrez.esearch(db="nucleotide", term="Cypripedi oideae", retmax=814, idtype="acc")[] [151] [152] [153] [154] [155] [156] [157]) [158] (./Tutorial/chapter_uniprot.tex Chapter 10. Overfull \hbox (216.73924pt too wide) in paragraph at lines 30--30 []\OT1/cmtt/m/n/10 >>> handle = TextIOWrapper(urlopen("https://raw.githubuserc ontent.com/biopython/biopython/master/Tests/SwissProt/F2CXE6.txt"))[] Overfull \hbox (137.98993pt too wide) in paragraph at lines 39--39 []\OT1/cmtt/m/n/10 >>> handle = urlopen("https://raw.githubusercontent.com/bio python/biopython/master/Tests/SwissProt/F2CXE6.txt")[] [159] Overfull \hbox (270.48853pt too wide) in paragraph at lines 79--79 []\OT1/cmtt/m/n/10 SubName: Full=Plasma membrane intrinsic protein {ECO:0000313 |EMBL:BAN04711.1}; SubName: Full=Predicted protein {ECO:0000313|EMBL:BAJ87517.1 };[] Overfull \hbox (359.73775pt too wide) in paragraph at lines 79--79 []\OT1/cmtt/m/n/10 authors: Matsumoto T., Tanaka T., Sakai H., Amano N., Kanamo ri H., Kurita K., Kikuta A., Kamiya K., Yamamoto M., Ikawa H., Fujii N., Hori K ., Itoh T., Sato K.[] Overfull \hbox (86.74013pt too wide) in paragraph at lines 79--79 []\OT1/cmtt/m/n/10 title: Comprehensive sequence analysis of 24,783 barley full -length cDNAs derived from 12 clone libraries.[] Overfull \hbox (553.98605pt too wide) in paragraph at lines 79--79 []\OT1/cmtt/m/n/10 ['Eukaryota', 'Viridiplantae', 'Streptophyta', 'Embryophyta' , 'Tracheophyta', 'Spermatophyta', 'Magnoliophyta', 'Liliopsida', 'Poales', 'Po aceae', 'BEP clade', 'Pooideae', 'Triticeae', 'Hordeum'][] Overfull \hbox (7.99081pt too wide) in paragraph at lines 79--79 []\OT1/cmtt/m/n/10 title: Functional characterization of a novel plasma membran e intrinsic protein2 in barley.[] Overfull \hbox (553.98605pt too wide) in paragraph at lines 79--79 []\OT1/cmtt/m/n/10 ['Eukaryota', 'Viridiplantae', 'Streptophyta', 'Embryophyta' , 'Tracheophyta', 'Spermatophyta', 'Magnoliophyta', 'Liliopsida', 'Poales', 'Po aceae', 'BEP clade', 'Pooideae', 'Triticeae', 'Hordeum'][] Overfull \hbox (553.98605pt too wide) in paragraph at lines 79--79 []\OT1/cmtt/m/n/10 ['Eukaryota', 'Viridiplantae', 'Streptophyta', 'Embryophyta' , 'Tracheophyta', 'Spermatophyta', 'Magnoliophyta', 'Liliopsida', 'Poales', 'Po aceae', 'BEP clade', 'Pooideae', 'Triticeae', 'Hordeum'][] [160] [161] [162] [163] [164] [165] Overfull \hbox (24.29903pt too wide) in paragraph at lines 366--367 []\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) 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 [166] Overfull \hbox (133.98972pt too wide) in paragraph at lines 493--493 []\OT1/cmtt/m/n/10 {'signature_ac': u'PS50948', 'level': u'0', 'stop': 98, 'seq uence_ac': u'USERSEQ1', 'start': 16, 'score': u'8.873'}[] [167]) [168] (./Tutorial/chapter_pdb.tex Chapter 11. [169] [170] Overfull \hbox (13.022pt too wide) in paragraph at lines 194--196 \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/-Mod-el/Chain/Residue/A tom) [171] Excluding 'htmlonly' comment. [172] [173 <./images/smcra.png (PNG copy)>] [174] [175] [176] [177] [178] [179] [180] [181] [182] LaTeX Warning: Command \r invalid in math mode on input line 901. [183] [184] [185] [186] [187]) [188] (./Tutorial/chapter_popgen.tex Chapter 12. [189]) [190] (./Tutorial/chapter_phylo.tex Chapter 13. [191] Excluding 'htmlonly' comment. [192] Overfull \hbox (25.13162pt too wide) in paragraph at lines 175--178 []\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 [193 <./images/phylo-simple-draw.png>] Excluding 'htmlonly' comment. [194 <./im ages/phylo-color-draw.png>] [195] Overfull \hbox (406.98734pt too wide) in paragraph at lines 328--328 []\OT1/cmtt/m/n/10 Phylogeny(description='phyloXML allows to use either a "bran ch_length" attribute...', name='example from Prof. Joe Felsenstein's book "Infe rring Phyl...', rooted=True)[] Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. [196] [197 <./images/phylo-draw-example.png> <./i mages/phylo-dot.png>] Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. [198 <./images/phylo-rooted.png> <./images/phylo- color.png>] [199 <./images/phylo-apaf.png> <./images/phylo-apaf-zoom.png>] Overfull \hbox (19.85507pt too wide) in paragraph at lines 559--566 \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"}) [200] Overfull \hbox (13.48741pt too wide) in paragraph at lines 614--617 []\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 , [201] [202] Overfull \hbox (4.04672pt too wide) in paragraph at lines 825--828 []\OT1/cmr/m/n/10 A sim-i-lar wrap-per for RAxML ([][]$\OT1/cmtt/m/n/10 https : / / sco . h-[]its . org / exelixis / software . html$[][]\OT1/cmr/m/n/10 ) was added in Biopy- [203] [204]) [205] (./Tutorial/chapter_motifs.tex Chapter 14. [206] [207] [208] [209] Overfull \hbox (128.73976pt too wide) in paragraph at lines 270--270 []\OT1/cmtt/m/n/10 [Seq('CACGTG', IUPACUnambiguousDNA()), Seq('CACGTG', IUPACUn ambiguousDNA()), Seq('CACGTG', IUPACUnambiguousDNA())][] [210] [211] [212] [213] [214] [215] Overfull \hbox (13.10551pt too wide) in paragraph at lines 582--586 \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 . [216] [217] [218] LaTeX Warning: `h' float specifier changed to `ht'. [219] [220] [221] [222] [223] [224] [225] [226] [227] [228] [229] [230]) [231] (./Tutorial/chapter_cluster.tex Chapter 15. [232] [233] [234] [235] [236] Overfull \hbox (78.60634pt too wide) in paragraph at lines 230--231 \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 $[]$ [237] [238] [239] [240] [241] Overfull \hbox (16.73593pt too wide) in paragraph at lines 413--414 [][]\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 $[]$, [242] [243] [244] [245] [246] Overfull \hbox (106.77225pt too wide) in paragraph at lines 648--650 \OT1/cmr/m/n/10 An ar-ray with di-men-sions $[]$ if rows are be-ing clus-tered, or $[]$ [247] Overfull \hbox (175.98935pt too wide) in paragraph at lines 707--707 []\OT1/cmtt/m/n/10 >>> handle = TextIOWrapper(urlopen("https://raw.githubuserco ntent.com/biopython/biopython/master/Tests/Cluster/cyano.txt"))[] Overfull \hbox (97.24004pt too wide) in paragraph at lines 715--715 []\OT1/cmtt/m/n/10 >>> handle = urlopen("https://raw.githubusercontent.com/biop ython/biopython/master/Tests/Cluster/cyano.txt")[] [248] Overfull \hbox (25.39864pt too wide) in paragraph at lines 740--751 [] [249] [250] [251] [252] Overfull \hbox (106.77225pt too wide) in paragraph at lines 930--932 \OT1/cmr/m/n/10 An ar-ray with di-men-sions $[]$ if rows are be-ing clus-tered, or $[]$ [253]) Overfull \hbox (26.21434pt too wide) in paragraph at lines 986--111 []\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 . [254] (./Tutorial/chapter_learning.tex Chapter 16. [255] [256] [257] [258] [259] Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding): (hyperref) removing `math shift' on input line 278. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding): (hyperref) removing `math shift' on input line 278. [260] Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding): (hyperref) removing `math shift' on input line 286. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding): (hyperref) removing `math shift' on input line 286. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding): (hyperref) removing `math shift' on input line 298. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding): (hyperref) removing `math shift' on input line 298. [261] [262]) [263] (./Tutorial/chapter_graphics.tex Chapter 17. [264] Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. [265] [266 <./images/plasmid_linear.png (PNG copy)> <./images/plasmid_circular.png (P NG copy)>] [267] Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. [268] [269 <./images/GD_sigil_labels.png (PNG copy)>] Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. [270] [271 <./images/GD_sigils.png>] [272 <./imag es/GD_sigil_arrow_shafts.png>] Excluding 'htmlonly' comment. [273 <./images/GD_ sigil_arrow_heads.png>] [274] Excluding 'htmlonly' comment. [275 <./images/plas mid_linear_nice.png (PNG copy)>] [276 <./images/plasmid_circular_nice.png>] Overfull \hbox (2.74086pt too wide) in paragraph at lines 605--605 []\OT1/cmtt/m/n/10 A_colors = [red]*5 + [grey]*7 + [orange]*2 + [grey]*2 + [ora nge] + [grey]*11 + [green]*4 \[] [277] Excluding 'htmlonly' comment. [278 <./images/three_track_simple.png>] [279] Overfull \hbox (28.99063pt too wide) in paragraph at lines 782--782 [] \OT1/cmtt/m/n/10 color = colors.linearlyInterpolatedColor(colors.whit e, colors.firebrick, 0, 100, score)[] Overfull \hbox (2.65141pt too wide) in paragraph at lines 784--790 []\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. Excluding 'htmlonly' comment. [280] [281 <./image s/three_track_cl.png>] [282 <./images/three_track_cl2a.png>] [283] [284 <./imag es/simple_chrom.pdf> <./images/tRNA_chrom.pdf>] [285] Excluding 'htmlonly' comment. [286] Excluding 'htmlonly' comment.) [287] (./Tutorial/chapter_kegg.tex Chapter 18. [288] [289]) [290] (./Tutorial/chapter_phenotype.tex Chapter 19. [291] Overfull \hbox (48.7407pt too wide) in paragraph at lines 102--102 []\OT1/cmtt/m/n/10 PlateRecord('WellRecord['A01'], WellRecord['A02'], WellReco rd['A03'], ..., WellRecord['A12']')[] Overfull \hbox (48.7407pt too wide) in paragraph at lines 102--102 []\OT1/cmtt/m/n/10 PlateRecord('WellRecord['A01'], WellRecord['B01'], WellReco rd['C01'], ..., WellRecord['H01']')[] Overfull \hbox (48.7407pt too wide) in paragraph at lines 102--102 []\OT1/cmtt/m/n/10 PlateRecord('WellRecord['A01'], WellRecord['A02'], WellReco rd['A03'], ..., WellRecord['C03']')[] [292] [293] [294]) [295] (./Tutorial/chapter_cookbook.tex Chapter 20. [296] [297] [298] [299] [300] [301] Overfull \hbox (5.83499pt too wide) in paragraph at lines 426--430 \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 Overfull \hbox (4.57849pt too wide) in paragraph at lines 444--446 \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 . [302] [303] [304] [305] Overfull \hbox (7.99081pt too wide) in paragraph at lines 765--765 []\OT1/cmtt/m/n/10 Seq('GTCCCAGTATTCGGATTTGTCTGCCAAAACAATGAAATTGACACAGTTTACAAC. ..CCG', SingleLetterAlphabet())[] [306] [307] [308] [309] Excluding 'htmlonly' comment. Overfull \hbox (4.00363pt too wide) in paragraph at lines 1057--1060 []\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(...) [310] Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. [311 <./image s/hist_plot.png>] [312 <./images/gc_plot.png>] Excluding 'htmlonly' comment. [313 <./images/dot_plot.png>] Excluding 'htmlonly' comment. [314] Excluding 'htmlonly' comment. [315 <./images/dot_plot_scatter.png>] [316 <./ima ges/SRR001666.png>] [317] Overfull \hbox (49.0755pt too wide) in paragraph at lines 1460--1461 []\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 . [318] [319] [320] [321]) [322] (./Tutorial/chapter_testing.tex Chapter 21. [323] [324] [325] [326] [327] [328] [329] (/usr/share/texlive/texmf-dist/tex/latex/base/omlcmr.fd)) [330] (./Tutorial/chapter_advanced.tex Chapter 22. [331] [332] Overfull \hbox (30.74179pt too wide) in paragraph at lines 198--199 [][][]\OT1/cmtt/m/n/10 factor[]\OT1/cmr/m/n/10 : fac-tor used to mul-ti-ply the log-odds val-ues. Each en-try is gen-er-ated by log(LOM[key])*factor [333] [334]) [335] (./Tutorial/chapter_contributing.tex Chapter 23. [336] [337]) [338] (./Tutorial/chapter_appendix.tex Chapter 24. [339]) [340] [341] [342] [343] (./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_advanced.aux) (./Tutorial/chapter_contributing.aux) (./Tutorial/chapter_appendix.aux)) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information)< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pfb> Output written on Tutorial.pdf (344 pages, 2487376 bytes). Transcript written on Tutorial.log. pdflatex Tutorial.tex This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Tutorial.tex LaTeX2e <2019-10-01> patch level 1 (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2019/08/27 v1.4j 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/listings/listings.sty (/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty) (/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 65. 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Excluding 'rawhtml' comment. [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.m ap} <./images/biopython_logo.pdf>] (./Tutorial.tocpdfTeX warning (ext4): destin ation with the same identifier (name{page.1}) has been already used, duplicate ignored \relax l.39 ...tions and locations}{40}{subsection.4.3.2} % [1] [2] [3] [4] [5] [6] [7]) [8] (./Tutorial/chapter_introduction.tex Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [9] [10] Excluding 'rawhtml' comment. Underfull \hbox (badness 10000) in paragraph at lines 141--147 Underfull \hbox (badness 10000) in paragraph at lines 153--155 [11 <./images/biopython_logo_old.jpg>] [12] Overfull \hbox (2.99303pt too wide) in paragraph at lines 246--248 \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 . [13]) [14] (./Tutorial/chapter_quick_start.tex Chapter 2. [15] [16] Overfull \hbox (7.99081pt too wide) in paragraph at lines 117--117 []\OT1/cmtt/m/n/10 Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGATGAGACCGTGG. ..CGC', SingleLetterAlphabet())[] Overfull \hbox (7.99081pt too wide) in paragraph at lines 117--117 []\OT1/cmtt/m/n/10 Seq('CATTGTTGAGATCACATAATAATTGATCGAGTTAATCTGGAGGATCTGTTTACT. ..GCC', SingleLetterAlphabet())[] [17] [18]) [19] (./Tutorial/chapter_seq_objects.tex Chapter 3. [20] [21] [22] [23] Overfull \hbox (39.49054pt too wide) in paragraph at lines 274--274 []\OT1/cmtt/m/n/10 >>> list_of_seqs = [Seq("ACGT", generic_dna), Seq("AACC", ge neric_dna), Seq("GGTT", generic_dna)][] Overfull \hbox (39.49054pt too wide) in paragraph at lines 285--285 []\OT1/cmtt/m/n/10 >>> list_of_seqs = [Seq("ACGT", generic_dna), Seq("AACC", ge neric_dna), Seq("GGTT", generic_dna)][] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33]) [34] (./Tutorial/chapter_seq_annot.tex Chapter 4. [35] [36] Overfull \hbox (2.74086pt too wide) in paragraph at lines 129--129 []\OT1/cmtt/m/n/10 >gi|45478711|ref|NC_005816.1| Yersinia pestis biovar Microtu s ... pPCP1, complete sequence[] Overfull \hbox (34.24059pt too wide) in paragraph at lines 144--144 []\OT1/cmtt/m/n/10 SingleLetterAlphabet()), id='gi|45478711|ref|NC_005816.1|', name='gi|45478711|ref|NC_005816.1|',[] Overfull \hbox (7.99081pt too wide) in paragraph at lines 153--153 []\OT1/cmtt/m/n/10 Seq('TGTAACGAACGGTGCAATAGTGATCCACACCCAACGCCTGAAATCAGATCCAGG. ..CTG', SingleLetterAlphabet())[] Overfull \hbox (7.99081pt too wide) in paragraph at lines 169--169 []\OT1/cmtt/m/n/10 'gi|45478711|ref|NC_005816.1| Yersinia pestis biovar Microtu s ... pPCP1, complete sequence'[] [37] Overfull \hbox (7.99081pt too wide) in paragraph at lines 226--226 []\OT1/cmtt/m/n/10 description='Yersinia pestis biovar Microtus str. 91001 plas mid pPCP1, complete sequence.',[] [38] [39] [40] [41] [42] Overfull \hbox (44.7405pt too wide) in paragraph at lines 536--536 []\OT1/cmtt/m/n/10 >>> example_parent = Seq("ACCGAGACGGCAAAGGCTAGCATAGGTATGAGAC TTCCTTCCTGCCAGTGCTGAGGAACTGGGAGCCTAC")[] Overfull \hbox (128.73976pt too wide) in paragraph at lines 546--546 []\OT1/cmtt/m/n/10 >>> feature_seq = example_parent[example_feature.location.st art:example_feature.location.end].reverse_complement()[] [43] Overfull \hbox (165.48944pt too wide) in paragraph at lines 618--618 []\OT1/cmtt/m/n/10 NotImplementedError: SeqRecord comparison is deliberately no t implemented. Explicitly compare the attributes of interest.[] [44] Overfull \hbox (2.74086pt too wide) in paragraph at lines 703--703 []\OT1/cmtt/m/n/10 description='Yersinia pestis biovar Microtus str. 91001 plas mid pPCP1, complete sequence',[] [45] Overfull \hbox (7.99081pt too wide) in paragraph at lines 762--762 []\OT1/cmtt/m/n/10 description='Yersinia pestis biovar Microtus str. 91001 plas mid pPCP1, complete sequence.',[] [46] Overfull \hbox (39.49054pt too wide) in paragraph at lines 839--839 []\OT1/cmtt/m/n/10 >>> sub_record.description = "Yersinia pestis biovar Microtu s str. 91001 plasmid pPCP1, partial."[] [47] Overfull \hbox (7.99081pt too wide) in paragraph at lines 930--930 []\OT1/cmtt/m/n/10 description='Yersinia pestis biovar Microtus str. 91001 plas mid pPCP1, complete sequence.',[] [48] Overfull \hbox (7.99081pt too wide) in paragraph at lines 960--960 []\OT1/cmtt/m/n/10 description='Yersinia pestis biovar Microtus str. 91001 plas mid pPCP1, complete sequence.',[] [49] Overfull \hbox (170.7394pt too wide) in paragraph at lines 1032--1032 []\OT1/cmtt/m/n/10 >>> print("%s %i %i %i %i" % (record.id, len(record), len(re cord.features), len(record.dbxrefs), len(record.annotations)))[] Overfull \hbox (65.74031pt too wide) in paragraph at lines 1042--1042 []\OT1/cmtt/m/n/10 >>> print("%s %i %i %i %i" % (rc.id, len(rc), len(rc.feature s), len(rc.dbxrefs), len(rc.annotations)))[] ) [50] (./Tutorial/chapter_seqio.tex Chapter 5. [51] Overfull \hbox (7.99081pt too wide) in paragraph at lines 66--66 []\OT1/cmtt/m/n/10 >>> identifiers = [seq_record.id for seq_record in SeqIO.par se("ls_orchid.gbk", "genbank")][] [52] [53] [54] [55] [56] Overfull \hbox (18.49072pt too wide) in paragraph at lines 391--391 []\OT1/cmtt/m/n/10 with Entrez.efetch(db="nucleotide", rettype="fasta", retmode ="text", id="6273291") as handle:[] [57] Overfull \hbox (23.74068pt too wide) in paragraph at lines 438--438 [] \OT1/cmtt/m/n/10 % (len(seq_record), len(seq_record.features), seq_record.annotations["source"]))[] Overfull \hbox (18.49072pt too wide) in paragraph at lines 482--482 []\OT1/cmtt/m/n/10 RecName: Full=Chalcone synthase 3; EC=2.3.1.74; AltName: Ful l=Naringenin-chalcone synthase 3;[] [58] [59] Overfull \hbox (34.24059pt too wide) in paragraph at lines 609--609 []\OT1/cmtt/m/n/10 orchid_dict = SeqIO.to_dict(SeqIO.parse("ls_orchid.fasta", " fasta"), key_function=get_accession)[] [60] [61] Overfull \hbox (9.93459pt too wide) in paragraph at lines 769--774 \OT1/cmr/m/n/10 FTP site ([][]$\OT1/cmtt/m/n/10 ftp : / / ftp . uniprot . org / pub / databases / uniprot / current _ release / knowledgebase / complete / [62] Overfull \hbox (4.48064pt too wide) in paragraph at lines 812--815 []\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 , [63] [64] [65] [66] [67] Overfull \hbox (13.24077pt too wide) in paragraph at lines 1174--1174 []\OT1/cmtt/m/n/10 >>> records = [rec.reverse_complement(id="rc_"+rec.id, descr iption = "reverse complement") \[] Overfull \hbox (13.24077pt too wide) in paragraph at lines 1184--1184 []\OT1/cmtt/m/n/10 >>> records = [rec.reverse_complement(id="rc_"+rec.id, descr iption = "reverse complement") \[] Overfull \hbox (13.24077pt too wide) in paragraph at lines 1192--1192 []\OT1/cmtt/m/n/10 >>> records = (rec.reverse_complement(id="rc_"+rec.id, descr iption = "reverse complement") \[] [68] Overfull \hbox (13.24077pt too wide) in paragraph at lines 1203--1203 []\OT1/cmtt/m/n/10 >>> records = (rec.reverse_complement(id="rc_"+rec.id, descr iption = "reverse complement") \[] Overfull \hbox (19.46596pt too wide) in paragraph at lines 1240--1242 \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(...) [69] Overfull \hbox (21.32593pt too wide) in paragraph at lines 1284--1288 []\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 ) [70] (./Tutorial/chapter_align.tex Chapter 6. [71] [72] [73] [74] [75] [76] [77] [78] Overfull \hbox (5.54102pt too wide) in paragraph at lines 435--436 \OT1/cmr/m/n/10 ever you can't do that when your records come from a gen-er-a-t or/it-er-a-tor. There-fore the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write() Overfull \hbox (39.68698pt too wide) in paragraph at lines 443--448 [][]\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() [79] [80] [81] Overfull \hbox (16.49278pt too wide) in paragraph at lines 619--622 []\OT1/cmr/m/n/10 Internally the [][]\OT1/cmtt/m/n/10 format() []\OT1/cmr/m/n/1 0 method is us-ing the [][]\OT1/cmtt/m/n/10 StringIO []\OT1/cmr/m/n/10 string b ased han-dle and call-ing [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write()[]\OT1/cmr/m/ n/10 . [82] [83] [84] [85] [86] [87] Overfull \hbox (8.40039pt too wide) in paragraph at lines 1057--1061 []\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 [88] [89] [90] Overfull \hbox (23.74068pt too wide) in paragraph at lines 1316--1316 []\OT1/cmtt/m/n/10 needle -outfile=needle.txt -asequence=alpha.faa -bsequence=b eta.faa -gapopen=10 -gapextend=0.5[] [91] Overfull \hbox (23.74068pt too wide) in paragraph at lines 1364--1364 []\OT1/cmtt/m/n/10 needle -outfile=needle.txt -asequence=alpha.faa -bsequence=b eta.faa -gapopen=10 -gapextend=0.5[] [92] [93] [94] [95] [96] Overfull \hbox (175.46193pt too wide) in paragraph at lines 1776--1813 [][] [97] [98] [99] [100] [101] Overfull \hbox (19.80069pt too wide) in paragraph at lines 2013--2014 \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) [102] [103]) [104] (./Tutorial/chapter_blast.tex Chapter 7. [105] [106] [107] LaTeX Warning: Reference `sec:parsing-blast-deprecated' on page 108 undefined o n input line 268. [108] [109] Overfull \hbox (55.2404pt too wide) in paragraph at lines 436--436 []\OT1/cmtt/m/n/10 sequence: >gb|AF283004.1|AF283004 Arabidopsis thaliana cold acclimation protein WCOR413-like protein[] [110] Excluding 'htmlonly' comment. Excluding 'htmlonly' comment.) [111] [112 <./images/BlastRecord.png>] [113 <./images/PSIBlastRecord.png>] (./Tutorial/chapter_searchio.tex Chapter 8. [114] 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 [115] [116] [117] [118] [119] Overfull \hbox (44.7405pt too wide) in paragraph at lines 462--462 []\OT1/cmtt/m/n/10 ... hit.id = hit.id.split("|")[3] # renames "gi|301171 322|ref|NR_035857.1|" to "NR_035857.1"[] [120] [121] [122] [123] Overfull \hbox (469.98679pt too wide) in paragraph at lines 731--731 []\OT1/cmtt/m/n/10 SeqRecord(seq=Seq('CCCTCTACAGGGAAGCGCTTTCTGTTGTCTGAAAGAAAAGA AAGTGCTTCCTTT...GGG', DNAAlphabet()), id='42291', name='aligned query sequence' , description='mystery_seq', dbxrefs=[])[] Overfull \hbox (769.23418pt too wide) in paragraph at lines 731--731 []\OT1/cmtt/m/n/10 SeqRecord(seq=Seq('CCCTCTACAGGGAAGCGCTTTCTGTTGTCTGAAAGAAAAGA AAGTGCTTCCTTT...GGG', DNAAlphabet()), id='gi|262205317|ref|NR_030195.1|', name= 'aligned hit sequence', description='Homo sapiens microRNA 520b (MIR520B), micr oRNA', dbxrefs=[])[] Overfull \hbox (27.24287pt too wide) in paragraph at lines 738--740 []\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 [124] [125] Overfull \hbox (65.74031pt too wide) in paragraph at lines 870--870 []\OT1/cmtt/m/n/10 >>> blat_hsp2.hit_inter_ranges # start and end coordinates of intervening regions in the hit sequence[] [126] Overfull \hbox (769.23418pt too wide) in paragraph at lines 962--962 []\OT1/cmtt/m/n/10 SeqRecord(seq=Seq('CCCTCTACAGGGAAGCGCTTTCTGTTGTCTGAAAGAAAAGA AAGTGCTTCCTTT...GGG', DNAAlphabet()), id='gi|262205317|ref|NR_030195.1|', name= 'aligned hit sequence', description='Homo sapiens microRNA 520b (MIR520B), micr oRNA', dbxrefs=[])[] [127] Overfull \hbox (14.20721pt too wide) in paragraph at lines 1050--1054 \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 , Overfull \hbox (20.13245pt too wide) in paragraph at lines 1080--1085 []\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 . [128] Overfull \hbox (13.24077pt too wide) in paragraph at lines 1123--1123 []\OT1/cmtt/m/n/10 >>> idx = SearchIO.index("tab_2226_tblastn_001.txt", "blast- tab", key_function=key_function)[] Overfull \hbox (11.82602pt too wide) in paragraph at lines 1160--1163 []\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 [129]) [130] (./Tutorial/chapter_entrez.tex Chapter 9. [131] [132] [133] [134] Overfull \hbox (70.99026pt too wide) in paragraph at lines 224--224 []\OT1/cmtt/m/n/10 >>> handle = Entrez.esearch(db="nucleotide", term="Cypripedi oideae[Orgn] AND matK[Gene]", idtype="acc")[] [135] [136] [137] [138] Overfull \hbox (13.24077pt too wide) in paragraph at lines 450--450 [] \OT1/cmtt/m/n/10 net_handle = Entrez.efetch(db="nucleotide", id="EU490707 ", rettype="gb", retmode="text")[] [139] [140] [141] [142] Overfull \hbox (312.48816pt too wide) in paragraph at lines 677--677 []\OT1/cmtt/m/n/10 Bio.Entrez.Parser.NotXMLError: Failed to parse the XML data (syntax error: line 1, column 0). Please make sure that the input data are in X ML format.[] [143] Overfull \hbox (249.48871pt too wide) in paragraph at lines 698--698 []\OT1/cmtt/m/n/10 [] Overfull \hbox (370.23766pt too wide) in paragraph at lines 705--705 []\OT1/cmtt/m/n/10 Bio.Entrez.Parser.CorruptedXMLError: Failed to parse the XML data (no element found: line 16, column 0). Please make sure that the input da ta are not corrupted.[] Overfull \hbox (249.48871pt too wide) in paragraph at lines 736--736 []\OT1/cmtt/m/n/10 [] [144] Overfull \hbox (585.48578pt too wide) in paragraph at lines 748--748 []\OT1/cmtt/m/n/10 Bio.Entrez.Parser.ValidationError: Failed to find tag 'Docsu mList' in the DTD. To skip all tags that are not represented in the DTD, please call Bio.Entrez.read or Bio.Entrez.parse with validate=False.[] [145] [146] [147] Overfull \hbox (133.98972pt too wide) in paragraph at lines 970--970 []\OT1/cmtt/m/n/10 EXPRESS bone| connective tissue| intestine| liver| live r tumor| normal| soft tissue/muscle tissue tumor| adult[] Overfull \hbox (102.48999pt too wide) in paragraph at lines 970--970 []\OT1/cmtt/m/n/10 SEQUENCE ACC=BG569293.1; NID=g13576946; CLONE=IMAGE:47225 96; END=5'; LID=6989; SEQTYPE=EST; TRACE=44157214[] [148] Overfull \hbox (160.23949pt too wide) in paragraph at lines 992--992 []\OT1/cmtt/m/n/10 ['bone', 'connective tissue', 'intestine', 'liver', 'liver t umor', 'normal', 'soft tissue/muscle tissue tumor', 'adult'][] [149] [150] Overfull \hbox (23.74068pt too wide) in paragraph at lines 1152--1152 []\OT1/cmtt/m/n/10 >>> handle = Entrez.esearch(db="nucleotide", term="Cypripedi oideae", retmax=814, idtype="acc")[] [151] [152] [153] [154] [155] [156] [157]) [158] (./Tutorial/chapter_uniprot.tex Chapter 10. Overfull \hbox (216.73924pt too wide) in paragraph at lines 30--30 []\OT1/cmtt/m/n/10 >>> handle = TextIOWrapper(urlopen("https://raw.githubuserc ontent.com/biopython/biopython/master/Tests/SwissProt/F2CXE6.txt"))[] Overfull \hbox (137.98993pt too wide) in paragraph at lines 39--39 []\OT1/cmtt/m/n/10 >>> handle = urlopen("https://raw.githubusercontent.com/bio python/biopython/master/Tests/SwissProt/F2CXE6.txt")[] [159] Overfull \hbox (270.48853pt too wide) in paragraph at lines 79--79 []\OT1/cmtt/m/n/10 SubName: Full=Plasma membrane intrinsic protein {ECO:0000313 |EMBL:BAN04711.1}; SubName: Full=Predicted protein {ECO:0000313|EMBL:BAJ87517.1 };[] Overfull \hbox (359.73775pt too wide) in paragraph at lines 79--79 []\OT1/cmtt/m/n/10 authors: Matsumoto T., Tanaka T., Sakai H., Amano N., Kanamo ri H., Kurita K., Kikuta A., Kamiya K., Yamamoto M., Ikawa H., Fujii N., Hori K ., Itoh T., Sato K.[] Overfull \hbox (86.74013pt too wide) in paragraph at lines 79--79 []\OT1/cmtt/m/n/10 title: Comprehensive sequence analysis of 24,783 barley full -length cDNAs derived from 12 clone libraries.[] Overfull \hbox (553.98605pt too wide) in paragraph at lines 79--79 []\OT1/cmtt/m/n/10 ['Eukaryota', 'Viridiplantae', 'Streptophyta', 'Embryophyta' , 'Tracheophyta', 'Spermatophyta', 'Magnoliophyta', 'Liliopsida', 'Poales', 'Po aceae', 'BEP clade', 'Pooideae', 'Triticeae', 'Hordeum'][] Overfull \hbox (7.99081pt too wide) in paragraph at lines 79--79 []\OT1/cmtt/m/n/10 title: Functional characterization of a novel plasma membran e intrinsic protein2 in barley.[] Overfull \hbox (553.98605pt too wide) in paragraph at lines 79--79 []\OT1/cmtt/m/n/10 ['Eukaryota', 'Viridiplantae', 'Streptophyta', 'Embryophyta' , 'Tracheophyta', 'Spermatophyta', 'Magnoliophyta', 'Liliopsida', 'Poales', 'Po aceae', 'BEP clade', 'Pooideae', 'Triticeae', 'Hordeum'][] Overfull \hbox (553.98605pt too wide) in paragraph at lines 79--79 []\OT1/cmtt/m/n/10 ['Eukaryota', 'Viridiplantae', 'Streptophyta', 'Embryophyta' , 'Tracheophyta', 'Spermatophyta', 'Magnoliophyta', 'Liliopsida', 'Poales', 'Po aceae', 'BEP clade', 'Pooideae', 'Triticeae', 'Hordeum'][] [160] [161] [162] [163] [164] [165] Overfull \hbox (24.29903pt too wide) in paragraph at lines 366--367 []\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) 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 [166] Overfull \hbox (133.98972pt too wide) in paragraph at lines 493--493 []\OT1/cmtt/m/n/10 {'signature_ac': u'PS50948', 'level': u'0', 'stop': 98, 'seq uence_ac': u'USERSEQ1', 'start': 16, 'score': u'8.873'}[] [167]) [168] (./Tutorial/chapter_pdb.tex Chapter 11. [169] [170] Overfull \hbox (13.022pt too wide) in paragraph at lines 194--196 \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/-Mod-el/Chain/Residue/A tom) [171] Excluding 'htmlonly' comment. [172] [173 <./images/smcra.png (PNG copy)>] [174] [175] [176] [177] [178] [179] [180] [181] [182] LaTeX Warning: Command \r invalid in math mode on input line 901. [183] [184] [185] [186] [187]) [188] (./Tutorial/chapter_popgen.tex Chapter 12. [189]) [190] (./Tutorial/chapter_phylo.tex Chapter 13. [191] Excluding 'htmlonly' comment. [192] Overfull \hbox (25.13162pt too wide) in paragraph at lines 175--178 []\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 [193 <./images/phylo-simple-draw.png>] Excluding 'htmlonly' comment. [194 <./im ages/phylo-color-draw.png>] [195] Overfull \hbox (406.98734pt too wide) in paragraph at lines 328--328 []\OT1/cmtt/m/n/10 Phylogeny(description='phyloXML allows to use either a "bran ch_length" attribute...', name='example from Prof. Joe Felsenstein's book "Infe rring Phyl...', rooted=True)[] Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. [196] [197 <./images/phylo-draw-example.png> <./i mages/phylo-dot.png>] Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. [198 <./images/phylo-rooted.png> <./images/phylo- color.png>] [199 <./images/phylo-apaf.png> <./images/phylo-apaf-zoom.png>] Overfull \hbox (19.85507pt too wide) in paragraph at lines 559--566 \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"}) [200] Overfull \hbox (13.48741pt too wide) in paragraph at lines 614--617 []\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 , [201] [202] Overfull \hbox (4.04672pt too wide) in paragraph at lines 825--828 []\OT1/cmr/m/n/10 A sim-i-lar wrap-per for RAxML ([][]$\OT1/cmtt/m/n/10 https : / / sco . h-[]its . org / exelixis / software . html$[][]\OT1/cmr/m/n/10 ) was added in Biopy- [203] [204]) [205] (./Tutorial/chapter_motifs.tex Chapter 14. [206] [207] [208] [209] Overfull \hbox (128.73976pt too wide) in paragraph at lines 270--270 []\OT1/cmtt/m/n/10 [Seq('CACGTG', IUPACUnambiguousDNA()), Seq('CACGTG', IUPACUn ambiguousDNA()), Seq('CACGTG', IUPACUnambiguousDNA())][] [210] [211] [212] [213] [214] [215] Overfull \hbox (13.10551pt too wide) in paragraph at lines 582--586 \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 . [216] [217] [218] LaTeX Warning: `h' float specifier changed to `ht'. [219] [220] [221] [222] [223] [224] [225] [226] [227] [228] [229] [230]) [231] (./Tutorial/chapter_cluster.tex Chapter 15. [232] [233] [234] [235] [236] Overfull \hbox (78.60634pt too wide) in paragraph at lines 230--231 \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 $[]$ [237] [238] [239] [240] [241] Overfull \hbox (16.73593pt too wide) in paragraph at lines 413--414 [][]\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 $[]$, [242] [243] [244] [245] [246] Overfull \hbox (106.77225pt too wide) in paragraph at lines 648--650 \OT1/cmr/m/n/10 An ar-ray with di-men-sions $[]$ if rows are be-ing clus-tered, or $[]$ [247] Overfull \hbox (175.98935pt too wide) in paragraph at lines 707--707 []\OT1/cmtt/m/n/10 >>> handle = TextIOWrapper(urlopen("https://raw.githubuserco ntent.com/biopython/biopython/master/Tests/Cluster/cyano.txt"))[] Overfull \hbox (97.24004pt too wide) in paragraph at lines 715--715 []\OT1/cmtt/m/n/10 >>> handle = urlopen("https://raw.githubusercontent.com/biop ython/biopython/master/Tests/Cluster/cyano.txt")[] [248] Overfull \hbox (25.39864pt too wide) in paragraph at lines 740--751 [] [249] [250] [251] [252] Overfull \hbox (106.77225pt too wide) in paragraph at lines 930--932 \OT1/cmr/m/n/10 An ar-ray with di-men-sions $[]$ if rows are be-ing clus-tered, or $[]$ [253]) Overfull \hbox (26.21434pt too wide) in paragraph at lines 986--111 []\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 . [254] (./Tutorial/chapter_learning.tex Chapter 16. [255] [256] [257] [258] [259] Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding): (hyperref) removing `math shift' on input line 278. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding): (hyperref) removing `math shift' on input line 278. [260] Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding): (hyperref) removing `math shift' on input line 286. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding): (hyperref) removing `math shift' on input line 286. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding): (hyperref) removing `math shift' on input line 298. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding): (hyperref) removing `math shift' on input line 298. [261] [262]) [263] (./Tutorial/chapter_graphics.tex Chapter 17. [264] Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. [265] [266 <./images/plasmid_linear.png (PNG copy)> <./images/plasmid_circular.png (P NG copy)>] [267] Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. [268] [269 <./images/GD_sigil_labels.png (PNG copy)>] Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. [270] [271 <./images/GD_sigils.png>] [272 <./imag es/GD_sigil_arrow_shafts.png>] Excluding 'htmlonly' comment. [273 <./images/GD_ sigil_arrow_heads.png>] [274] Excluding 'htmlonly' comment. [275 <./images/plas mid_linear_nice.png (PNG copy)>] [276 <./images/plasmid_circular_nice.png>] Overfull \hbox (2.74086pt too wide) in paragraph at lines 605--605 []\OT1/cmtt/m/n/10 A_colors = [red]*5 + [grey]*7 + [orange]*2 + [grey]*2 + [ora nge] + [grey]*11 + [green]*4 \[] [277] Excluding 'htmlonly' comment. [278 <./images/three_track_simple.png>] [279] Overfull \hbox (28.99063pt too wide) in paragraph at lines 782--782 [] \OT1/cmtt/m/n/10 color = colors.linearlyInterpolatedColor(colors.whit e, colors.firebrick, 0, 100, score)[] Overfull \hbox (2.65141pt too wide) in paragraph at lines 784--790 []\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. Excluding 'htmlonly' comment. [280] [281 <./image s/three_track_cl.png>] [282 <./images/three_track_cl2a.png>] [283] [284 <./imag es/simple_chrom.pdf> <./images/tRNA_chrom.pdf>] [285] Excluding 'htmlonly' comment. [286] Excluding 'htmlonly' comment.) [287] (./Tutorial/chapter_kegg.tex Chapter 18. [288] [289]) [290] (./Tutorial/chapter_phenotype.tex Chapter 19. [291] Overfull \hbox (48.7407pt too wide) in paragraph at lines 102--102 []\OT1/cmtt/m/n/10 PlateRecord('WellRecord['A01'], WellRecord['A02'], WellReco rd['A03'], ..., WellRecord['A12']')[] Overfull \hbox (48.7407pt too wide) in paragraph at lines 102--102 []\OT1/cmtt/m/n/10 PlateRecord('WellRecord['A01'], WellRecord['B01'], WellReco rd['C01'], ..., WellRecord['H01']')[] Overfull \hbox (48.7407pt too wide) in paragraph at lines 102--102 []\OT1/cmtt/m/n/10 PlateRecord('WellRecord['A01'], WellRecord['A02'], WellReco rd['A03'], ..., WellRecord['C03']')[] [292] [293] [294]) [295] (./Tutorial/chapter_cookbook.tex Chapter 20. [296] [297] [298] [299] [300] [301] Overfull \hbox (5.83499pt too wide) in paragraph at lines 426--430 \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 Overfull \hbox (4.57849pt too wide) in paragraph at lines 444--446 \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 . [302] [303] [304] [305] Overfull \hbox (7.99081pt too wide) in paragraph at lines 765--765 []\OT1/cmtt/m/n/10 Seq('GTCCCAGTATTCGGATTTGTCTGCCAAAACAATGAAATTGACACAGTTTACAAC. ..CCG', SingleLetterAlphabet())[] [306] [307] [308] [309] Excluding 'htmlonly' comment. Overfull \hbox (4.00363pt too wide) in paragraph at lines 1057--1060 []\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(...) [310] Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. [311 <./image s/hist_plot.png>] [312 <./images/gc_plot.png>] Excluding 'htmlonly' comment. [313 <./images/dot_plot.png>] Excluding 'htmlonly' comment. [314] Excluding 'htmlonly' comment. [315 <./images/dot_plot_scatter.png>] [316 <./ima ges/SRR001666.png>] [317] Overfull \hbox (49.0755pt too wide) in paragraph at lines 1460--1461 []\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 . [318] [319] [320] [321]) [322] (./Tutorial/chapter_testing.tex Chapter 21. [323] [324] [325] [326] [327] [328] [329] (/usr/share/texlive/texmf-dist/tex/latex/base/omlcmr.fd)) [330] (./Tutorial/chapter_advanced.tex Chapter 22. [331] [332] Overfull \hbox (30.74179pt too wide) in paragraph at lines 198--199 [][][]\OT1/cmtt/m/n/10 factor[]\OT1/cmr/m/n/10 : fac-tor used to mul-ti-ply the log-odds val-ues. Each en-try is gen-er-ated by log(LOM[key])*factor [333] [334]) [335] (./Tutorial/chapter_contributing.tex Chapter 23. [336] [337]) [338] (./Tutorial/chapter_appendix.tex Chapter 24. [339]) [340] [341] [342] [343] (./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_advanced.aux) (./Tutorial/chapter_contributing.aux) (./Tutorial/chapter_appendix.aux)) LaTeX Warning: There were undefined references. ) (see the transcript file for additional information)< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pfb> Output written on Tutorial.pdf (344 pages, 2487370 bytes). Transcript written on Tutorial.log. pdflatex biopdb_faq.tex This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./biopdb_faq.tex LaTeX2e <2019-10-01> patch level 1 (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2019/08/27 v1.4j 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/base/t1enc.def)) (/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/oberdiek/ifpdf.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.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/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 56. 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[9] LaTeX Warning: Reference `sub:Analysis' on page 10 undefined on input line 805. [10] Overfull \hbox (45.08351pt too wide) in paragraph at lines 960--964 \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 968--973 \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 LaTeX Warning: Reference `cap:DSSP-codes' on page 11 undefined on input line 99 0. [11] Overfull \hbox (87.74638pt too wide) in paragraph at lines 1097--1098 []\T1/pcr/m/n/10 # Calculate classical coordination number exp_fs=hse.calc_fs_e xposure(model) [12] Overfull \hbox (20.6135pt too wide) in paragraph at lines 1118--1123 \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 1280--1288 []\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) Package rerunfilecheck Warning: File `biopdb_faq.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. 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The se-quence of each polypep-tide can then eas-ily be ob- tained from the \T1/pcr/m/n/10 Polypeptide [11] Overfull \hbox (87.74638pt too wide) in paragraph at lines 1097--1098 []\T1/pcr/m/n/10 # Calculate classical coordination number exp_fs=hse.calc_fs_e xposure(model) [12] Overfull \hbox (20.6135pt too wide) in paragraph at lines 1118--1123 \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 1280--1288 []\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, 164414 bytes). 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(/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/switch.def) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def)))) (./biopdb_faq.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pbk.fd) *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/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.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/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./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/omspbk.fd) [2] Overfull \hbox (21.75009pt too wide) in paragraph at lines 257--262 \T1/pbk/l/n/10 file to their val-ues. 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The se-quence of each polypep-tide can then eas-ily be ob- tained from the \T1/pcr/m/n/10 Polypeptide [11] Overfull \hbox (87.74638pt too wide) in paragraph at lines 1097--1098 []\T1/pcr/m/n/10 # Calculate classical coordination number exp_fs=hse.calc_fs_e xposure(model) [12] Overfull \hbox (20.6135pt too wide) in paragraph at lines 1118--1123 \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 1280--1288 []\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, 164414 bytes). Transcript written on biopdb_faq.log. make -C install make[3]: Entering directory '/<>/python-biopython-1.73+dfsg/Doc/install' pdflatex Installation.tex This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Installation.tex LaTeX2e <2019-10-01> patch level 1 (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2019/08/27 v1.4j 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/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 52. 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Overfull \hbox (9.0224pt too wide) in paragraph at lines 540--541 []\OT1/cmr/m/n/10 For Python 2.6 we cur-rently use Mi-crosoft's free VC++ 2008 Ex-press Edi-tion from [][]$\OT1/cmtt/m/n/10 http : / / www . microsoft . LaTeX Warning: Reference `sec:is_working' on page 8 undefined on input line 558 . Overfull \hbox (27.57379pt too wide) in paragraph at lines 563--565 [][]\OT1/cmtt/m/n/10 PYTHONPATH []\OT1/cmr/m/n/10 with some-thing like [][]\OT1 /cmtt/m/n/10 export PYTHONPATH = $PYTHONPATH':/directory/where/you/put/Biopytho n' [8] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) Overfull \hbox (9.6602pt too wide) in paragraph at lines 600--601 []\OT1/cmr/m/n/10 NCBI Stan-dalone BLAST, which can used with the [][]\OT1/cmtt /m/n/10 Bio.Blast []\OT1/cmr/m/n/10 mod-ule and parsed with the [][]\OT1/cmtt/m /n/10 Bio.SearchIO [9] [10] (./Installation.aux) Package rerunfilecheck Warning: File `Installation.out' has changed. 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Transcript written on Installation.log. pdflatex Installation.tex This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Installation.tex LaTeX2e <2019-10-01> patch level 1 (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2019/08/27 v1.4j 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/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 52. (./Installation.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/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.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/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./Installation.out) (./Installation.out) (./Installation.toc) [1{/var/lib/texm f/fonts/map/pdftex/updmap/pdftex.map}] [2] [3] [4] [5] [6] [7] Overfull \hbox (9.0224pt too wide) in paragraph at lines 540--541 []\OT1/cmr/m/n/10 For Python 2.6 we cur-rently use Mi-crosoft's free VC++ 2008 Ex-press Edi-tion from [][]$\OT1/cmtt/m/n/10 http : / / www . microsoft . [8] Overfull \hbox (27.57379pt too wide) in paragraph at lines 563--565 [][]\OT1/cmtt/m/n/10 PYTHONPATH []\OT1/cmr/m/n/10 with some-thing like [][]\OT1 /cmtt/m/n/10 export PYTHONPATH = $PYTHONPATH':/directory/where/you/put/Biopytho n' (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) Overfull \hbox (9.6602pt too wide) in paragraph at lines 600--601 []\OT1/cmr/m/n/10 NCBI Stan-dalone BLAST, which can used with the [][]\OT1/cmtt /m/n/10 Bio.Blast []\OT1/cmr/m/n/10 mod-ule and parsed with the [][]\OT1/cmtt/m /n/10 Bio.SearchIO [9] [10] (./Installation.aux) LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on Installation.pdf (10 pages, 150357 bytes). Transcript written on Installation.log. pdflatex Installation.tex This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Installation.tex LaTeX2e <2019-10-01> patch level 1 (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2019/08/27 v1.4j 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/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 52. (./Installation.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/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.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/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./Installation.out) (./Installation.out) (./Installation.toc) [1{/var/lib/texm f/fonts/map/pdftex/updmap/pdftex.map}] [2] [3] [4] [5] [6] [7] Overfull \hbox (9.0224pt too wide) in paragraph at lines 540--541 []\OT1/cmr/m/n/10 For Python 2.6 we cur-rently use Mi-crosoft's free VC++ 2008 Ex-press Edi-tion from [][]$\OT1/cmtt/m/n/10 http : / / www . microsoft . [8] Overfull \hbox (27.57379pt too wide) in paragraph at lines 563--565 [][]\OT1/cmtt/m/n/10 PYTHONPATH []\OT1/cmr/m/n/10 with some-thing like [][]\OT1 /cmtt/m/n/10 export PYTHONPATH = $PYTHONPATH':/directory/where/you/put/Biopytho n' (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) Overfull \hbox (9.6602pt too wide) in paragraph at lines 600--601 []\OT1/cmr/m/n/10 NCBI Stan-dalone BLAST, which can used with the [][]\OT1/cmtt /m/n/10 Bio.Blast []\OT1/cmr/m/n/10 mod-ule and parsed with the [][]\OT1/cmtt/m /n/10 Bio.SearchIO [9] [10] (./Installation.aux) ) (see the transcript file for additional information) Output written on Installation.pdf (10 pages, 150502 bytes). Transcript written on Installation.log. hevea -fix Installation.tex Exclude comment 'comment' ./Installation.tex:67: Warning: Suppressing nested a element ./Installation.tex:67: Warning: Suppressing nested a element ./Installation.tex:108: Warning: Undefined label: 'sec:windows_install' ./Installation.tex:114: Warning: Suppressing nested a element ./Installation.tex:114: Warning: Suppressing nested a element ./Installation.tex:140: Warning: Suppressing nested a element ./Installation.tex:140: Warning: Suppressing nested a element ./Installation.tex:218: Warning: Suppressing nested a element ./Installation.tex:218: Warning: Suppressing nested a element ./Installation.tex:230: Warning: Suppressing nested a element ./Installation.tex:230: Warning: Suppressing nested a element ./Installation.tex:255: Warning: Suppressing nested a element ./Installation.tex:255: Warning: Suppressing nested a element ./Installation.tex:314: Warning: Suppressing nested a element ./Installation.tex:314: Warning: Suppressing nested a element ./Installation.tex:317: Warning: Suppressing nested a element ./Installation.tex:317: Warning: Suppressing nested a element ./Installation.tex:387: Warning: Suppressing nested a element ./Installation.tex:387: Warning: Suppressing nested a element ./Installation.tex:400: Warning: Suppressing nested a element ./Installation.tex:400: Warning: Suppressing nested a element ./Installation.tex:406: Warning: Suppressing nested a element ./Installation.tex:406: Warning: Suppressing nested a element ./Installation.tex:413: Warning: Suppressing nested a element ./Installation.tex:413: Warning: Suppressing nested a element ./Installation.tex:419: Warning: Suppressing nested a element ./Installation.tex:419: Warning: Suppressing nested a element ./Installation.tex:421: Warning: Suppressing nested a element ./Installation.tex:421: Warning: Suppressing nested a element ./Installation.tex:430: Warning: '_' occurring outside math mode ./Installation.tex:456: Warning: Suppressing nested a element ./Installation.tex:456: Warning: Suppressing nested a element ./Installation.tex:460: Warning: Undefined label: 'sec:is_working' ./Installation.tex:467: Warning: Suppressing nested a element ./Installation.tex:467: Warning: Suppressing nested a element ./Installation.tex:497: Warning: Suppressing nested a element ./Installation.tex:497: Warning: Suppressing nested a element ./Installation.tex:516: Warning: Suppressing nested a element ./Installation.tex:516: Warning: Suppressing nested a element ./Installation.tex:535: Warning: '_' occurring outside math mode ./Installation.tex:537: Warning: Undefined label: 'sec:unix_install' ./Installation.tex:540: Warning: Suppressing nested a element ./Installation.tex:540: Warning: Suppressing nested a element ./Installation.tex:548: Warning: Suppressing nested a element ./Installation.tex:548: Warning: Suppressing nested a element ./Installation.tex:556: Warning: Suppressing nested a element ./Installation.tex:556: Warning: Suppressing nested a element ./Installation.tex:558: Warning: Undefined label: 'sec:is_working' ./Installation.tex:561: Warning: '_' occurring outside math mode ./Installation.tex:609: Warning: Suppressing nested a element ./Installation.tex:609: Warning: Suppressing nested a element HeVeA Warning: Label(s) may have changed. Rerun me to get cross-references right. Run, run, again... Exclude comment 'comment' ./Installation.tex:67: Warning: Suppressing nested a element ./Installation.tex:67: Warning: Suppressing nested a element ./Installation.tex:114: Warning: Suppressing nested a element ./Installation.tex:114: Warning: Suppressing nested a element ./Installation.tex:140: Warning: Suppressing nested a element ./Installation.tex:140: Warning: Suppressing nested a element ./Installation.tex:218: Warning: Suppressing nested a element ./Installation.tex:218: Warning: Suppressing nested a element ./Installation.tex:230: Warning: Suppressing nested a element ./Installation.tex:230: Warning: Suppressing nested a element ./Installation.tex:255: Warning: Suppressing nested a element ./Installation.tex:255: Warning: Suppressing nested a element ./Installation.tex:314: Warning: Suppressing nested a element ./Installation.tex:314: Warning: Suppressing nested a element ./Installation.tex:317: Warning: Suppressing nested a element ./Installation.tex:317: Warning: Suppressing nested a element ./Installation.tex:387: Warning: Suppressing nested a element ./Installation.tex:387: Warning: Suppressing nested a element ./Installation.tex:400: Warning: Suppressing nested a element ./Installation.tex:400: Warning: Suppressing nested a element ./Installation.tex:406: Warning: Suppressing nested a element ./Installation.tex:406: Warning: Suppressing nested a element ./Installation.tex:413: Warning: Suppressing nested a element ./Installation.tex:413: Warning: Suppressing nested a element ./Installation.tex:419: Warning: Suppressing nested a element ./Installation.tex:419: Warning: Suppressing nested a element ./Installation.tex:421: Warning: Suppressing nested a element ./Installation.tex:421: Warning: Suppressing nested a element ./Installation.tex:430: Warning: '_' occurring outside math mode ./Installation.tex:456: Warning: Suppressing nested a element ./Installation.tex:456: Warning: Suppressing nested a element ./Installation.tex:467: Warning: Suppressing nested a element ./Installation.tex:467: Warning: Suppressing nested a element ./Installation.tex:497: Warning: Suppressing nested a element ./Installation.tex:497: Warning: Suppressing nested a element ./Installation.tex:516: Warning: Suppressing nested a element ./Installation.tex:516: Warning: Suppressing nested a element ./Installation.tex:535: Warning: '_' occurring outside math mode ./Installation.tex:540: Warning: Suppressing nested a element ./Installation.tex:540: Warning: Suppressing nested a element ./Installation.tex:548: Warning: Suppressing nested a element ./Installation.tex:548: Warning: Suppressing nested a element ./Installation.tex:556: Warning: Suppressing nested a element ./Installation.tex:556: Warning: Suppressing nested a element ./Installation.tex:561: Warning: '_' occurring outside math mode ./Installation.tex:609: Warning: Suppressing nested a element ./Installation.tex:609: Warning: Suppressing nested a element Fixpoint reached in 2 step(s) hevea -fix -text Installation.tex Exclude comment 'comment' ./Installation.tex:55: Warning: tt_mode is an empty style ./Installation.tex:61: Warning: No date given ./Installation.tex:430: Warning: '_' occurring outside math mode ./Installation.tex:535: Warning: '_' occurring outside math mode ./Installation.tex:561: Warning: '_' occurring outside math mode HeVeA Warning: Label(s) may have changed. Rerun me to get cross-references right. Run, run, again... Exclude comment 'comment' ./Installation.tex:55: Warning: tt_mode is an empty style ./Installation.tex:61: Warning: No date given ./Installation.tex:430: Warning: '_' occurring outside math mode ./Installation.tex:535: Warning: '_' occurring outside math mode ./Installation.tex:561: Warning: '_' occurring outside math mode Fixpoint reached in 2 step(s) make[3]: Leaving directory '/<>/python-biopython-1.73+dfsg/Doc/install' make[2]: Leaving directory '/<>/python-biopython-1.73+dfsg/Doc' make[1]: Leaving directory '/<>/python-biopython-1.73+dfsg' rm -f debian/python-biopython.debhelper.log debian/python3-biopython.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/<>/python-biopython-1.73+dfsg' mkdir -p Tests_avoid for avoid in PAML_tools EmbossPhylipNew MSAProbs_tool NACCESS_tool PopGen_DFDist PopGen_FDist PopGen_GenePop PopGen_GenePop_EasyController PopGen_SimCoal XXmotif_tool BWA_tool raxml_tool BioSQL_MySQLdb BioSQL_psycopg2 phyml_tool \ ; do \ mv Tests/test_${avoid}.py Tests_avoid ; \ done mv: cannot stat 'Tests/test_PopGen_DFDist.py': No such file or directory mv: cannot stat 'Tests/test_PopGen_FDist.py': No such file or directory mv: cannot stat 'Tests/test_PopGen_SimCoal.py': No such file or directory # For the doc package we need a clean testsuite without all the remaining files. So keep a clean copy here mkdir -p debian/tmp_tests cp -a Tests debian/tmp_tests # remove duplicated file rm -f debian/tmp_tests/Tests/Quality/example.fastq.gz # We also keep the tests we need to avoid for later inspection cp -a Tests_avoid debian/tmp_tests # in the Debian package dialign it is not needed to set DIALIGN2_DIR but the test is verifying this dir # to run the EMBOSS test test_Emboss also requires to have the environment variable EMBOSS_ROOT set LC_ALL=C.UTF-8 dh_auto_test -- --test --system=custom \ --test-args='set -e; \ mkdir -p {build_dir}/home; \ mkdir -p {build_dir}/Doc/examples; \ cp -a Doc/Tutorial.tex {build_dir}/Doc; \ cp -a Doc/Tutorial {build_dir}/Doc; \ cp -a Doc/examples {build_dir}/Doc; \ cp -a Tests {build_dir}; \ cd {build_dir}/Tests; \ env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME={build_dir}/home {interpreter} run_tests.py --offline' pybuild --test -i python{version} -p 2.7 --test --system=custom "--test-args=set -e; \\\ mkdir -p {build_dir}/home; \\\ mkdir -p {build_dir}/Doc/examples; \\\ cp -a Doc/Tutorial.tex {build_dir}/Doc; \\\ cp -a Doc/Tutorial {build_dir}/Doc; \\\ cp -a Doc/examples {build_dir}/Doc; \\\ cp -a Tests {build_dir}; \\\ cd {build_dir}/Tests; \\\ env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME={build_dir}/home {interpreter} run_tests.py --offline" I: pybuild base:217: set -e; \ mkdir -p /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/home; \ mkdir -p /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Doc/examples; \ cp -a Doc/Tutorial.tex /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Doc; \ cp -a Doc/Tutorial /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Doc; \ cp -a Doc/examples /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Doc; \ cp -a Tests /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build; \ cd /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Tests; \ env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=/<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/home python2.7 run_tests.py --offline test_Ace ... ok test_Affy ... ok test_AlignIO ... ok test_AlignIO_ClustalIO ... ok test_AlignIO_EmbossIO ... ok test_AlignIO_FastaIO ... ok test_AlignIO_MauveIO ... ok test_AlignIO_PhylipIO ... ok test_AlignIO_convert ... ok test_AlignInfo ... ok test_Application ... ok test_BioSQL_MySQLdb_online ... skipping. internet not available test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) test_BioSQL_mysql_connector_online ... skipping. internet not available test_BioSQL_psycopg2_online ... skipping. internet not available test_BioSQL_sqlite3 ... ok test_BioSQL_sqlite3_online ... skipping. internet not available test_CAPS ... ok test_CelFile ... ok test_Chi2 ... ok test_ClustalOmega_tool ... ok test_Clustalw_tool ... ok test_Cluster ... ok test_CodonTable ... ok test_CodonUsage ... ok test_ColorSpiral ... ok test_Compass ... ok test_Consensus ... ok test_Crystal ... ok test_DSSP_tool ... ok test_Dialign_tool ... ok test_EMBL_unittest ... ok test_Emboss ... ok test_EmbossPrimer ... ok test_Entrez ... ok test_Entrez_online ... skipping. internet not available test_Entrez_parser ... ok test_Enzyme ... ok test_ExPASy ... skipping. internet not available test_FSSP ... ok test_Fasttree_tool ... ok test_File ... ok test_GenBank ... ok test_GenBank_unittest ... ok test_GenomeDiagram ... x_order_2: colinear! x_order_2: colinear! x_order_2: colinear! x_order_2: colinear! x_order_2: colinear! x_order_2: colinear! x_order_2: colinear! ok test_GraphicsBitmaps ... ok test_GraphicsChromosome ... ok test_GraphicsDistribution ... ok test_GraphicsGeneral ... ok test_HMMCasino ... ok test_HMMGeneral ... ok test_KDTree ... ok test_KEGG ... ok test_KEGG_online ... skipping. internet not available test_KGML_graphics ... ok test_KGML_graphics_online ... skipping. internet not available test_KGML_nographics ... ok test_KeyWList ... ok test_Location ... ok test_LogisticRegression ... ok test_MafIO_index ... ok test_Mafft_tool ... ok test_MarkovModel ... ok test_Medline ... ok test_Muscle_tool ... ok test_NCBITextParser ... ok test_NCBIXML ... ok test_NCBI_BLAST_tools ... /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Tests/test_NCBI_BLAST_tools.py:401: UserWarning: NCBI BLAST+ blastn and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids) ",".join(sorted(missing)))) /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Tests/test_NCBI_BLAST_tools.py:401: UserWarning: NCBI BLAST+ blastp and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -ipglist,-negative_ipglist,-negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids) ",".join(sorted(missing)))) /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Tests/test_NCBI_BLAST_tools.py:401: UserWarning: NCBI BLAST+ blastx and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -ipglist,-negative_ipglist,-negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids) ",".join(sorted(missing)))) /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Tests/test_NCBI_BLAST_tools.py:401: UserWarning: NCBI BLAST+ deltablast and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids) ",".join(sorted(missing)))) /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Tests/test_NCBI_BLAST_tools.py:401: UserWarning: NCBI BLAST+ makeblastdb and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -blastdb_version) ",".join(sorted(missing)))) /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Tests/test_NCBI_BLAST_tools.py:401: UserWarning: NCBI BLAST+ psiblast and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -ipglist,-negative_ipglist,-negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids) ",".join(sorted(missing)))) /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Tests/test_NCBI_BLAST_tools.py:401: UserWarning: NCBI BLAST+ rpsblast and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -sorthits,-sorthsps,-subject_besthit) ",".join(sorted(missing)))) /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Tests/test_NCBI_BLAST_tools.py:401: UserWarning: NCBI BLAST+ rpstblastn and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -sorthits,-sorthsps) ",".join(sorted(missing)))) /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Tests/test_NCBI_BLAST_tools.py:401: UserWarning: NCBI BLAST+ tblastn and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids) ",".join(sorted(missing)))) /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Tests/test_NCBI_BLAST_tools.py:401: UserWarning: NCBI BLAST+ tblastx and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids) ",".join(sorted(missing)))) ok test_NCBI_qblast ... skipping. internet not available test_NaiveBayes ... ok test_Nexus ... ok test_PAML_baseml ... ok test_PAML_codeml ... ok test_PAML_yn00 ... ok test_PDB ... ok test_PDBList ... skipping. internet not available test_PDB_FragmentMapper ... ok test_PDB_KDTree ... ok test_PDB_MMCIF2Dict ... ok test_PDB_MMCIFParser ... ok test_PDB_Polypetide ... ok test_PDB_ResidueDepth ... skipping. Install MSMS if you want to use it in Biopython. test_PDB_StructureAlignment ... /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB/StructureBuilder.py:91: PDBConstructionWarning: WARNING: Chain A is discontinuous at line 13298. PDBConstructionWarning) /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB/StructureBuilder.py:91: PDBConstructionWarning: WARNING: Chain B is discontinuous at line 13344. PDBConstructionWarning) ok test_PDB_Superimposer ... ok test_PDB_vectors ... ok test_Pathway ... ok test_Phd ... ok test_Phylo ... ok test_PhyloXML ... ok test_Phylo_CDAO ... ok test_Phylo_NeXML ... ok test_Phylo_matplotlib ... ok test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo test_PopGen_GenePop_nodepend ... ok test_Prank_tool ... ok test_Probcons_tool ... ok test_ProtParam ... ok test_QCPSuperimposer ... ok test_RCSBFormats ... ok test_Restriction ... skipping. Under Python 2 this test needs the unittest2 library test_SCOP_Astral ... ok test_SCOP_Cla ... ok test_SCOP_Des ... ok test_SCOP_Dom ... ok test_SCOP_Hie ... ok test_SCOP_Raf ... ok test_SCOP_Residues ... ok test_SCOP_Scop ... ok test_SCOP_online ... skipping. internet not available test_SVDSuperimposer ... ok test_SearchIO_blast_tab ... ok test_SearchIO_blast_tab_index ... ok test_SearchIO_blast_text ... ok test_SearchIO_blast_xml ... ok test_SearchIO_blast_xml_index ... ok test_SearchIO_blat_psl ... ok test_SearchIO_blat_psl_index ... ok test_SearchIO_exonerate ... ok test_SearchIO_exonerate_text_index ... ok test_SearchIO_exonerate_vulgar_index ... ok test_SearchIO_fasta_m10 ... ok test_SearchIO_fasta_m10_index ... ok test_SearchIO_hmmer2_text ... ok test_SearchIO_hmmer2_text_index ... ok test_SearchIO_hmmer3_domtab ... ok test_SearchIO_hmmer3_domtab_index ... ok test_SearchIO_hmmer3_tab ... ok test_SearchIO_hmmer3_tab_index ... ok test_SearchIO_hmmer3_text ... ok test_SearchIO_hmmer3_text_index ... ok test_SearchIO_interproscan_xml ... ok test_SearchIO_legacy ... ok test_SearchIO_model ... ok test_SearchIO_write ... ok test_SeqFeature ... ok test_SeqIO ... ok test_SeqIO_AbiIO ... ok test_SeqIO_FastaIO ... ok test_SeqIO_Insdc ... ok test_SeqIO_PdbIO ... ok test_SeqIO_QualityIO ... ok test_SeqIO_SeqXML ... ok test_SeqIO_convert ... ok test_SeqIO_features ... ok test_SeqIO_index ... ok test_SeqIO_online ... skipping. internet not available test_SeqIO_write ... ok test_SeqRecord ... ok test_SeqUtils ... ok test_Seq_objs ... ok test_SffIO ... ok test_SubsMat ... ok test_SwissProt ... ok test_TCoffee_tool ... ok test_TogoWS ... skipping. internet not available test_TreeConstruction ... ok test_Tutorial ... ok test_UniGene ... ok test_Uniprot ... ok test_Wise ... ok test_align ... ok test_bgzf ... ok test_cellosaurus ... ok test_codonalign ... /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Seq.py:2589: BiopythonWarning: This table contains 6 codon(s) which code(s) for both STOP and an amino acid (e.g. 'TAA' -> 'stop' or STOP). Such codons will be translated as amino acid. BiopythonWarning) ok test_geo ... ok test_kNN ... ok test_lowess ... ok test_mmtf ... skipping. Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) test_mmtf_online ... skipping. Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) test_motifs ... ok test_motifs_online ... skipping. internet not available test_pairwise2 ... ok test_pairwise_aligner ... ok test_phenotype ... ok test_phenotype_fit ... ok test_prodoc ... ok test_prosite1 ... ok test_prosite2 ... ok test_psw ... ok test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython test_seq ... skipping. Under Python 2 this test needs the unittest2 library test_translate ... ok test_trie ... ok Bio.Align docstring test ... ok Bio.Align.Applications._Clustalw docstring test ... ok Bio.Align.Applications._ClustalOmega docstring test ... ok Bio.Align.Applications._Dialign docstring test ... ok Bio.Align.Applications._MSAProbs docstring test ... ok Bio.Align.Applications._Mafft docstring test ... ok Bio.Align.Applications._Muscle docstring test ... ok Bio.Align.Applications._Probcons docstring test ... ok Bio.Align.Applications._Prank docstring test ... ok Bio.Align.Applications._TCoffee docstring test ... ok Bio.AlignIO docstring test ... ok Bio.AlignIO.StockholmIO docstring test ... ok Bio.Alphabet docstring test ... ok Bio.Alphabet.Reduced docstring test ... ok Bio.Application docstring test ... ok Bio.bgzf docstring test ... ok Bio.codonalign docstring test ... ok Bio.codonalign.codonalignment docstring test ... ok Bio.codonalign.codonalphabet docstring test ... ok Bio.codonalign.codonseq docstring test ... ok Bio.Blast.Applications docstring test ... ok Bio.Emboss.Applications docstring test ... ok Bio.GenBank docstring test ... ok Bio.Graphics.GenomeDiagram._Colors docstring test ... ok Bio.KEGG.Compound docstring test ... ok Bio.KEGG.Enzyme docstring test ... ok Bio.KEGG.Gene docstring test ... ok Bio.KEGG.KGML.KGML_parser docstring test ... ok Bio.Nexus.Nexus docstring test ... ok Bio.NMR.xpktools docstring test ... ok Bio.motifs docstring test ... ok Bio.motifs.applications._xxmotif docstring test ... ok Bio.pairwise2 docstring test ... ok Bio.Phylo.Applications._Raxml docstring test ... ok Bio.Phylo.Consensus docstring test ... ok Bio.Phylo.BaseTree docstring test ... ok Bio.SearchIO docstring test ... ok Bio.SearchIO._model docstring test ... ok Bio.SearchIO._model.query docstring test ... ok Bio.SearchIO._model.hit docstring test ... ok Bio.SearchIO._model.hsp docstring test ... ok Bio.SearchIO.BlastIO docstring test ... ok Bio.SearchIO.HmmerIO docstring test ... ok Bio.SearchIO.FastaIO docstring test ... ok Bio.SearchIO.BlatIO docstring test ... ok Bio.SearchIO.ExonerateIO docstring test ... ok Bio.SeqIO docstring test ... ok Bio.SeqIO.AceIO docstring test ... ok Bio.SeqIO.FastaIO docstring test ... ok Bio.SeqIO.IgIO docstring test ... ok Bio.SeqIO.InsdcIO docstring test ... ok Bio.SeqIO.PhdIO docstring test ... ok Bio.SeqIO.PirIO docstring test ... ok Bio.SeqIO.QualityIO docstring test ... ok Bio.SeqIO.SffIO docstring test ... ok Bio.SeqIO.TabIO docstring test ... ok Bio.SeqFeature docstring test ... /<>/python-biopython-1.73+dfsg/.pybuild/cpython2_2.7/build/Bio/Seq.py:2609: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. BiopythonWarning) ok Bio.SeqRecord docstring test ... ok Bio.SeqUtils docstring test ... ok Bio.SeqUtils.CheckSum docstring test ... ok Bio.SeqUtils.MeltingTemp docstring test ... ok Bio.SeqUtils.ProtParam docstring test ... ok Bio.Sequencing.Applications._Novoalign docstring test ... ok Bio.Sequencing.Applications._bwa docstring test ... ok Bio.Sequencing.Applications._samtools docstring test ... ok Bio.SwissProt docstring test ... ok Bio.UniProt.GOA docstring test ... ok Bio.Wise docstring test ... ok Bio.Wise.psw docstring test ... ok Bio.Affy.CelFile docstring test ... ok Bio.MaxEntropy docstring test ... ok Bio.PDB.Polypeptide docstring test ... ok Bio.PDB.Selection docstring test ... ok Bio.SeqIO.PdbIO docstring test ... ok Bio.Statistics.lowess docstring test ... ok Bio.SVDSuperimposer docstring test ... ok ---------------------------------------------------------------------- Ran 259 tests in 755.963 seconds Skipping any tests requiring internet access Python version: 2.7.17 (default, Oct 19 2019, 23:36:22) [GCC 9.2.1 20191008] Operating system: posix linux2 pybuild --test -i python{version} -p "3.8 3.7" --test --system=custom "--test-args=set -e; \\\ mkdir -p {build_dir}/home; \\\ mkdir -p {build_dir}/Doc/examples; \\\ cp -a Doc/Tutorial.tex {build_dir}/Doc; \\\ cp -a Doc/Tutorial {build_dir}/Doc; \\\ cp -a Doc/examples {build_dir}/Doc; \\\ cp -a Tests {build_dir}; \\\ cd {build_dir}/Tests; \\\ env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME={build_dir}/home {interpreter} run_tests.py --offline" I: pybuild base:217: set -e; \ mkdir -p /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/home; \ mkdir -p /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Doc/examples; \ cp -a Doc/Tutorial.tex /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Doc; \ cp -a Doc/Tutorial /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Doc; \ cp -a Doc/examples /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Doc; \ cp -a Tests /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build; \ cd /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests; \ env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/home python3.8 run_tests.py --offline x_order_2: colinear! x_order_2: colinear! x_order_2: colinear! x_order_2: colinear! x_order_2: colinear! x_order_2: colinear! x_order_2: colinear! x_order_2: colinear! x_order_2: colinear! test_Ace ... ok test_Affy ... ok test_AlignIO ... /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Nexus/Nexus.py:939: SyntaxWarning: "is" with a literal. Did you mean "=="? elif state is ',': ok test_AlignIO_ClustalIO ... ok test_AlignIO_EmbossIO ... ok test_AlignIO_FastaIO ... ok test_AlignIO_MauveIO ... ok test_AlignIO_PhylipIO ... ok test_AlignIO_convert ... ok test_AlignInfo ... ok test_Application ... ok test_BioSQL_MySQLdb_online ... skipping. internet not available test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) test_BioSQL_mysql_connector_online ... skipping. internet not available test_BioSQL_psycopg2_online ... skipping. internet not available test_BioSQL_sqlite3 ... FAIL test_BioSQL_sqlite3_online ... skipping. internet not available test_CAPS ... ok test_CelFile ... ok test_Chi2 ... ok test_ClustalOmega_tool ... ok test_Clustalw_tool ... ok test_Cluster ... ok test_CodonTable ... ok test_CodonUsage ... ok test_ColorSpiral ... ok test_Compass ... ok test_Consensus ... ok test_Crystal ... ok test_DSSP_tool ... ok test_Dialign_tool ... ok test_EMBL_unittest ... ok test_Emboss ... ok test_EmbossPrimer ... ok test_Entrez ... ok test_Entrez_online ... skipping. internet not available test_Entrez_parser ... ok test_Enzyme ... ok test_ExPASy ... skipping. internet not available test_FSSP ... ok test_Fasttree_tool ... ok test_File ... ok test_GenBank ... FAIL test_GenBank_unittest ... ok test_GenomeDiagram ... ok test_GraphicsBitmaps ... ok test_GraphicsChromosome ... ok test_GraphicsDistribution ... ok test_GraphicsGeneral ... ok test_HMMCasino ... ok test_HMMGeneral ... ok test_KDTree ... ok test_KEGG ... /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/KEGG/__init__.py:82: SyntaxWarning: "is not" with a literal. Did you mean "!="? if item is not "": # ensure item is only written on first line ok test_KEGG_online ... skipping. internet not available test_KGML_graphics ... ok test_KGML_graphics_online ... skipping. internet not available test_KGML_nographics ... ok test_KeyWList ... ok test_Location ... FAIL test_LogisticRegression ... ok test_MafIO_index ... ok test_Mafft_tool ... ok test_MarkovModel ... ok test_Medline ... ok test_Muscle_tool ... ok test_NCBITextParser ... ok test_NCBIXML ... ok test_NCBI_BLAST_tools ... /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:396: UserWarning: NCBI BLAST+ blastn and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids) warnings.warn("NCBI BLAST+ %s and Biopython out sync. Please " /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:396: UserWarning: NCBI BLAST+ blastp and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -ipglist,-negative_ipglist,-negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids) warnings.warn("NCBI BLAST+ %s and Biopython out sync. Please " /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:396: UserWarning: NCBI BLAST+ blastx and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -ipglist,-negative_ipglist,-negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids) warnings.warn("NCBI BLAST+ %s and Biopython out sync. Please " /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:396: UserWarning: NCBI BLAST+ deltablast and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids) warnings.warn("NCBI BLAST+ %s and Biopython out sync. Please " /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:396: UserWarning: NCBI BLAST+ makeblastdb and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -blastdb_version) warnings.warn("NCBI BLAST+ %s and Biopython out sync. Please " /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:396: UserWarning: NCBI BLAST+ psiblast and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -ipglist,-negative_ipglist,-negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids) warnings.warn("NCBI BLAST+ %s and Biopython out sync. Please " /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:396: UserWarning: NCBI BLAST+ rpsblast and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -sorthits,-sorthsps,-subject_besthit) warnings.warn("NCBI BLAST+ %s and Biopython out sync. Please " /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:396: UserWarning: NCBI BLAST+ rpstblastn and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -sorthits,-sorthsps) warnings.warn("NCBI BLAST+ %s and Biopython out sync. Please " /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:396: UserWarning: NCBI BLAST+ tblastn and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids) warnings.warn("NCBI BLAST+ %s and Biopython out sync. Please " /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:396: UserWarning: NCBI BLAST+ tblastx and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids) warnings.warn("NCBI BLAST+ %s and Biopython out sync. Please " ok test_NCBI_qblast ... skipping. internet not available test_NaiveBayes ... ok test_Nexus ... ok test_PAML_baseml ... ok test_PAML_codeml ... ok test_PAML_yn00 ... ok test_PDB ... ok test_PDBList ... skipping. internet not available test_PDB_FragmentMapper ... ok test_PDB_KDTree ... ok test_PDB_MMCIF2Dict ... ok test_PDB_MMCIFParser ... ok test_PDB_Polypetide ... ok test_PDB_ResidueDepth ... skipping. Install MSMS if you want to use it in Biopython. test_PDB_StructureAlignment ... /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB/StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain A is discontinuous at line 13298. warnings.warn("WARNING: Chain %s is discontinuous at line %i." /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB/StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain B is discontinuous at line 13344. warnings.warn("WARNING: Chain %s is discontinuous at line %i." ok test_PDB_Superimposer ... ok test_PDB_vectors ... ok test_Pathway ... ok test_Phd ... ok test_Phylo ... ok test_PhyloXML ... ok test_Phylo_CDAO ... ok test_Phylo_NeXML ... ok test_Phylo_matplotlib ... ok test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo test_PopGen_GenePop_nodepend ... ok test_Prank_tool ... ok test_Probcons_tool ... ok test_ProtParam ... ok test_QCPSuperimposer ... ok test_RCSBFormats ... ok test_Restriction ... ok test_SCOP_Astral ... ok test_SCOP_Cla ... ok test_SCOP_Des ... ok test_SCOP_Dom ... ok test_SCOP_Hie ... ok test_SCOP_Raf ... ok test_SCOP_Residues ... ok test_SCOP_Scop ... ok test_SCOP_online ... skipping. internet not available test_SVDSuperimposer ... ok test_SearchIO_blast_tab ... ok test_SearchIO_blast_tab_index ... ok test_SearchIO_blast_text ... ok test_SearchIO_blast_xml ... ok test_SearchIO_blast_xml_index ... ok test_SearchIO_blat_psl ... ok test_SearchIO_blat_psl_index ... ok test_SearchIO_exonerate ... ok test_SearchIO_exonerate_text_index ... ok test_SearchIO_exonerate_vulgar_index ... ok test_SearchIO_fasta_m10 ... ok test_SearchIO_fasta_m10_index ... ok test_SearchIO_hmmer2_text ... ok test_SearchIO_hmmer2_text_index ... ok test_SearchIO_hmmer3_domtab ... ok test_SearchIO_hmmer3_domtab_index ... ok test_SearchIO_hmmer3_tab ... ok test_SearchIO_hmmer3_tab_index ... ok test_SearchIO_hmmer3_text ... ok test_SearchIO_hmmer3_text_index ... ok test_SearchIO_interproscan_xml ... ok test_SearchIO_legacy ... ok test_SearchIO_model ... ok test_SearchIO_write ... ok test_SeqFeature ... ok test_SeqIO ... ok test_SeqIO_AbiIO ... ok test_SeqIO_FastaIO ... ok test_SeqIO_Insdc ... /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/GenBank/Scanner.py:286: BiopythonParserWarning: Non-standard feature line wrapping (didn't break on comma)? warnings.warn("Non-standard feature line wrapping (didn't break on comma)?", ok test_SeqIO_PdbIO ... ok test_SeqIO_QualityIO ... ok test_SeqIO_SeqXML ... ok test_SeqIO_convert ... ok test_SeqIO_features ... ok test_SeqIO_index ... ok test_SeqIO_online ... skipping. internet not available test_SeqIO_write ... ok test_SeqRecord ... ok test_SeqUtils ... ok test_Seq_objs ... ok test_SffIO ... ok test_SubsMat ... ERROR test_SwissProt ... ok test_TCoffee_tool ... ok test_TogoWS ... skipping. internet not available test_TreeConstruction ... ok test_Tutorial ... FAIL test_UniGene ... ok test_Uniprot ... ok test_Wise ... ok test_align ... ok test_bgzf ... ok test_cellosaurus ... ok test_codonalign ... /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Seq.py:2585: BiopythonWarning: This table contains 6 codon(s) which code(s) for both STOP and an amino acid (e.g. 'TAA' -> 'stop' or STOP). Such codons will be translated as amino acid. warnings.warn("This table contains {} codon(s) which code(s) for both " ok test_geo ... ok test_kNN ... ok test_lowess ... ok test_mmtf ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) test_mmtf_online ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) test_motifs ... ok test_motifs_online ... skipping. internet not available test_pairwise2 ... ok test_pairwise_aligner ... ok test_phenotype ... ok test_phenotype_fit ... ok test_prodoc ... ok test_prosite1 ... ok test_prosite2 ... ok test_psw ... ok test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython test_seq ... ok test_translate ... ok test_trie ... ok Bio.Align docstring test ... ok Bio.Align.Applications._Clustalw docstring test ... ok Bio.Align.Applications._ClustalOmega docstring test ... ok Bio.Align.Applications._Dialign docstring test ... ok Bio.Align.Applications._MSAProbs docstring test ... ok Bio.Align.Applications._Mafft docstring test ... ok Bio.Align.Applications._Muscle docstring test ... ok Bio.Align.Applications._Probcons docstring test ... ok Bio.Align.Applications._Prank docstring test ... ok Bio.Align.Applications._TCoffee docstring test ... ok Bio.AlignIO docstring test ... ok Bio.AlignIO.StockholmIO docstring test ... ok Bio.Alphabet docstring test ... ok Bio.Alphabet.Reduced docstring test ... ok Bio.Application docstring test ... ok Bio.bgzf docstring test ... ok Bio.codonalign docstring test ... /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Seq.py:2585: BiopythonWarning: This table contains 6 codon(s) which code(s) for both STOP and an amino acid (e.g. 'TAA' -> 'stop' or STOP). Such codons will be translated as amino acid. warnings.warn("This table contains {} codon(s) which code(s) for both " ok Bio.codonalign.codonalignment docstring test ... ok Bio.codonalign.codonalphabet docstring test ... ok Bio.codonalign.codonseq docstring test ... ok Bio.Blast.Applications docstring test ... ok Bio.Emboss.Applications docstring test ... ok Bio.GenBank docstring test ... FAIL Bio.Graphics.GenomeDiagram._Colors docstring test ... ok Bio.KEGG.Compound docstring test ... ok Bio.KEGG.Enzyme docstring test ... ok Bio.KEGG.Gene docstring test ... ok Bio.KEGG.KGML.KGML_parser docstring test ... ok Bio.Nexus.Nexus docstring test ... ok Bio.NMR.xpktools docstring test ... ok Bio.motifs docstring test ... ok Bio.motifs.applications._xxmotif docstring test ... ok Bio.pairwise2 docstring test ... ok Bio.Phylo.Applications._Raxml docstring test ... ok Bio.Phylo.Consensus docstring test ... ok Bio.Phylo.BaseTree docstring test ... ok Bio.SearchIO docstring test ... ok Bio.SearchIO._model docstring test ... ok Bio.SearchIO._model.query docstring test ... ok Bio.SearchIO._model.hit docstring test ... ok Bio.SearchIO._model.hsp docstring test ... ok Bio.SearchIO.BlastIO docstring test ... ok Bio.SearchIO.HmmerIO docstring test ... ok Bio.SearchIO.FastaIO docstring test ... ok Bio.SearchIO.BlatIO docstring test ... ok Bio.SearchIO.ExonerateIO docstring test ... ok Bio.Seq docstring test ... /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Seq.py:2585: BiopythonWarning: This table contains 2 codon(s) which code(s) for both STOP and an amino acid (e.g. 'TGA' -> 'W' or STOP). Such codons will be translated as amino acid. warnings.warn("This table contains {} codon(s) which code(s) for both " ok Bio.SeqIO docstring test ... ok Bio.SeqIO.AceIO docstring test ... ok Bio.SeqIO.FastaIO docstring test ... ok Bio.SeqIO.IgIO docstring test ... ok Bio.SeqIO.InsdcIO docstring test ... ok Bio.SeqIO.PhdIO docstring test ... ok Bio.SeqIO.PirIO docstring test ... ok Bio.SeqIO.QualityIO docstring test ... ok Bio.SeqIO.SffIO docstring test ... ok Bio.SeqIO.TabIO docstring test ... ok Bio.SeqFeature docstring test ... /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/Seq.py:2606: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. warnings.warn("Partial codon, len(sequence) not a multiple of three. " FAIL Bio.SeqRecord docstring test ... FAIL Bio.SeqUtils docstring test ... ok Bio.SeqUtils.CheckSum docstring test ... ok Bio.SeqUtils.MeltingTemp docstring test ... ok Bio.SeqUtils.ProtParam docstring test ... ok Bio.Sequencing.Applications._Novoalign docstring test ... ok Bio.Sequencing.Applications._bwa docstring test ... ok Bio.Sequencing.Applications._samtools docstring test ... ok Bio.SwissProt docstring test ... ok Bio.UniProt.GOA docstring test ... ok Bio.Wise docstring test ... ok Bio.Wise.psw docstring test ... ok Bio.Affy.CelFile docstring test ... ok Bio.MaxEntropy docstring test ... ok Bio.PDB.Polypeptide docstring test ... ok Bio.PDB.Selection docstring test ... ok Bio.SeqIO.PdbIO docstring test ... ok Bio.Statistics.lowess docstring test ... ok Bio.SVDSuperimposer docstring test ... ok ====================================================================== ERROR: test_SeqIO_loading (common_BioSQL.AutoSeqIOTests) ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 1184, in test_SeqIO_loading self.check('genbank', 'GenBank/cor6_6.gb', 6) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 1112, in check count = db.load(iterator) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/BioSeqDatabase.py", line 920, in load db_loader.load_seqrecord(cur_record) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 73, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 836, in _load_reference start = 1 + int(str(reference.location[0].start)) ValueError: invalid literal for int() with base 10: 'ExactPosition(0)' ====================================================================== ERROR: test_NC_000932 (common_BioSQL.ClosedLoopTest) From GenBank file to BioSQL and back to a GenBank file, NC_000932. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 815, in test_NC_000932 self.loop("GenBank/NC_000932.gb", "gb") File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 852, in loop count = db.load(original_records) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/BioSeqDatabase.py", line 920, in load db_loader.load_seqrecord(cur_record) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 73, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 836, in _load_reference start = 1 + int(str(reference.location[0].start)) ValueError: invalid literal for int() with base 10: 'ExactPosition(0)' ====================================================================== ERROR: test_NC_005816 (common_BioSQL.ClosedLoopTest) From GenBank file to BioSQL and back to a GenBank file, NC_005816. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 811, in test_NC_005816 self.loop("GenBank/NC_005816.gb", "gb") File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 852, in loop count = db.load(original_records) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/BioSeqDatabase.py", line 920, in load db_loader.load_seqrecord(cur_record) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 73, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 836, in _load_reference start = 1 + int(str(reference.location[0].start)) ValueError: invalid literal for int() with base 10: 'ExactPosition(0)' ====================================================================== ERROR: test_NT_019265 (common_BioSQL.ClosedLoopTest) From GenBank file to BioSQL and back to a GenBank file, NT_019265. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 819, in test_NT_019265 self.loop("GenBank/NT_019265.gb", "gb") File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 852, in loop count = db.load(original_records) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/BioSeqDatabase.py", line 920, in load db_loader.load_seqrecord(cur_record) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 73, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 836, in _load_reference start = 1 + int(str(reference.location[0].start)) ValueError: invalid literal for int() with base 10: 'ExactPosition(0)' ====================================================================== ERROR: test_arab1 (common_BioSQL.ClosedLoopTest) From GenBank file to BioSQL and back to a GenBank file, arab1. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 842, in test_arab1 self.loop("GenBank/arab1.gb", "gb") File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 852, in loop count = db.load(original_records) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/BioSeqDatabase.py", line 920, in load db_loader.load_seqrecord(cur_record) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 73, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 836, in _load_reference start = 1 + int(str(reference.location[0].start)) ValueError: invalid literal for int() with base 10: 'ExactPosition(0)' ====================================================================== ERROR: test_cor6_6 (common_BioSQL.ClosedLoopTest) From GenBank file to BioSQL and back to a GenBank file, cor6_6. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 838, in test_cor6_6 self.loop("GenBank/cor6_6.gb", "gb") File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 852, in loop count = db.load(original_records) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/BioSeqDatabase.py", line 920, in load db_loader.load_seqrecord(cur_record) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 73, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 836, in _load_reference start = 1 + int(str(reference.location[0].start)) ValueError: invalid literal for int() with base 10: 'ExactPosition(0)' ====================================================================== ERROR: test_one_of (common_BioSQL.ClosedLoopTest) From GenBank file to BioSQL and back to a GenBank file, one_of. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 834, in test_one_of self.loop("GenBank/one_of.gb", "gb") File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 852, in loop count = db.load(original_records) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/BioSeqDatabase.py", line 920, in load db_loader.load_seqrecord(cur_record) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 73, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 836, in _load_reference start = 1 + int(str(reference.location[0].start)) ValueError: invalid literal for int() with base 10: 'ExactPosition(0)' ====================================================================== ERROR: test_protein_refseq2 (common_BioSQL.ClosedLoopTest) From GenBank file to BioSQL and back to a GenBank file, protein_refseq2. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 826, in test_protein_refseq2 self.loop("GenBank/protein_refseq2.gb", "gb") File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 852, in loop count = db.load(original_records) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/BioSeqDatabase.py", line 920, in load db_loader.load_seqrecord(cur_record) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 73, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 836, in _load_reference start = 1 + int(str(reference.location[0].start)) ValueError: invalid literal for int() with base 10: 'ExactPosition(0)' ====================================================================== ERROR: test_del_db_items (common_BioSQL.DeleteTest) Check all associated data is deleted from an item. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 671, in setUp load_database("GenBank/cor6_6.gb") File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 251, in load_database count = db.load(iterator) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/BioSeqDatabase.py", line 920, in load db_loader.load_seqrecord(cur_record) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 73, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 836, in _load_reference start = 1 + int(str(reference.location[0].start)) ValueError: invalid literal for int() with base 10: 'ExactPosition(0)' ====================================================================== ERROR: test_server (common_BioSQL.DeleteTest) Check BioSeqDatabase methods. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 671, in setUp load_database("GenBank/cor6_6.gb") File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 251, in load_database count = db.load(iterator) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/BioSeqDatabase.py", line 920, in load db_loader.load_seqrecord(cur_record) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 73, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 836, in _load_reference start = 1 + int(str(reference.location[0].start)) ValueError: invalid literal for int() with base 10: 'ExactPosition(0)' ====================================================================== ERROR: test_record_loading (common_BioSQL.InDepthLoadTest) Make sure all records are correctly loaded. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 964, in setUp load_database(gb_file) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 251, in load_database count = db.load(iterator) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/BioSeqDatabase.py", line 920, in load db_loader.load_seqrecord(cur_record) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 73, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 836, in _load_reference start = 1 + int(str(reference.location[0].start)) ValueError: invalid literal for int() with base 10: 'ExactPosition(0)' ====================================================================== ERROR: test_reload (common_BioSQL.InDepthLoadTest) Make sure can't reimport existing records. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 964, in setUp load_database(gb_file) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 251, in load_database count = db.load(iterator) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/BioSeqDatabase.py", line 920, in load db_loader.load_seqrecord(cur_record) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 73, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 836, in _load_reference start = 1 + int(str(reference.location[0].start)) ValueError: invalid literal for int() with base 10: 'ExactPosition(0)' ====================================================================== ERROR: test_seq_feature (common_BioSQL.InDepthLoadTest) In depth check that SeqFeatures are transmitted through the db. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 964, in setUp load_database(gb_file) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 251, in load_database count = db.load(iterator) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/BioSeqDatabase.py", line 920, in load db_loader.load_seqrecord(cur_record) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 73, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 836, in _load_reference start = 1 + int(str(reference.location[0].start)) ValueError: invalid literal for int() with base 10: 'ExactPosition(0)' ====================================================================== ERROR: test_transfer (common_BioSQL.InDepthLoadTest) Make sure can load record into another namespace. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 964, in setUp load_database(gb_file) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 251, in load_database count = db.load(iterator) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/BioSeqDatabase.py", line 920, in load db_loader.load_seqrecord(cur_record) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 73, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 836, in _load_reference start = 1 + int(str(reference.location[0].start)) ValueError: invalid literal for int() with base 10: 'ExactPosition(0)' ====================================================================== ERROR: test_load_database (common_BioSQL.LoaderTest) Load SeqRecord objects into a BioSQL database. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 644, in test_load_database self.db.load(self.iterator) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/BioSeqDatabase.py", line 920, in load db_loader.load_seqrecord(cur_record) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 73, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 836, in _load_reference start = 1 + int(str(reference.location[0].start)) ValueError: invalid literal for int() with base 10: 'ExactPosition(0)' ====================================================================== ERROR: test_cross_retrieval_of_items (common_BioSQL.MultiReadTest) Test that valid ids can't be retrieved between namespaces. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 294, in setUp load_multi_database("GenBank/cor6_6.gb", "GenBank/NC_000932.gb") File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 273, in load_multi_database count = db.load(iterator) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/BioSeqDatabase.py", line 920, in load db_loader.load_seqrecord(cur_record) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 73, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 836, in _load_reference start = 1 + int(str(reference.location[0].start)) ValueError: invalid literal for int() with base 10: 'ExactPosition(0)' ====================================================================== ERROR: test_get_db_items (common_BioSQL.MultiReadTest) Check list, keys, length etc. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 294, in setUp load_multi_database("GenBank/cor6_6.gb", "GenBank/NC_000932.gb") File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 273, in load_multi_database count = db.load(iterator) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/BioSeqDatabase.py", line 920, in load db_loader.load_seqrecord(cur_record) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 73, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 836, in _load_reference start = 1 + int(str(reference.location[0].start)) ValueError: invalid literal for int() with base 10: 'ExactPosition(0)' ====================================================================== ERROR: test_server (common_BioSQL.MultiReadTest) Check BioSeqDatabase methods. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 294, in setUp load_multi_database("GenBank/cor6_6.gb", "GenBank/NC_000932.gb") File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 273, in load_multi_database count = db.load(iterator) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/BioSeqDatabase.py", line 920, in load db_loader.load_seqrecord(cur_record) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 73, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 836, in _load_reference start = 1 + int(str(reference.location[0].start)) ValueError: invalid literal for int() with base 10: 'ExactPosition(0)' ====================================================================== ERROR: test_get_db_items (common_BioSQL.ReadTest) Check list, keys, length etc. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 376, in setUp load_database("GenBank/cor6_6.gb") File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 251, in load_database count = db.load(iterator) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/BioSeqDatabase.py", line 920, in load db_loader.load_seqrecord(cur_record) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 73, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 836, in _load_reference start = 1 + int(str(reference.location[0].start)) ValueError: invalid literal for int() with base 10: 'ExactPosition(0)' ====================================================================== ERROR: test_lookup_items (common_BioSQL.ReadTest) Test retrieval of items using various ids. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 376, in setUp load_database("GenBank/cor6_6.gb") File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 251, in load_database count = db.load(iterator) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/BioSeqDatabase.py", line 920, in load db_loader.load_seqrecord(cur_record) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 73, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 836, in _load_reference start = 1 + int(str(reference.location[0].start)) ValueError: invalid literal for int() with base 10: 'ExactPosition(0)' ====================================================================== ERROR: test_server (common_BioSQL.ReadTest) Check BioSeqDatabase methods. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 376, in setUp load_database("GenBank/cor6_6.gb") File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 251, in load_database count = db.load(iterator) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/BioSeqDatabase.py", line 920, in load db_loader.load_seqrecord(cur_record) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 73, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 836, in _load_reference start = 1 + int(str(reference.location[0].start)) ValueError: invalid literal for int() with base 10: 'ExactPosition(0)' ====================================================================== ERROR: test_addition (common_BioSQL.SeqInterfaceTest) Check can add DBSeq objects together. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 458, in setUp load_database("GenBank/cor6_6.gb") File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 251, in load_database count = db.load(iterator) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/BioSeqDatabase.py", line 920, in load db_loader.load_seqrecord(cur_record) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 73, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 836, in _load_reference start = 1 + int(str(reference.location[0].start)) ValueError: invalid literal for int() with base 10: 'ExactPosition(0)' ====================================================================== ERROR: test_convert (common_BioSQL.SeqInterfaceTest) Check can turn a DBSeq object into a Seq or MutableSeq. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 458, in setUp load_database("GenBank/cor6_6.gb") File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 251, in load_database count = db.load(iterator) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/BioSeqDatabase.py", line 920, in load db_loader.load_seqrecord(cur_record) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 73, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 836, in _load_reference start = 1 + int(str(reference.location[0].start)) ValueError: invalid literal for int() with base 10: 'ExactPosition(0)' ====================================================================== ERROR: test_multiplication (common_BioSQL.SeqInterfaceTest) Check can multiply DBSeq objects by integers. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 458, in setUp load_database("GenBank/cor6_6.gb") File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 251, in load_database count = db.load(iterator) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/BioSeqDatabase.py", line 920, in load db_loader.load_seqrecord(cur_record) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 73, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 836, in _load_reference start = 1 + int(str(reference.location[0].start)) ValueError: invalid literal for int() with base 10: 'ExactPosition(0)' ====================================================================== ERROR: test_record_slicing (common_BioSQL.SeqInterfaceTest) Check that slices of DBSeqRecord are retrieved properly. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 458, in setUp load_database("GenBank/cor6_6.gb") File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 251, in load_database count = db.load(iterator) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/BioSeqDatabase.py", line 920, in load db_loader.load_seqrecord(cur_record) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 73, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 836, in _load_reference start = 1 + int(str(reference.location[0].start)) ValueError: invalid literal for int() with base 10: 'ExactPosition(0)' ====================================================================== ERROR: test_seq (common_BioSQL.SeqInterfaceTest) Make sure Seqs from BioSQL implement the right interface. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 458, in setUp load_database("GenBank/cor6_6.gb") File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 251, in load_database count = db.load(iterator) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/BioSeqDatabase.py", line 920, in load db_loader.load_seqrecord(cur_record) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 73, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 836, in _load_reference start = 1 + int(str(reference.location[0].start)) ValueError: invalid literal for int() with base 10: 'ExactPosition(0)' ====================================================================== ERROR: test_seq_features (common_BioSQL.SeqInterfaceTest) Check SeqFeatures of a sequence. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 458, in setUp load_database("GenBank/cor6_6.gb") File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 251, in load_database count = db.load(iterator) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/BioSeqDatabase.py", line 920, in load db_loader.load_seqrecord(cur_record) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 73, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 836, in _load_reference start = 1 + int(str(reference.location[0].start)) ValueError: invalid literal for int() with base 10: 'ExactPosition(0)' ====================================================================== ERROR: test_seq_record (common_BioSQL.SeqInterfaceTest) Make sure SeqRecords from BioSQL implement the right interface. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 458, in setUp load_database("GenBank/cor6_6.gb") File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 251, in load_database count = db.load(iterator) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/BioSeqDatabase.py", line 920, in load db_loader.load_seqrecord(cur_record) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 73, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 836, in _load_reference start = 1 + int(str(reference.location[0].start)) ValueError: invalid literal for int() with base 10: 'ExactPosition(0)' ====================================================================== ERROR: test_seq_slicing (common_BioSQL.SeqInterfaceTest) Check that slices of sequences are retrieved properly. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 458, in setUp load_database("GenBank/cor6_6.gb") File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 251, in load_database count = db.load(iterator) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/BioSeqDatabase.py", line 920, in load db_loader.load_seqrecord(cur_record) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 73, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 836, in _load_reference start = 1 + int(str(reference.location[0].start)) ValueError: invalid literal for int() with base 10: 'ExactPosition(0)' ====================================================================== ERROR: test_NC_000932 (common_BioSQL.TransferTest) From GenBank file to BioSQL, then again to a new namespace, NC_000932. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 897, in test_NC_000932 self.trans("GenBank/NC_000932.gb", "gb") File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 934, in trans count = db.load(original_records) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/BioSeqDatabase.py", line 920, in load db_loader.load_seqrecord(cur_record) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 73, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 836, in _load_reference start = 1 + int(str(reference.location[0].start)) ValueError: invalid literal for int() with base 10: 'ExactPosition(0)' ====================================================================== ERROR: test_NC_005816 (common_BioSQL.TransferTest) From GenBank file to BioSQL, then again to a new namespace, NC_005816. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 893, in test_NC_005816 self.trans("GenBank/NC_005816.gb", "gb") File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 934, in trans count = db.load(original_records) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/BioSeqDatabase.py", line 920, in load db_loader.load_seqrecord(cur_record) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 73, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 836, in _load_reference start = 1 + int(str(reference.location[0].start)) ValueError: invalid literal for int() with base 10: 'ExactPosition(0)' ====================================================================== ERROR: test_NT_019265 (common_BioSQL.TransferTest) From GenBank file to BioSQL, then again to a new namespace, NT_019265. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 901, in test_NT_019265 self.trans("GenBank/NT_019265.gb", "gb") File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 934, in trans count = db.load(original_records) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/BioSeqDatabase.py", line 920, in load db_loader.load_seqrecord(cur_record) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 73, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 836, in _load_reference start = 1 + int(str(reference.location[0].start)) ValueError: invalid literal for int() with base 10: 'ExactPosition(0)' ====================================================================== ERROR: test_arab1 (common_BioSQL.TransferTest) From GenBank file to BioSQL, then again to a new namespace, arab1. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 924, in test_arab1 self.trans("GenBank/arab1.gb", "gb") File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 934, in trans count = db.load(original_records) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/BioSeqDatabase.py", line 920, in load db_loader.load_seqrecord(cur_record) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 73, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 836, in _load_reference start = 1 + int(str(reference.location[0].start)) ValueError: invalid literal for int() with base 10: 'ExactPosition(0)' ====================================================================== ERROR: test_cor6_6 (common_BioSQL.TransferTest) From GenBank file to BioSQL, then again to a new namespace, cor6_6. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 920, in test_cor6_6 self.trans("GenBank/cor6_6.gb", "gb") File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 934, in trans count = db.load(original_records) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/BioSeqDatabase.py", line 920, in load db_loader.load_seqrecord(cur_record) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 73, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 836, in _load_reference start = 1 + int(str(reference.location[0].start)) ValueError: invalid literal for int() with base 10: 'ExactPosition(0)' ====================================================================== ERROR: test_one_of (common_BioSQL.TransferTest) From GenBank file to BioSQL, then again to a new namespace, one_of. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 916, in test_one_of self.trans("GenBank/one_of.gb", "gb") File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 934, in trans count = db.load(original_records) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/BioSeqDatabase.py", line 920, in load db_loader.load_seqrecord(cur_record) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 73, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 836, in _load_reference start = 1 + int(str(reference.location[0].start)) ValueError: invalid literal for int() with base 10: 'ExactPosition(0)' ====================================================================== ERROR: test_protein_refseq2 (common_BioSQL.TransferTest) From GenBank file to BioSQL, then again to a new namespace, protein_refseq2. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 908, in test_protein_refseq2 self.trans("GenBank/protein_refseq2.gb", "gb") File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/common_BioSQL.py", line 934, in trans count = db.load(original_records) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/BioSeqDatabase.py", line 920, in load db_loader.load_seqrecord(cur_record) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 73, in load_seqrecord self._load_reference(reference, rank, bioentry_id) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/BioSQL/Loader.py", line 836, in _load_reference start = 1 + int(str(reference.location[0].start)) ValueError: invalid literal for int() with base 10: 'ExactPosition(0)' ====================================================================== ERROR: runTest (__main__.ComparisonTestCase) test_GenBank ---------------------------------------------------------------------- Traceback (most recent call last): File "run_tests.py", line 378, in runTest raise ValueError("\nOutput : %s\nExpected: %s\n%s line %s" ValueError: Output : 'location: [ExactPosition(0):ExactPosition(1622)](+)' Expected: 'location: [0:1622](+)' /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/output/test_GenBank line 34 ====================================================================== ERROR: runTest (__main__.ComparisonTestCase) test_Location ---------------------------------------------------------------------- Traceback (most recent call last): File "run_tests.py", line 378, in runTest raise ValueError("\nOutput : %s\nExpected: %s\n%s line %s" ValueError: Output : 'Exact: ExactPosition(5)' Expected: 'Exact: 5' /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/output/test_Location line 3 ====================================================================== ERROR: test_SubsMat ---------------------------------------------------------------------- Traceback (most recent call last): File "run_tests.py", line 459, in runTest suite = loader.loadTestsFromName(name) File "/usr/lib/python3.8/unittest/loader.py", line 154, in loadTestsFromName module = __import__(module_name) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/test_SubsMat.py", line 68, in mat = SubsMat.SeqMat(getattr(MatrixInfo, i)) File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SubsMat/__init__.py", line 204, in __init__ self._correct_matrix() File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SubsMat/__init__.py", line 210, in _correct_matrix for key in self: RuntimeError: dictionary keys changed during iteration ====================================================================== ERROR: test_doctests (test_Tutorial.TutorialTestCase) Run tutorial doctests. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests/test_Tutorial.py", line 257, in test_doctests raise ValueError("%i Tutorial doctests failed: %s" % ValueError: 2 Tutorial doctests failed: test_chapter_seq_annot_line_00416, test_chapter_seq_annot_line_00691 ====================================================================== FAIL: _pos (Bio.GenBank) Doctest: Bio.GenBank._pos ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3.8/doctest.py", line 2196, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.GenBank._pos File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/GenBank/__init__.py", line 154, in _pos ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/GenBank/__init__.py", line 185, in Bio.GenBank._pos Failed example: print(p) Expected: one-of(5,8,11) Got: one-of(ExactPosition(5),ExactPosition(8),ExactPosition(11)) ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/GenBank/__init__.py", line 208, in Bio.GenBank._pos Failed example: print(p) Expected: one-of(4,7,10) Got: one-of(ExactPosition(4),ExactPosition(7),ExactPosition(10)) ====================================================================== FAIL: __add__ (Bio.SeqFeature.CompoundLocation) Doctest: Bio.SeqFeature.CompoundLocation.__add__ ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3.8/doctest.py", line 2196, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.SeqFeature.CompoundLocation.__add__ File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 1205, in __add__ ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 1210, in Bio.SeqFeature.CompoundLocation.__add__ Failed example: print(f1) Expected: join{[15:17], [20:30]} Got: join{[ExactPosition(15):ExactPosition(17)], [ExactPosition(20):ExactPosition(30)]} ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 1215, in Bio.SeqFeature.CompoundLocation.__add__ Failed example: print(f1 + FeatureLocation(40, 50)) Expected: join{[15:17], [20:30], [40:50]} Got: join{[ExactPosition(15):ExactPosition(17)], [ExactPosition(20):ExactPosition(30)], [ExactPosition(40):ExactPosition(50)]} ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 1217, in Bio.SeqFeature.CompoundLocation.__add__ Failed example: print(FeatureLocation(5, 10) + f1) Expected: join{[5:10], [15:17], [20:30]} Got: join{[ExactPosition(5):ExactPosition(10)], [ExactPosition(15):ExactPosition(17)], [ExactPosition(20):ExactPosition(30)]} ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 1223, in Bio.SeqFeature.CompoundLocation.__add__ Failed example: print(f2) Expected: join{[40:50], [60:70]} Got: join{[ExactPosition(40):ExactPosition(50)], [ExactPosition(60):ExactPosition(70)]} ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 1225, in Bio.SeqFeature.CompoundLocation.__add__ Failed example: print(f1 + f2) Expected: join{[15:17], [20:30], [40:50], [60:70]} Got: join{[ExactPosition(15):ExactPosition(17)], [ExactPosition(20):ExactPosition(30)], [ExactPosition(40):ExactPosition(50)], [ExactPosition(60):ExactPosition(70)]} ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 1231, in Bio.SeqFeature.CompoundLocation.__add__ Failed example: print(f1 + 100) Expected: join{[115:117], [120:130]} Got: join{[ExactPosition(115):ExactPosition(117)], [ExactPosition(120):ExactPosition(130)]} ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 1233, in Bio.SeqFeature.CompoundLocation.__add__ Failed example: print(200 + f1) Expected: join{[215:217], [220:230]} Got: join{[ExactPosition(215):ExactPosition(217)], [ExactPosition(220):ExactPosition(230)]} ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 1235, in Bio.SeqFeature.CompoundLocation.__add__ Failed example: print(f1 + (-5)) Expected: join{[10:12], [15:25]} Got: join{[ExactPosition(10):ExactPosition(12)], [ExactPosition(15):ExactPosition(25)]} ====================================================================== FAIL: _flip (Bio.SeqFeature.CompoundLocation) Doctest: Bio.SeqFeature.CompoundLocation._flip ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3.8/doctest.py", line 2196, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.SeqFeature.CompoundLocation._flip File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 1314, in _flip ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 1332, in Bio.SeqFeature.CompoundLocation._flip Failed example: print(small) Expected: [5:20](+) Got: [ExactPosition(5):ExactPosition(20)](+) ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 1334, in Bio.SeqFeature.CompoundLocation._flip Failed example: print(large) Expected: [28:52](+) Got: [ExactPosition(28):ExactPosition(52)](+) ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 1336, in Bio.SeqFeature.CompoundLocation._flip Failed example: print(location) Expected: join{[5:20](+), [28:52](+)} Got: join{[ExactPosition(5):ExactPosition(20)](+), [ExactPosition(28):ExactPosition(52)](+)} ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 1378, in Bio.SeqFeature.CompoundLocation._flip Failed example: print(flipped_location) Expected: join{[37:52](-), [5:29](-)} Got: join{[ExactPosition(37):ExactPosition(52)](-), [ExactPosition(5):ExactPosition(29)](-)} ====================================================================== FAIL: ExactPosition (Bio.SeqFeature) Doctest: Bio.SeqFeature.ExactPosition ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3.8/doctest.py", line 2196, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.SeqFeature.ExactPosition File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 1489, in ExactPosition ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 1503, in Bio.SeqFeature.ExactPosition Failed example: print(p) Expected: 5 Got: ExactPosition(5) ====================================================================== FAIL: FeatureLocation (Bio.SeqFeature) Doctest: Bio.SeqFeature.FeatureLocation ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3.8/doctest.py", line 2196, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.SeqFeature.FeatureLocation File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 614, in FeatureLocation ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 630, in Bio.SeqFeature.FeatureLocation Failed example: print(f) Expected: [122:150] Got: [ExactPosition(122):ExactPosition(150)] ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 632, in Bio.SeqFeature.FeatureLocation Failed example: print(f.start) Expected: 122 Got: ExactPosition(122) ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 634, in Bio.SeqFeature.FeatureLocation Failed example: print(f.end) Expected: 150 Got: ExactPosition(150) ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 644, in Bio.SeqFeature.FeatureLocation Failed example: print(f) Expected: [122:150](+) Got: [ExactPosition(122):ExactPosition(150)](+) ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 657, in Bio.SeqFeature.FeatureLocation Failed example: print(r) Expected: [122:150](-) Got: [ExactPosition(122):ExactPosition(150)](-) ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 659, in Bio.SeqFeature.FeatureLocation Failed example: print(r.start) Expected: 122 Got: ExactPosition(122) ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 661, in Bio.SeqFeature.FeatureLocation Failed example: print(r.end) Expected: 150 Got: ExactPosition(150) ====================================================================== FAIL: __add__ (Bio.SeqFeature.FeatureLocation) Doctest: Bio.SeqFeature.FeatureLocation.__add__ ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3.8/doctest.py", line 2196, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.SeqFeature.FeatureLocation.__add__ File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 804, in __add__ ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 813, in Bio.SeqFeature.FeatureLocation.__add__ Failed example: print(combined) Expected: join{[5:10], [20:30]} Got: join{[ExactPosition(5):ExactPosition(10)], [ExactPosition(20):ExactPosition(30)]} ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 820, in Bio.SeqFeature.FeatureLocation.__add__ Failed example: print(join) Expected: join{[5:10], [20:30]} Got: join{[ExactPosition(5):ExactPosition(10)], [ExactPosition(20):ExactPosition(30)]} ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 826, in Bio.SeqFeature.FeatureLocation.__add__ Failed example: print(join) Expected: join{[5:10], [20:30]} Got: join{[ExactPosition(5):ExactPosition(10)], [ExactPosition(20):ExactPosition(30)]} ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 835, in Bio.SeqFeature.FeatureLocation.__add__ Failed example: print(f1) Expected: [5:10] Got: [ExactPosition(5):ExactPosition(10)] ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 837, in Bio.SeqFeature.FeatureLocation.__add__ Failed example: print(f1 + 100) Expected: [105:110] Got: [ExactPosition(105):ExactPosition(110)] ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 839, in Bio.SeqFeature.FeatureLocation.__add__ Failed example: print(200 + f1) Expected: [205:210] Got: [ExactPosition(205):ExactPosition(210)] ====================================================================== FAIL: __init__ (Bio.SeqFeature.FeatureLocation) Doctest: Bio.SeqFeature.FeatureLocation.__init__ ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3.8/doctest.py", line 2196, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.SeqFeature.FeatureLocation.__init__ File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 678, in __init__ ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 692, in Bio.SeqFeature.FeatureLocation.__init__ Failed example: print(loc) Expected: [5:10](-) Got: [ExactPosition(5):ExactPosition(10)](-) ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 699, in Bio.SeqFeature.FeatureLocation.__init__ Failed example: print(loc) Expected: [5:10](-) Got: [ExactPosition(5):ExactPosition(10)](-) ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 717, in Bio.SeqFeature.FeatureLocation.__init__ Failed example: print(loc) Expected: [5:10](+) Got: [ExactPosition(5):ExactPosition(10)](+) ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 727, in Bio.SeqFeature.FeatureLocation.__init__ Failed example: print(loc) Expected: AL391218.9[105172:108462](+) Got: AL391218.9[ExactPosition(105172):ExactPosition(108462)](+) ====================================================================== FAIL: __contains__ (Bio.SeqFeature.SeqFeature) Doctest: Bio.SeqFeature.SeqFeature.__contains__ ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3.8/doctest.py", line 2196, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.SeqFeature.SeqFeature.__contains__ File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 485, in __contains__ ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 500, in Bio.SeqFeature.SeqFeature.__contains__ Failed example: for f in record.features: if 1750 in f: print("%s %s" % (f.type, f.location)) Expected: source [0:154478](+) gene [1716:4347](-) tRNA join{[4310:4347](-), [1716:1751](-)} Got: source [ExactPosition(0):ExactPosition(154478)](+) gene [ExactPosition(1716):ExactPosition(4347)](-) tRNA join{[ExactPosition(4310):ExactPosition(4347)](-), [ExactPosition(1716):ExactPosition(1751)](-)} ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqFeature.py", line 513, in Bio.SeqFeature.SeqFeature.__contains__ Failed example: for f in record.features: if 1760 in f: print("%s %s" % (f.type, f.location)) Expected: source [0:154478](+) gene [1716:4347](-) Got: source [ExactPosition(0):ExactPosition(154478)](+) gene [ExactPosition(1716):ExactPosition(4347)](-) ====================================================================== FAIL: __getitem__ (Bio.SeqRecord.SeqRecord) Doctest: Bio.SeqRecord.SeqRecord.__getitem__ ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3.8/doctest.py", line 2196, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.SeqRecord.SeqRecord.__getitem__ File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqRecord.py", line 323, in __getitem__ ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqRecord.py", line 374, in Bio.SeqRecord.SeqRecord.__getitem__ Failed example: print(rec.features[0].location) Expected: [20:21] Got: [ExactPosition(20):ExactPosition(21)] ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqRecord.py", line 390, in Bio.SeqRecord.SeqRecord.__getitem__ Failed example: print(sub.features[0].location) Expected: [9:10] Got: [ExactPosition(9):ExactPosition(10)] ====================================================================== FAIL: reverse_complement (Bio.SeqRecord.SeqRecord) Doctest: Bio.SeqRecord.SeqRecord.reverse_complement ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3.8/doctest.py", line 2196, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.SeqRecord.SeqRecord.reverse_complement File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqRecord.py", line 1004, in reverse_complement ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqRecord.py", line 1078, in Bio.SeqRecord.SeqRecord.reverse_complement Failed example: print(plasmid.features[1]) Expected: type: CDS location: [1081:1960](-) qualifiers: Key: label, Value: ['araC'] Key: note, Value: ['araC regulator of the arabinose BAD promoter'] Key: vntifkey, Value: ['4'] Got: type: CDS location: [ExactPosition(1081):ExactPosition(1960)](-) qualifiers: Key: label, Value: ['araC'] Key: note, Value: ['araC regulator of the arabinose BAD promoter'] Key: vntifkey, Value: ['4'] ---------------------------------------------------------------------- File "/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqRecord.py", line 1086, in Bio.SeqRecord.SeqRecord.reverse_complement Failed example: print(rc_plasmid.features[-2]) Expected: type: CDS location: [2963:3842](+) qualifiers: Key: label, Value: ['araC'] Key: note, Value: ['araC regulator of the arabinose BAD promoter'] Key: vntifkey, Value: ['4'] Got: type: CDS location: [ExactPosition(2963):ExactPosition(3842)](+) qualifiers: Key: label, Value: ['araC'] Key: note, Value: ['araC regulator of the arabinose BAD promoter'] Key: vntifkey, Value: ['4'] ---------------------------------------------------------------------- Ran 260 tests in 608.496 seconds FAILED (failures = 8) Skipping any tests requiring internet access Python version: 3.8.0 (default, Oct 27 2019, 15:36:55) [GCC 9.2.1 20191025] Operating system: posix linux E: pybuild pybuild:341: test: plugin custom failed with: exit code=1: set -e; \ mkdir -p /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/home; \ mkdir -p /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Doc/examples; \ cp -a Doc/Tutorial.tex /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Doc; \ cp -a Doc/Tutorial /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Doc; \ cp -a Doc/examples /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Doc; \ cp -a Tests /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build; \ cd /<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/Tests; \ env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=/<>/python-biopython-1.73+dfsg/.pybuild/cpython3_3.8/build/home python3.8 run_tests.py --offline dh_auto_test: pybuild --test -i python{version} -p "3.8 3.7" --test --system=custom "--test-args=set -e; \\\ mkdir -p {build_dir}/home; \\\ mkdir -p {build_dir}/Doc/examples; \\\ cp -a Doc/Tutorial.tex {build_dir}/Doc; \\\ cp -a Doc/Tutorial {build_dir}/Doc; \\\ cp -a Doc/examples {build_dir}/Doc; \\\ cp -a Tests {build_dir}; \\\ cd {build_dir}/Tests; \\\ env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME={build_dir}/home {interpreter} run_tests.py --offline" returned exit code 13 make[1]: *** [debian/rules:100: override_dh_auto_test] Error 255 make[1]: Leaving directory '/<>/python-biopython-1.73+dfsg' make: *** [debian/rules:48: build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 20191103-1024 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build-Space: 262888 Build-Time: 1606 Distribution: focal-proposed Fail-Stage: build Host Architecture: armhf Install-Time: 200 Job: python-biopython_1.73+dfsg-1ubuntu2.dsc Machine Architecture: arm64 Package: python-biopython Package-Time: 1810 Source-Version: 1.73+dfsg-1ubuntu2 Space: 262888 Status: attempted Version: 1.73+dfsg-1ubuntu2 -------------------------------------------------------------------------------- Finished at 20191103-1024 Build needed 00:30:10, 262888k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=focal --arch=armhf PACKAGEBUILD-17940165 Scanning for processes to kill in build PACKAGEBUILD-17940165