https://launchpad.net/ubuntu/+source/python-biopython/1.78+dfsg-5ubuntu2/+build/22291105 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-ppc64el-022 4.15.0-161-generic #169-Ubuntu SMP Fri Oct 15 13:40:22 UTC 2021 ppc64le Buildd toolchain package versions: launchpad-buildd_203~505~ubuntu18.04.1 python3-lpbuildd_203~505~ubuntu18.04.1 sbuild_0.75.0-1ubuntu1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu16.04.1 bzr_2.7.0+bzr6622-10 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu18.04.1 git_1:2.17.1-1ubuntu0.9 dpkg-dev_1.19.0.5ubuntu2.3 python-debian_0.1.32 python3-debian_0.1.32. Syncing the system clock with the buildd NTP service... 22 Oct 10:36:00 ntpdate[2105]: adjust time server 10.211.37.1 offset 0.008144 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=jammy --arch=ppc64el PACKAGEBUILD-22291105 --image-type chroot /home/buildd/filecache-default/104362a8a1d4d9793492e39ad0c0e733056a927b Creating target for build PACKAGEBUILD-22291105 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=jammy --arch=ppc64el PACKAGEBUILD-22291105 Starting target for build PACKAGEBUILD-22291105 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=jammy --arch=ppc64el PACKAGEBUILD-22291105 'deb http://ftpmaster.internal/ubuntu jammy main universe' 'deb http://ftpmaster.internal/ubuntu jammy-security main universe' 'deb http://ftpmaster.internal/ubuntu jammy-updates main universe' 'deb http://ftpmaster.internal/ubuntu jammy-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-22291105 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=jammy --arch=ppc64el PACKAGEBUILD-22291105 Updating target for build PACKAGEBUILD-22291105 Get:1 http://ftpmaster.internal/ubuntu jammy InRelease [224 kB] Get:2 http://ftpmaster.internal/ubuntu jammy-security InRelease [74.9 kB] Get:3 http://ftpmaster.internal/ubuntu jammy-updates InRelease [74.9 kB] Get:4 http://ftpmaster.internal/ubuntu jammy-proposed InRelease [74.9 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main ppc64el Packages [1356 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main Translation-en [512 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/universe ppc64el Packages [13.3 MB] Get:8 http://ftpmaster.internal/ubuntu jammy/universe Translation-en [5503 kB] Get:9 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el Packages [355 kB] Get:10 http://ftpmaster.internal/ubuntu jammy-proposed/main Translation-en [120 kB] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/universe ppc64el Packages [1777 kB] Get:12 http://ftpmaster.internal/ubuntu jammy-proposed/universe Translation-en [908 kB] Fetched 24.3 MB in 5s (5023 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt bsdutils ca-certificates cpp-11 debianutils g++-11 gcc-11 gcc-11-base libapparmor1 libapt-pkg6.0 libasan6 libatomic1 libattr1 libblkid1 libcc1-0 libgcc-11-dev libgcc-s1 libgdbm-compat4 libgdbm6 libgomp1 libgpg-error0 libgssapi-krb5-2 libidn2-0 libisl23 libitm1 libk5crypto3 libkrb5-3 libkrb5support0 liblsan0 libmount1 libmpc3 libncurses6 libncursesw6 libp11-kit0 libquadmath0 libseccomp2 libselinux1 libsmartcols1 libsqlite3-0 libstdc++-11-dev libstdc++6 libtasn1-6 libtinfo6 libtsan0 libubsan1 libuuid1 libzstd1 lockfile-progs make mount ncurses-base ncurses-bin sensible-utils util-linux 54 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 171 MB of archives. After this operation, 135 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el bsdutils ppc64el 1:2.36.1-8ubuntu2 [86.1 kB] Get:2 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el debianutils ppc64el 5.5-1 [78.2 kB] Get:3 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libncursesw6 ppc64el 6.2+20210905-1 [183 kB] Get:4 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libncurses6 ppc64el 6.2+20210905-1 [144 kB] Get:5 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libtinfo6 ppc64el 6.2+20210905-1 [129 kB] Get:6 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el ncurses-bin ppc64el 6.2+20210905-1 [193 kB] Get:7 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el util-linux ppc64el 2.36.1-8ubuntu2 [1080 kB] Get:8 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el ncurses-base all 6.2+20210905-1 [19.9 kB] Get:9 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libcc1-0 ppc64el 11.2.0-10ubuntu1 [48.1 kB] Get:10 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el gcc-11-base ppc64el 11.2.0-10ubuntu1 [21.0 kB] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libgcc-s1 ppc64el 11.2.0-10ubuntu1 [34.7 kB] Get:12 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libgomp1 ppc64el 11.2.0-10ubuntu1 [129 kB] Get:13 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libitm1 ppc64el 11.2.0-10ubuntu1 [33.1 kB] Get:14 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libatomic1 ppc64el 11.2.0-10ubuntu1 [10.7 kB] Get:15 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libasan6 ppc64el 11.2.0-10ubuntu1 [2303 kB] Get:16 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el liblsan0 ppc64el 11.2.0-10ubuntu1 [997 kB] Get:17 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libtsan0 ppc64el 11.2.0-10ubuntu1 [2284 kB] Get:18 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libubsan1 ppc64el 11.2.0-10ubuntu1 [947 kB] Get:19 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libquadmath0 ppc64el 11.2.0-10ubuntu1 [166 kB] Get:20 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el g++-11 ppc64el 11.2.0-10ubuntu1 [50.9 MB] Get:21 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libstdc++-11-dev ppc64el 11.2.0-10ubuntu1 [2180 kB] Get:22 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libgcc-11-dev ppc64el 11.2.0-10ubuntu1 [1490 kB] Get:23 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el gcc-11 ppc64el 11.2.0-10ubuntu1 [53.8 MB] Get:24 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el cpp-11 ppc64el 11.2.0-10ubuntu1 [46.2 MB] Get:25 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libstdc++6 ppc64el 11.2.0-10ubuntu1 [759 kB] Get:26 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libisl23 ppc64el 0.24-2 [835 kB] Get:27 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libmpc3 ppc64el 1.2.1-1 [52.9 kB] Get:28 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libzstd1 ppc64el 1.4.8+dfsg-3 [364 kB] Get:29 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libapt-pkg6.0 ppc64el 2.3.11 [1030 kB] Get:30 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libseccomp2 ppc64el 2.5.1-1ubuntu2 [59.8 kB] Get:31 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el apt ppc64el 2.3.11 [1438 kB] Get:32 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el mount ppc64el 2.36.1-8ubuntu2 [117 kB] Get:33 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libattr1 ppc64el 1:2.5.1-1 [14.3 kB] Get:34 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libblkid1 ppc64el 2.36.1-8ubuntu2 [123 kB] Get:35 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libgpg-error0 ppc64el 1.42-3 [84.4 kB] Get:36 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libk5crypto3 ppc64el 1.18.3-7 [117 kB] Get:37 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libkrb5support0 ppc64el 1.18.3-7 [37.6 kB] Get:38 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libkrb5-3 ppc64el 1.18.3-7 [436 kB] Get:39 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libgssapi-krb5-2 ppc64el 1.18.3-7 [183 kB] Get:40 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libselinux1 ppc64el 3.1-3build3 [93.8 kB] Get:41 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libmount1 ppc64el 2.36.1-8ubuntu2 [140 kB] Get:42 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libsmartcols1 ppc64el 2.36.1-8ubuntu2 [59.5 kB] Get:43 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libuuid1 ppc64el 2.36.1-8ubuntu2 [26.5 kB] Get:44 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libidn2-0 ppc64el 2.3.2-2 [70.4 kB] Get:45 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libp11-kit0 ppc64el 0.24.0-5 [264 kB] Get:46 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libtasn1-6 ppc64el 4.17.0-2 [56.1 kB] Get:47 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el sensible-utils all 0.0.17 [20.1 kB] Get:48 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el ca-certificates all 20211016 [148 kB] Get:49 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libapparmor1 ppc64el 3.0.3-0ubuntu2 [43.8 kB] Get:50 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libsqlite3-0 ppc64el 3.36.0-2 [744 kB] Get:51 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libgdbm6 ppc64el 1.22-1 [43.1 kB] Get:52 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libgdbm-compat4 ppc64el 1.22-1 [6864 B] Get:53 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el lockfile-progs ppc64el 0.1.19 [10.2 kB] Get:54 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el make ppc64el 4.3-4ubuntu2 [211 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 171 MB in 4s (38.6 MB/s) (Reading database ... 13185 files and directories currently installed.) 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Setting up libgomp1:ppc64el (11.2.0-10ubuntu1) ... Setting up libasan6:ppc64el (11.2.0-10ubuntu1) ... Setting up ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 7 added, 8 removed; done. Setting up make (4.3-4ubuntu2) ... Setting up libncurses6:ppc64el (6.2+20210905-1) ... Setting up libquadmath0:ppc64el (11.2.0-10ubuntu1) ... Setting up libmpc3:ppc64el (1.2.1-1) ... Setting up lockfile-progs (0.1.19) ... Setting up libatomic1:ppc64el (11.2.0-10ubuntu1) ... Setting up libncursesw6:ppc64el (6.2+20210905-1) ... Setting up libubsan1:ppc64el (11.2.0-10ubuntu1) ... Setting up mount (2.36.1-8ubuntu2) ... Setting up sensible-utils (0.0.17) ... Setting up libisl23:ppc64el (0.24-2) ... Setting up libcc1-0:ppc64el (11.2.0-10ubuntu1) ... Setting up liblsan0:ppc64el (11.2.0-10ubuntu1) ... Setting up libitm1:ppc64el (11.2.0-10ubuntu1) ... Setting up libgdbm6:ppc64el (1.22-1) ... Setting up libtsan0:ppc64el (11.2.0-10ubuntu1) ... Setting up cpp-11 (11.2.0-10ubuntu1) ... Setting up libgdbm-compat4:ppc64el (1.22-1) ... Setting up libgcc-11-dev:ppc64el (11.2.0-10ubuntu1) ... Setting up gcc-11 (11.2.0-10ubuntu1) ... Setting up libstdc++-11-dev:ppc64el (11.2.0-10ubuntu1) ... Setting up g++-11 (11.2.0-10ubuntu1) ... Processing triggers for libc-bin (2.34-0ubuntu3) ... Processing triggers for ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-22291105 ppc64el jammy-proposed -c chroot:build-PACKAGEBUILD-22291105 --arch=ppc64el --dist=jammy-proposed --nolog python-biopython_1.78+dfsg-5ubuntu2.dsc Initiating build PACKAGEBUILD-22291105 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-161-generic #169-Ubuntu SMP Fri Oct 15 13:40:22 UTC 2021 ppc64le sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on bos02-ppc64el-022.buildd +===============================================================================+ | python-biopython 1.78+dfsg-5ubuntu2 (ppc64el) Fri, 22 Oct 2021 10:36:32 +0000 | +===============================================================================+ Package: python-biopython Version: 1.78+dfsg-5ubuntu2 Source Version: 1.78+dfsg-5ubuntu2 Distribution: jammy-proposed Machine Architecture: ppc64el Host Architecture: ppc64el Build Architecture: ppc64el Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-22291105/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- python-biopython_1.78+dfsg-5ubuntu2.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/python-biopython-6IvcQW/python-biopython-1.78+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/python-biopython-6IvcQW' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-5VwOil/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-5VwOil/apt_archive ./ InRelease Get:2 copy:/<>/resolver-5VwOil/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-5VwOil/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-5VwOil/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-5VwOil/apt_archive ./ Packages [434 B] Fetched 1740 B in 0s (75.4 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 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 652 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-5VwOil/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [652 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 652 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 13187 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_ppc64el.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (ppc64el included in any all) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-python, python3-all-dev, python3-numpy, flex, python3-reportlab, hevea, texlive-latex-base, texlive-latex-extra, texlive-fonts-recommended, bwa, clustalo, clustalw, dialign, dssp (>= 4.0.0), emboss, fasttree, mafft, muscle, ncbi-blast+ (>= 2.10.1-3), phylip, prank, probcons, python3-networkx, python3-mysqldb, python3-matplotlib, python3-mmtf, python3-pil, python3-rdflib, python3-renderpm, python3-psycopg2, python3-pygments, python3-scipy, python3-setuptools, python3-unittest2, samtools, t-coffee, wise Filtered Build-Depends: debhelper-compat (= 13), dh-python, python3-all-dev, python3-numpy, flex, python3-reportlab, hevea, texlive-latex-base, texlive-latex-extra, texlive-fonts-recommended, bwa, clustalo, clustalw, dialign, dssp (>= 4.0.0), emboss, fasttree, mafft, muscle, ncbi-blast+ (>= 2.10.1-3), phylip, prank, probcons, python3-networkx, python3-mysqldb, python3-matplotlib, python3-mmtf, python3-pil, python3-rdflib, python3-renderpm, python3-psycopg2, python3-pygments, python3-scipy, python3-setuptools, python3-unittest2, samtools, t-coffee, wise dpkg-deb: building package 'sbuild-build-depends-python-biopython-dummy' in '/<>/resolver-5VwOil/apt_archive/sbuild-build-depends-python-biopython-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-python-biopython-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-5VwOil/apt_archive ./ InRelease Get:2 copy:/<>/resolver-5VwOil/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-5VwOil/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-5VwOil/apt_archive ./ Sources [795 B] Get:5 copy:/<>/resolver-5VwOil/apt_archive ./ Packages [824 B] Fetched 2582 B in 0s (138 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 additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils bwa clustalo clustalw debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dialign dssp dwz emboss emboss-data emboss-lib fasttree file flex fontconfig-config fonts-lmodern fonts-lyx fonts-urw-base35 gettext gettext-base ghostscript groff-base hevea intltool-debian libapache-pom-java libarchive-zip-perl libargtable2-0 libavahi-client3 libavahi-common-data libavahi-common3 libblas3 libboost-iostreams1.74.0 libboost-program-options1.74.0 libbrotli1 libbsd0 libcairo2 libcifpp1 libcommons-logging-java libcommons-parent-java libcups2 libcurl3-gnutls libdbus-1-3 libdebhelper-perl libdeflate0 libdw1 libedit2 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfreetype6 libfribidi0 libgd3 libgfortran5 libglib2.0-0 libgraphite2-3 libgs9 libgs9-common libharfbuzz0b libhpdf-2.3.0 libhts3 libhtscodecs2 libice6 libicu67 libidn11 libijs-0.35 libimagequant0 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libkpathsea6 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblmdb0 libmagic-mgc libmagic1 libmbedcrypto3 libmbedtls12 libmbedx509-0 libmd0 libmpdec3 libmysqlclient21 libnetpbm10 libnghttp2-14 libopenjp2-7 libpaper-utils libpaper1 libpdfbox-java libpipeline1 libpixman-1-0 libpq5 libpsl5 libptexenc1 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.10 libpython3.10-dev libpython3.10-minimal libpython3.10-stdlib libpython3.9 libpython3.9-dev libpython3.9-minimal libpython3.9-stdlib libraqm0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libssh-4 libsub-override-perl libsynctex2 libteckit0 libtexlua53 libtiff5 libtool libuchardet0 libwebp6 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxt6 libzzip-0-13 m4 mafft mailcap man-db media-types mime-support muscle mysql-common ncbi-blast+ ncbi-data netpbm phylip po-debconf poppler-data prank preview-latex-style probcons python-matplotlib-data python3 python3-all python3-all-dev python3-cycler python3-dateutil python3-decorator python3-dev python3-distutils python3-isodate python3-kiwisolver python3-lib2to3 python3-linecache2 python3-matplotlib python3-minimal python3-mmtf python3-msgpack python3-mysqldb python3-networkx python3-numpy python3-pil python3-pkg-resources python3-psycopg2 python3-pygments python3-pyparsing python3-rdflib python3-renderpm python3-reportlab python3-reportlab-accel python3-scipy python3-setuptools python3-six python3-traceback2 python3-unittest2 python3.10 python3.10-dev python3.10-minimal python3.9 python3.9-dev python3.9-minimal samtools t-coffee t1utils tex-common texlive-base texlive-binaries texlive-fonts-recommended texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures ttf-bitstream-vera ucf wise wise-data x11-common xdg-utils zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc clustalx seaview dh-make flit python3-toml emboss-doc emboss-test embassy bison flex-doc fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre gettext-doc libasprintf-dev libgettextpo-dev ghostscript-x groff hevea-doc libavalon-framework-java libcommons-logging-java-doc libexcalibur-logkit-java liblog4j1.2-java cups-common libgd-tools libjs-jquery-ui-docs liblcms2-utils libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser phylip-doc libmail-box-perl poppler-utils fonts-japanese-mincho | fonts-ipafont-mincho fonts-japanese-gothic | fonts-ipafont-gothic fonts-arphic-ukai fonts-arphic-uming fonts-nanum probcons-extra python3-doc python3-tk python3-venv python-cycler-doc dvipng ffmpeg gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-nose python3-pyqt5 python3-sip python3-tornado texlive-extra-utils ttf-staypuft default-mysql-server | virtual-mysql-server python3-mysqldb-dbg python-networkx-doc python3-gdal python3-pydot python3-pygraphviz gfortran python-numpy-doc python3-numpy-dbg python3-pytest python-pil-doc python-psycopg2-doc python-pygments-doc python-pyparsing-doc python-rdflib-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc python-scipy-doc python-setuptools-doc python3.10-venv python3.10-doc binfmt-support python3.9-venv python3.9-doc cwltool boxshade t-coffee-examples perl-tk xpdf | pdf-viewer xzdec texlive-fonts-recommended-doc texlive-latex-base-doc 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 dbus libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs fonts-droid-fallback javascript-common libldap-common publicsuffix libsasl2-modules libltdl-dev blast2 libwww-perl lynx ruby libmail-sendmail-perl python3-tk python3-yaml 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 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 bsdextrautils bwa clustalo clustalw debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dialign dssp dwz emboss emboss-data emboss-lib fasttree file flex fontconfig-config fonts-lmodern fonts-lyx fonts-urw-base35 gettext gettext-base ghostscript groff-base hevea intltool-debian libapache-pom-java libarchive-zip-perl libargtable2-0 libavahi-client3 libavahi-common-data libavahi-common3 libblas3 libboost-iostreams1.74.0 libboost-program-options1.74.0 libbrotli1 libbsd0 libcairo2 libcifpp1 libcommons-logging-java libcommons-parent-java libcups2 libcurl3-gnutls libdbus-1-3 libdebhelper-perl libdeflate0 libdw1 libedit2 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfreetype6 libfribidi0 libgd3 libgfortran5 libglib2.0-0 libgraphite2-3 libgs9 libgs9-common libharfbuzz0b libhpdf-2.3.0 libhts3 libhtscodecs2 libice6 libicu67 libidn11 libijs-0.35 libimagequant0 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libkpathsea6 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblmdb0 libmagic-mgc libmagic1 libmbedcrypto3 libmbedtls12 libmbedx509-0 libmd0 libmpdec3 libmysqlclient21 libnetpbm10 libnghttp2-14 libopenjp2-7 libpaper-utils libpaper1 libpdfbox-java libpipeline1 libpixman-1-0 libpq5 libpsl5 libptexenc1 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.10 libpython3.10-dev libpython3.10-minimal libpython3.10-stdlib libpython3.9 libpython3.9-dev libpython3.9-minimal libpython3.9-stdlib libraqm0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libssh-4 libsub-override-perl libsynctex2 libteckit0 libtexlua53 libtiff5 libtool libuchardet0 libwebp6 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxt6 libzzip-0-13 m4 mafft mailcap man-db media-types mime-support muscle mysql-common ncbi-blast+ ncbi-data netpbm phylip po-debconf poppler-data prank preview-latex-style probcons python-matplotlib-data python3 python3-all python3-all-dev python3-cycler python3-dateutil python3-decorator python3-dev python3-distutils python3-isodate python3-kiwisolver python3-lib2to3 python3-linecache2 python3-matplotlib python3-minimal python3-mmtf python3-msgpack python3-mysqldb python3-networkx python3-numpy python3-pil python3-pkg-resources python3-psycopg2 python3-pygments python3-pyparsing python3-rdflib python3-renderpm python3-reportlab python3-reportlab-accel python3-scipy python3-setuptools python3-six python3-traceback2 python3-unittest2 python3.10 python3.10-dev python3.10-minimal python3.9 python3.9-dev python3.9-minimal samtools 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, 230 newly installed, 0 to remove and 0 not upgraded. Need to get 298 MB of archives. After this operation, 1470 MB of additional disk space will be used. Get:1 copy:/<>/resolver-5VwOil/apt_archive ./ sbuild-build-depends-python-biopython-dummy 0.invalid.0 [900 B] Get:2 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libpython3.9-minimal ppc64el 3.9.7-4 [780 kB] Get:3 http://ftpmaster.internal/ubuntu jammy/main ppc64el libexpat1 ppc64el 2.4.1-2 [108 kB] Get:4 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el python3.9-minimal ppc64el 3.9.7-4 [2118 kB] Get:5 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el python3-minimal ppc64el 3.9.4-1ubuntu2 [24.6 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main ppc64el media-types all 4.0.0 [22.2 kB] Get:7 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el mailcap all 3.70ubuntu1 [23.7 kB] Get:8 http://ftpmaster.internal/ubuntu jammy/main ppc64el mime-support all 3.66 [3696 B] Get:9 http://ftpmaster.internal/ubuntu jammy/main ppc64el libmpdec3 ppc64el 2.5.1-2build1 [112 kB] Get:10 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libpython3.9-stdlib ppc64el 3.9.7-4 [1805 kB] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el python3.9 ppc64el 3.9.7-4 [433 kB] Get:12 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libpython3-stdlib ppc64el 3.9.4-1ubuntu2 [7186 B] Get:13 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el python3 ppc64el 3.9.4-1ubuntu2 [22.8 kB] Get:14 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el bsdextrautils ppc64el 2.36.1-8ubuntu2 [81.1 kB] Get:15 http://ftpmaster.internal/ubuntu jammy/main ppc64el libuchardet0 ppc64el 0.0.7-1build1 [80.3 kB] Get:16 http://ftpmaster.internal/ubuntu jammy/main ppc64el groff-base ppc64el 1.22.4-7 [1033 kB] Get:17 http://ftpmaster.internal/ubuntu jammy/main ppc64el libpipeline1 ppc64el 1.5.3-1build1 [27.0 kB] Get:18 http://ftpmaster.internal/ubuntu jammy/main ppc64el man-db ppc64el 2.9.4-2build1 [1231 kB] Get:19 http://ftpmaster.internal/ubuntu jammy/main ppc64el libsigsegv2 ppc64el 2.13-1ubuntu2 [15.3 kB] Get:20 http://ftpmaster.internal/ubuntu jammy/main ppc64el m4 ppc64el 1.4.18-5ubuntu1 [213 kB] Get:21 http://ftpmaster.internal/ubuntu jammy/main ppc64el flex ppc64el 2.6.4-8build1 [309 kB] Get:22 http://ftpmaster.internal/ubuntu jammy/main ppc64el poppler-data all 0.4.11-1 [2171 kB] Get:23 http://ftpmaster.internal/ubuntu jammy/main ppc64el libpython3.10-minimal ppc64el 3.10.0-3 [799 kB] Get:24 http://ftpmaster.internal/ubuntu jammy/main ppc64el python3.10-minimal ppc64el 3.10.0-3 [2159 kB] Get:25 http://ftpmaster.internal/ubuntu jammy/main ppc64el ucf all 3.0043 [56.1 kB] Get:26 http://ftpmaster.internal/ubuntu jammy-proposed/universe ppc64el tex-common all 6.17 [33.7 kB] Get:27 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libmd0 ppc64el 1.0.4-1 [29.4 kB] Get:28 http://ftpmaster.internal/ubuntu jammy/main ppc64el libbsd0 ppc64el 0.11.3-1ubuntu3 [59.3 kB] Get:29 http://ftpmaster.internal/ubuntu jammy/main ppc64el libdbus-1-3 ppc64el 1.12.20-2ubuntu2 [219 kB] Get:30 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libelf1 ppc64el 0.185-2 [62.6 kB] Get:31 http://ftpmaster.internal/ubuntu jammy/main ppc64el libfribidi0 ppc64el 1.0.8-2ubuntu2 [27.2 kB] Get:32 http://ftpmaster.internal/ubuntu jammy/main ppc64el libglib2.0-0 ppc64el 2.68.4-1ubuntu1 [1612 kB] Get:33 http://ftpmaster.internal/ubuntu jammy/main ppc64el libicu67 ppc64el 67.1-7ubuntu1 [10.4 MB] Get:34 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libxml2 ppc64el 2.9.12+dfsg-5 [838 kB] Get:35 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el python3-pkg-resources all 58.2.0-1 [130 kB] Get:36 http://ftpmaster.internal/ubuntu jammy/main ppc64el libmagic-mgc ppc64el 1:5.39-3build1 [236 kB] Get:37 http://ftpmaster.internal/ubuntu jammy/main ppc64el libmagic1 ppc64el 1:5.39-3build1 [105 kB] Get:38 http://ftpmaster.internal/ubuntu jammy/main ppc64el file ppc64el 1:5.39-3build1 [25.6 kB] Get:39 http://ftpmaster.internal/ubuntu jammy/main ppc64el gettext-base ppc64el 0.21-4ubuntu3 [40.5 kB] Get:40 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libedit2 ppc64el 3.1-20210910-1 [124 kB] Get:41 http://ftpmaster.internal/ubuntu jammy/main ppc64el liblmdb0 ppc64el 0.9.24-1build1 [62.6 kB] Get:42 http://ftpmaster.internal/ubuntu jammy/main ppc64el libpsl5 ppc64el 0.21.0-1.2build1 [59.6 kB] Get:43 http://ftpmaster.internal/ubuntu jammy/main ppc64el libxau6 ppc64el 1:1.0.9-1build4 [8132 B] Get:44 http://ftpmaster.internal/ubuntu jammy/main ppc64el libxdmcp6 ppc64el 1:1.1.3-0ubuntu4 [12.4 kB] Get:45 http://ftpmaster.internal/ubuntu jammy/main ppc64el libxcb1 ppc64el 1.14-3ubuntu2 [57.1 kB] Get:46 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libx11-data all 2:1.7.2-2 [123 kB] Get:47 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libx11-6 ppc64el 2:1.7.2-2 [759 kB] Get:48 http://ftpmaster.internal/ubuntu jammy/main ppc64el libxext6 ppc64el 2:1.3.4-0ubuntu4 [39.2 kB] Get:49 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el autoconf all 2.71-2 [338 kB] Get:50 http://ftpmaster.internal/ubuntu jammy/main ppc64el autotools-dev all 20180224.1+nmu1 [39.4 kB] Get:51 http://ftpmaster.internal/ubuntu jammy/main ppc64el automake all 1:1.16.4-2 [557 kB] Get:52 http://ftpmaster.internal/ubuntu jammy/main ppc64el autopoint all 0.21-4ubuntu3 [422 kB] Get:53 http://ftpmaster.internal/ubuntu jammy/universe ppc64el bwa ppc64el 0.7.17-6 [210 kB] Get:54 http://ftpmaster.internal/ubuntu jammy/universe ppc64el libargtable2-0 ppc64el 13-1.1 [17.1 kB] Get:55 http://ftpmaster.internal/ubuntu jammy/universe ppc64el clustalo ppc64el 1.2.4-7 [292 kB] Get:56 http://ftpmaster.internal/ubuntu jammy/universe ppc64el clustalw ppc64el 2.1+lgpl-7 [313 kB] Get:57 http://ftpmaster.internal/ubuntu jammy/main ppc64el libdebhelper-perl all 13.3.4ubuntu2 [62.5 kB] Get:58 http://ftpmaster.internal/ubuntu jammy/main ppc64el libtool all 2.4.6-15build1 [164 kB] Get:59 http://ftpmaster.internal/ubuntu jammy/main ppc64el dh-autoreconf all 20 [16.1 kB] Get:60 http://ftpmaster.internal/ubuntu jammy/main ppc64el libarchive-zip-perl all 1.68-1 [90.2 kB] Get:61 http://ftpmaster.internal/ubuntu jammy/main ppc64el libsub-override-perl all 0.09-2 [9532 B] Get:62 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libfile-stripnondeterminism-perl all 1.12.0-2 [18.0 kB] Get:63 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el dh-strip-nondeterminism all 1.12.0-2 [5208 B] Get:64 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libdw1 ppc64el 0.185-2 [289 kB] Get:65 http://ftpmaster.internal/ubuntu jammy/main ppc64el debugedit ppc64el 1:5.0-0ubuntu2 [52.4 kB] Get:66 http://ftpmaster.internal/ubuntu jammy/main ppc64el dwz ppc64el 0.14-1build1 [125 kB] Get:67 http://ftpmaster.internal/ubuntu jammy/main ppc64el gettext ppc64el 0.21-4ubuntu3 [895 kB] Get:68 http://ftpmaster.internal/ubuntu jammy/main ppc64el intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:69 http://ftpmaster.internal/ubuntu jammy/main ppc64el po-debconf all 1.0.21+nmu1 [233 kB] Get:70 http://ftpmaster.internal/ubuntu jammy/main ppc64el debhelper all 13.3.4ubuntu2 [921 kB] Get:71 http://ftpmaster.internal/ubuntu jammy/main ppc64el python3-lib2to3 all 3.9.7-1 [77.9 kB] Get:72 http://ftpmaster.internal/ubuntu jammy/main ppc64el python3-distutils all 3.9.7-1 [144 kB] Get:73 http://ftpmaster.internal/ubuntu jammy-proposed/universe ppc64el dh-python all 5.20211021 [99.5 kB] Get:74 http://ftpmaster.internal/ubuntu jammy/universe ppc64el dialign ppc64el 2.2.1-11 [142 kB] Get:75 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libboost-iostreams1.74.0 ppc64el 1.74.0-8ubuntu8 [244 kB] Get:76 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libboost-program-options1.74.0 ppc64el 1.74.0-8ubuntu8 [315 kB] Get:77 http://ftpmaster.internal/ubuntu jammy/universe ppc64el libcifpp1 ppc64el 1.0.1-3 [1410 kB] Get:78 http://ftpmaster.internal/ubuntu jammy/universe ppc64el dssp ppc64el 4.0.0-2 [131 kB] Get:79 http://ftpmaster.internal/ubuntu jammy/main ppc64el libbrotli1 ppc64el 1.0.9-2build4 [372 kB] Get:80 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libfreetype6 ppc64el 2.11.0+dfsg-1 [523 kB] Get:81 http://ftpmaster.internal/ubuntu jammy/universe ppc64el ttf-bitstream-vera all 1.10-8.1 [223 kB] Get:82 http://ftpmaster.internal/ubuntu jammy/main ppc64el fonts-urw-base35 all 20200910-1 [6367 kB] Get:83 http://ftpmaster.internal/ubuntu jammy/main ppc64el fontconfig-config all 2.13.1-4.2ubuntu4 [29.1 kB] Get:84 http://ftpmaster.internal/ubuntu jammy/main ppc64el libfontconfig1 ppc64el 2.13.1-4.2ubuntu4 [183 kB] Get:85 http://ftpmaster.internal/ubuntu jammy/main ppc64el libjpeg-turbo8 ppc64el 2.0.6-0ubuntu3 [209 kB] Get:86 http://ftpmaster.internal/ubuntu jammy/main ppc64el libjpeg8 ppc64el 8c-2ubuntu8 [2146 B] Get:87 http://ftpmaster.internal/ubuntu jammy/main ppc64el libdeflate0 ppc64el 1.7-2ubuntu2 [49.7 kB] Get:88 http://ftpmaster.internal/ubuntu jammy/main ppc64el libjbig0 ppc64el 2.1-3.1build2 [33.4 kB] Get:89 http://ftpmaster.internal/ubuntu jammy/main ppc64el libwebp6 ppc64el 0.6.1-2.1build1 [301 kB] Get:90 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libtiff5 ppc64el 4.3.0-2 [251 kB] Get:91 http://ftpmaster.internal/ubuntu jammy/main ppc64el libxpm4 ppc64el 1:3.5.12-1build1 [47.4 kB] Get:92 http://ftpmaster.internal/ubuntu jammy/main ppc64el libgd3 ppc64el 2.3.0-2ubuntu1 [167 kB] Get:93 http://ftpmaster.internal/ubuntu jammy/universe ppc64el libhpdf-2.3.0 ppc64el 2.3.0+dfsg-1build1 [367 kB] Get:94 http://ftpmaster.internal/ubuntu jammy/main ppc64el mysql-common all 5.8+1.0.5ubuntu3 [7578 B] Get:95 http://ftpmaster.internal/ubuntu jammy/main ppc64el libmysqlclient21 ppc64el 8.0.26-0ubuntu1 [1331 kB] Get:96 http://ftpmaster.internal/ubuntu jammy/main ppc64el libsasl2-modules-db ppc64el 2.1.27+dfsg-2.1build1 [16.8 kB] Get:97 http://ftpmaster.internal/ubuntu jammy/main ppc64el libsasl2-2 ppc64el 2.1.27+dfsg-2.1build1 [57.3 kB] Get:98 http://ftpmaster.internal/ubuntu jammy/main ppc64el libldap-2.5-0 ppc64el 2.5.6+dfsg-1~exp1ubuntu1 [222 kB] Get:99 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libpq5 ppc64el 14.0-1 [238 kB] Get:100 http://ftpmaster.internal/ubuntu jammy/universe ppc64el emboss-lib ppc64el 6.6.0+dfsg-9ubuntu1 [3287 kB] Get:101 http://ftpmaster.internal/ubuntu jammy/universe ppc64el emboss-data all 6.6.0+dfsg-9ubuntu1 [61.0 MB] Get:102 http://ftpmaster.internal/ubuntu jammy/universe ppc64el emboss ppc64el 6.6.0+dfsg-9ubuntu1 [1023 kB] Get:103 http://ftpmaster.internal/ubuntu jammy/universe ppc64el fonts-lmodern all 2.004.5-6.1 [4532 kB] Get:104 http://ftpmaster.internal/ubuntu jammy/universe ppc64el fonts-lyx all 2.3.6-1 [159 kB] Get:105 http://ftpmaster.internal/ubuntu jammy/main ppc64el libgs9-common all 9.54.0~dfsg1-0ubuntu2 [747 kB] Get:106 http://ftpmaster.internal/ubuntu jammy/main ppc64el libavahi-common-data ppc64el 0.8-5ubuntu4 [24.2 kB] Get:107 http://ftpmaster.internal/ubuntu jammy/main ppc64el libavahi-common3 ppc64el 0.8-5ubuntu4 [25.7 kB] Get:108 http://ftpmaster.internal/ubuntu jammy/main ppc64el libavahi-client3 ppc64el 0.8-5ubuntu4 [31.5 kB] Get:109 http://ftpmaster.internal/ubuntu jammy/main ppc64el libcups2 ppc64el 2.3.3op2-7ubuntu2 [332 kB] Get:110 http://ftpmaster.internal/ubuntu jammy/main ppc64el libidn11 ppc64el 1.33-3build1 [64.8 kB] Get:111 http://ftpmaster.internal/ubuntu jammy/main ppc64el libijs-0.35 ppc64el 0.35-15build1 [17.8 kB] Get:112 http://ftpmaster.internal/ubuntu jammy/main ppc64el libjbig2dec0 ppc64el 0.19-3build1 [91.5 kB] Get:113 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libopenjp2-7 ppc64el 2.4.0-3 [215 kB] Get:114 http://ftpmaster.internal/ubuntu jammy/main ppc64el libpaper1 ppc64el 1.1.28build1 [13.9 kB] Get:115 http://ftpmaster.internal/ubuntu jammy/main ppc64el libgs9 ppc64el 9.54.0~dfsg1-0ubuntu2 [5983 kB] Get:116 http://ftpmaster.internal/ubuntu jammy/main ppc64el ghostscript ppc64el 9.54.0~dfsg1-0ubuntu2 [50.0 kB] Get:117 http://ftpmaster.internal/ubuntu jammy/universe ppc64el libnetpbm10 ppc64el 2:10.0-15.4 [67.4 kB] Get:118 http://ftpmaster.internal/ubuntu jammy/universe ppc64el netpbm ppc64el 2:10.0-15.4 [1108 kB] Get:119 http://ftpmaster.internal/ubuntu jammy/main ppc64el libpaper-utils ppc64el 1.1.28build1 [8712 B] Get:120 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libkpathsea6 ppc64el 2021.20210626.59705-1 [67.9 kB] Get:121 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libptexenc1 ppc64el 2021.20210626.59705-1 [40.7 kB] Get:122 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libsynctex2 ppc64el 2021.20210626.59705-1 [63.6 kB] Get:123 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libtexlua53 ppc64el 2021.20210626.59705-1 [161 kB] Get:124 http://ftpmaster.internal/ubuntu jammy/main ppc64el t1utils ppc64el 1.41-4build1 [69.1 kB] Get:125 http://ftpmaster.internal/ubuntu jammy/main ppc64el libpixman-1-0 ppc64el 0.40.0-1build3 [305 kB] Get:126 http://ftpmaster.internal/ubuntu jammy/main ppc64el libxcb-render0 ppc64el 1.14-3ubuntu2 [17.2 kB] Get:127 http://ftpmaster.internal/ubuntu jammy/main ppc64el libxcb-shm0 ppc64el 1.14-3ubuntu2 [6002 B] Get:128 http://ftpmaster.internal/ubuntu jammy/main ppc64el libxrender1 ppc64el 1:0.9.10-1build3 [23.2 kB] Get:129 http://ftpmaster.internal/ubuntu jammy/main ppc64el libcairo2 ppc64el 1.16.0-5ubuntu2 [787 kB] Get:130 http://ftpmaster.internal/ubuntu jammy/main ppc64el libgraphite2-3 ppc64el 1.3.14-1build1 [85.5 kB] Get:131 http://ftpmaster.internal/ubuntu jammy/main ppc64el libharfbuzz0b ppc64el 2.7.4-1ubuntu2 [448 kB] Get:132 http://ftpmaster.internal/ubuntu jammy/universe ppc64el libteckit0 ppc64el 2.5.10+ds1-3 [306 kB] Get:133 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el x11-common all 1:7.7+23ubuntu1 [23.5 kB] Get:134 http://ftpmaster.internal/ubuntu jammy/main ppc64el libice6 ppc64el 2:1.0.10-1build1 [50.1 kB] Get:135 http://ftpmaster.internal/ubuntu jammy/main ppc64el libsm6 ppc64el 2:1.2.3-1build1 [18.6 kB] Get:136 http://ftpmaster.internal/ubuntu jammy/main ppc64el libxt6 ppc64el 1:1.2.0-1build1 [203 kB] Get:137 http://ftpmaster.internal/ubuntu jammy/main ppc64el libxmu6 ppc64el 2:1.1.3-0ubuntu2 [57.8 kB] Get:138 http://ftpmaster.internal/ubuntu jammy/main ppc64el libxaw7 ppc64el 2:1.0.13-1.1build1 [227 kB] Get:139 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libxi6 ppc64el 2:1.8-1 [38.4 kB] Get:140 http://ftpmaster.internal/ubuntu jammy/universe ppc64el libzzip-0-13 ppc64el 0.13.72+dfsg.1-1.1 [29.7 kB] Get:141 http://ftpmaster.internal/ubuntu jammy-proposed/universe ppc64el texlive-binaries ppc64el 2021.20210626.59705-1 [12.5 MB] Get:142 http://ftpmaster.internal/ubuntu jammy/main ppc64el xdg-utils all 1.1.3-2ubuntu2 [61.5 kB] Get:143 http://ftpmaster.internal/ubuntu jammy-proposed/universe ppc64el texlive-base all 2021.20210921-1 [20.9 MB] Get:144 http://ftpmaster.internal/ubuntu jammy-proposed/universe ppc64el hevea ppc64el 2.35-1 [2104 kB] Get:145 http://ftpmaster.internal/ubuntu jammy/universe ppc64el libapache-pom-java all 18-1 [4720 B] Get:146 http://ftpmaster.internal/ubuntu jammy/main ppc64el libblas3 ppc64el 3.9.0-3ubuntu3 [149 kB] Get:147 http://ftpmaster.internal/ubuntu jammy/universe ppc64el libcommons-parent-java all 43-1 [10.8 kB] Get:148 http://ftpmaster.internal/ubuntu jammy/universe ppc64el libcommons-logging-java all 1.2-2 [60.3 kB] Get:149 http://ftpmaster.internal/ubuntu jammy/main ppc64el libnghttp2-14 ppc64el 1.43.0-1build1 [89.0 kB] Get:150 http://ftpmaster.internal/ubuntu jammy/main ppc64el librtmp1 ppc64el 2.4+20151223.gitfa8646d.1-2build3 [65.8 kB] Get:151 http://ftpmaster.internal/ubuntu jammy/main ppc64el libssh-4 ppc64el 0.9.6-1 [237 kB] Get:152 http://ftpmaster.internal/ubuntu jammy/main ppc64el libcurl3-gnutls ppc64el 7.74.0-1.3ubuntu2 [347 kB] Get:153 http://ftpmaster.internal/ubuntu jammy/main ppc64el libexpat1-dev ppc64el 2.4.1-2 [155 kB] Get:154 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libgfortran5 ppc64el 11.2.0-10ubuntu1 [507 kB] Get:155 http://ftpmaster.internal/ubuntu jammy-proposed/universe ppc64el libhtscodecs2 ppc64el 1.1.1-3 [80.0 kB] Get:156 http://ftpmaster.internal/ubuntu jammy/universe ppc64el libhts3 ppc64el 1.13+ds-2 [507 kB] Get:157 http://ftpmaster.internal/ubuntu jammy/main ppc64el libimagequant0 ppc64el 2.12.2-1.1build1 [38.2 kB] Get:158 http://ftpmaster.internal/ubuntu jammy/main ppc64el libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [314 kB] Get:159 http://ftpmaster.internal/ubuntu jammy/universe ppc64el libjs-jquery-ui all 1.12.1+dfsg-8 [231 kB] Get:160 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libjs-underscore all 1.9.1~dfsg-4 [103 kB] Get:161 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libjs-sphinxdoc all 4.2.0-4build1 [137 kB] Get:162 http://ftpmaster.internal/ubuntu jammy/main ppc64el liblapack3 ppc64el 3.9.0-3ubuntu3 [2028 kB] Get:163 http://ftpmaster.internal/ubuntu jammy/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.3-9 [29.3 kB] Get:164 http://ftpmaster.internal/ubuntu jammy/main ppc64el liblcms2-2 ppc64el 2.12~rc1-2build1 [224 kB] Get:165 http://ftpmaster.internal/ubuntu jammy/universe ppc64el libmbedcrypto3 ppc64el 2.16.9-0.1ubuntu1 [183 kB] Get:166 http://ftpmaster.internal/ubuntu jammy/universe ppc64el libmbedx509-0 ppc64el 2.16.9-0.1ubuntu1 [44.5 kB] Get:167 http://ftpmaster.internal/ubuntu jammy/universe ppc64el libmbedtls12 ppc64el 2.16.9-0.1ubuntu1 [74.2 kB] Get:168 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libpython3.9 ppc64el 3.9.7-4 [2102 kB] Get:169 http://ftpmaster.internal/ubuntu jammy/main ppc64el zlib1g-dev ppc64el 1:1.2.11.dfsg-2ubuntu7 [177 kB] Get:170 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libpython3.9-dev ppc64el 3.9.7-4 [4926 kB] Get:171 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libpython3-dev ppc64el 3.9.4-1ubuntu2 [7446 B] Get:172 http://ftpmaster.internal/ubuntu jammy/main ppc64el libpython3.10-stdlib ppc64el 3.10.0-3 [1814 kB] Get:173 http://ftpmaster.internal/ubuntu jammy/main ppc64el libpython3.10 ppc64el 3.10.0-3 [2157 kB] Get:174 http://ftpmaster.internal/ubuntu jammy/main ppc64el libpython3.10-dev ppc64el 3.10.0-3 [4994 kB] Get:175 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libpython3-all-dev ppc64el 3.9.4-1ubuntu2 [928 B] Get:176 http://ftpmaster.internal/ubuntu jammy/universe ppc64el libraqm0 ppc64el 0.7.0-4 [12.7 kB] Get:177 http://ftpmaster.internal/ubuntu jammy/main ppc64el libwebpdemux2 ppc64el 0.6.1-2.1build1 [11.5 kB] Get:178 http://ftpmaster.internal/ubuntu jammy/main ppc64el libwebpmux3 ppc64el 0.6.1-2.1build1 [25.5 kB] Get:179 http://ftpmaster.internal/ubuntu jammy-proposed/universe ppc64el mafft ppc64el 7.487-1 [974 kB] Get:180 http://ftpmaster.internal/ubuntu jammy/universe ppc64el muscle ppc64el 1:3.8.1551-2build1 [275 kB] Get:181 http://ftpmaster.internal/ubuntu jammy/universe ppc64el ncbi-data all 6.1.20170106+dfsg1-9 [3519 kB] Get:182 http://ftpmaster.internal/ubuntu jammy-proposed/universe ppc64el ncbi-blast+ ppc64el 2.11.0+ds-1 [12.0 MB] Get:183 http://ftpmaster.internal/ubuntu jammy/universe ppc64el phylip ppc64el 1:3.697+dfsg-2 [888 kB] Get:184 http://ftpmaster.internal/ubuntu jammy/universe ppc64el prank ppc64el 0.0.170427+dfsg-3 [353 kB] Get:185 http://ftpmaster.internal/ubuntu jammy/universe ppc64el preview-latex-style all 12.2-1ubuntu1 [185 kB] Get:186 http://ftpmaster.internal/ubuntu jammy-proposed/universe ppc64el probcons ppc64el 1.12-14 [174 kB] Get:187 http://ftpmaster.internal/ubuntu jammy-proposed/universe ppc64el python-matplotlib-data all 3.3.4-2 [4036 kB] Get:188 http://ftpmaster.internal/ubuntu jammy/main ppc64el python3.10 ppc64el 3.10.0-3 [473 kB] Get:189 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el python3-all ppc64el 3.9.4-1ubuntu2 [920 B] Get:190 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el python3.9-dev ppc64el 3.9.7-4 [507 kB] Get:191 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el python3-dev ppc64el 3.9.4-1ubuntu2 [25.5 kB] Get:192 http://ftpmaster.internal/ubuntu jammy/main ppc64el python3.10-dev ppc64el 3.10.0-3 [509 kB] Get:193 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el python3-all-dev ppc64el 3.9.4-1ubuntu2 [928 B] Get:194 http://ftpmaster.internal/ubuntu jammy/main ppc64el python3-six all 1.16.0-2 [12.6 kB] Get:195 http://ftpmaster.internal/ubuntu jammy/universe ppc64el python3-cycler all 0.10.0-3 [8132 B] Get:196 http://ftpmaster.internal/ubuntu jammy/main ppc64el python3-dateutil all 2.8.1-6 [78.4 kB] Get:197 http://ftpmaster.internal/ubuntu jammy/main ppc64el python3-decorator all 4.4.2-0ubuntu1 [10.3 kB] Get:198 http://ftpmaster.internal/ubuntu jammy/universe ppc64el python3-isodate all 0.6.0-2 [24.0 kB] Get:199 http://ftpmaster.internal/ubuntu jammy-proposed/universe ppc64el python3-kiwisolver ppc64el 1.3.2-1 [67.8 kB] Get:200 http://ftpmaster.internal/ubuntu jammy/main ppc64el python3-linecache2 all 1.0.0-4ubuntu2 [13.3 kB] Get:201 http://ftpmaster.internal/ubuntu jammy/main ppc64el python3-pyparsing all 2.4.7-1 [61.4 kB] Get:202 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el python3-numpy ppc64el 1:1.20.2-1ubuntu1 [11.5 MB] Get:203 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el python3-pil ppc64el 8.3.2-1 [466 kB] Get:204 http://ftpmaster.internal/ubuntu jammy-proposed/universe ppc64el python3-matplotlib ppc64el 3.3.4-2 [6751 kB] Get:205 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el python3-msgpack ppc64el 1.0.2-2 [87.5 kB] Get:206 http://ftpmaster.internal/ubuntu jammy/universe ppc64el python3-mmtf all 1.1.2-3 [15.9 kB] Get:207 http://ftpmaster.internal/ubuntu jammy/main ppc64el python3-mysqldb ppc64el 1.4.4-2build5 [50.4 kB] Get:208 http://ftpmaster.internal/ubuntu jammy/main ppc64el python3-networkx all 2.4-4ubuntu1 [855 kB] Get:209 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el python3-psycopg2 ppc64el 2.9.1-1 [160 kB] Get:210 http://ftpmaster.internal/ubuntu jammy/main ppc64el python3-pygments all 2.7.1+dfsg-2.1 [639 kB] Get:211 http://ftpmaster.internal/ubuntu jammy/universe ppc64el python3-rdflib all 5.0.0-1.1build1 [174 kB] Get:212 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el python3-renderpm ppc64el 3.6.1-1 [75.5 kB] Get:213 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el python3-reportlab-accel ppc64el 3.6.1-1 [23.2 kB] Get:214 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el python3-reportlab all 3.6.1-1 [560 kB] Get:215 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el python3-setuptools all 58.2.0-1 [336 kB] Get:216 http://ftpmaster.internal/ubuntu jammy/main ppc64el python3-traceback2 all 1.4.0-6 [16.6 kB] Get:217 http://ftpmaster.internal/ubuntu jammy/main ppc64el python3-unittest2 all 1.1.0-7 [75.5 kB] Get:218 http://ftpmaster.internal/ubuntu jammy/universe ppc64el samtools ppc64el 1.13-2 [588 kB] Get:219 http://ftpmaster.internal/ubuntu jammy/universe ppc64el t-coffee ppc64el 13.41.0.28bdc39+dfsg-4 [1038 kB] Get:220 http://ftpmaster.internal/ubuntu jammy-proposed/universe ppc64el texlive-fonts-recommended all 2021.20210921-1 [4972 kB] Get:221 http://ftpmaster.internal/ubuntu jammy-proposed/universe ppc64el texlive-latex-base all 2021.20210921-1 [1119 kB] Get:222 http://ftpmaster.internal/ubuntu jammy/universe ppc64el libfontbox-java all 1:1.8.16-2 [207 kB] Get:223 http://ftpmaster.internal/ubuntu jammy/universe ppc64el libpdfbox-java all 1:1.8.16-2 [5199 kB] Get:224 http://ftpmaster.internal/ubuntu jammy-proposed/universe ppc64el texlive-latex-recommended all 2021.20210921-1 [14.4 MB] Get:225 http://ftpmaster.internal/ubuntu jammy-proposed/universe ppc64el texlive-pictures all 2021.20210921-1 [8679 kB] Get:226 http://ftpmaster.internal/ubuntu jammy-proposed/universe ppc64el texlive-latex-extra all 2021.20210921-1 [14.1 MB] Get:227 http://ftpmaster.internal/ubuntu jammy/universe ppc64el wise-data all 2.4.1-23 [76.8 kB] Get:228 http://ftpmaster.internal/ubuntu jammy/universe ppc64el wise ppc64el 2.4.1-23 [1340 kB] Get:229 http://ftpmaster.internal/ubuntu jammy/universe ppc64el fasttree ppc64el 2.1.11-2 [218 kB] Get:230 http://ftpmaster.internal/ubuntu jammy/universe ppc64el python3-scipy ppc64el 1.6.0-2 [13.3 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 298 MB in 18s (16.1 MB/s) Selecting previously unselected package libpython3.9-minimal:ppc64el. (Reading database ... 13187 files and directories currently installed.) Preparing to unpack .../libpython3.9-minimal_3.9.7-4_ppc64el.deb ... Unpacking libpython3.9-minimal:ppc64el (3.9.7-4) ... Selecting previously unselected package libexpat1:ppc64el. Preparing to unpack .../libexpat1_2.4.1-2_ppc64el.deb ... Unpacking libexpat1:ppc64el (2.4.1-2) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../python3.9-minimal_3.9.7-4_ppc64el.deb ... Unpacking python3.9-minimal (3.9.7-4) ... Setting up libpython3.9-minimal:ppc64el (3.9.7-4) ... Setting up libexpat1:ppc64el (2.4.1-2) ... Setting up python3.9-minimal (3.9.7-4) ... Selecting previously unselected package python3-minimal. (Reading database ... 13480 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.4-1ubuntu2_ppc64el.deb ... Unpacking python3-minimal (3.9.4-1ubuntu2) ... Selecting previously unselected package media-types. 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Setting up libxau6:ppc64el (1:1.0.9-1build4) ... Setting up libhpdf-2.3.0:ppc64el (2.3.0+dfsg-1build1) ... Setting up libpsl5:ppc64el (0.21.0-1.2build1) ... Setting up ttf-bitstream-vera (1.10-8.1) ... Setting up bsdextrautils (2.36.1-8ubuntu2) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up probcons (1.12-14) ... Setting up libicu67:ppc64el (67.1-7ubuntu1) ... Setting up libmagic-mgc (1:5.39-3build1) ... Setting up libtexlua53:ppc64el (2021.20210626.59705-1) ... Setting up mafft (7.487-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:ppc64el (2.68.4-1ubuntu1) ... No schema files found: doing nothing. Setting up bwa (0.7.17-6) ... Setting up libboost-iostreams1.74.0:ppc64el (1.74.0-8ubuntu8) ... Setting up libboost-program-options1.74.0:ppc64el (1.74.0-8ubuntu8) ... Setting up fonts-lyx (2.3.6-1) ... Setting up libijs-0.35:ppc64el (0.35-15build1) ... Setting up libdebhelper-perl (13.3.4ubuntu2) ... Setting up libbrotli1:ppc64el (1.0.9-2build4) ... Setting up libfontbox-java (1:1.8.16-2) ... Setting up phylip (1:3.697+dfsg-2) ... Setting up x11-common (1:7.7+23ubuntu1) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libnghttp2-14:ppc64el (1.43.0-1build1) ... Setting up libmagic1:ppc64el (1:5.39-3build1) ... Setting up libdeflate0:ppc64el (1.7-2ubuntu2) ... Setting up gettext-base (0.21-4ubuntu3) ... Setting up libzzip-0-13:ppc64el (0.13.72+dfsg.1-1.1) ... Setting up file (1:5.39-3build1) ... Setting up libnetpbm10 (2:10.0-15.4) ... Setting up fonts-urw-base35 (20200910-1) ... Setting up muscle (1:3.8.1551-2build1) ... Setting up emboss-data (6.6.0+dfsg-9ubuntu1) ... Setting up libjbig0:ppc64el (2.1-3.1build2) ... Setting up t-coffee (13.41.0.28bdc39+dfsg-4) ... Setting up poppler-data (0.4.11-1) ... Setting up libsasl2-modules-db:ppc64el (2.1.27+dfsg-2.1build1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libblas3:ppc64el (3.9.0-3ubuntu3) ... update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode Setting up libexpat1-dev:ppc64el (2.4.1-2) ... Setting up libfreetype6:ppc64el (2.11.0+dfsg-1) ... Setting up libx11-data (2:1.7.2-2) ... Setting up libjbig2dec0:ppc64el (0.19-3build1) ... Setting up librtmp1:ppc64el (2.4+20151223.gitfa8646d.1-2build3) ... Setting up libidn11:ppc64el (1.33-3build1) ... Setting up libteckit0:ppc64el (2.5.10+ds1-3) ... Setting up libapache-pom-java (18-1) ... Setting up libavahi-common-data:ppc64el (0.8-5ubuntu4) ... Setting up libdbus-1-3:ppc64el (1.12.20-2ubuntu2) ... Setting up libsigsegv2:ppc64el (2.13-1ubuntu2) ... Setting up libfribidi0:ppc64el (1.0.8-2ubuntu2) ... Setting up t1utils (1.41-4build1) ... Setting up libimagequant0:ppc64el (2.12.2-1.1build1) ... Setting up libpython3.10-minimal:ppc64el (3.10.0-3) ... Setting up autopoint (0.21-4ubuntu3) ... Setting up libwebp6:ppc64el (0.6.1-2.1build1) ... Setting up ucf (3.0043) ... Setting up wise-data (2.4.1-23) ... Setting up libjpeg-turbo8:ppc64el (2.0.6-0ubuntu3) ... Setting up libkpathsea6:ppc64el (2021.20210626.59705-1) ... Setting up libsasl2-2:ppc64el (2.1.27+dfsg-2.1build1) ... Setting up libssh-4:ppc64el (0.9.6-1) ... Setting up libgfortran5:ppc64el (11.2.0-10ubuntu1) ... Setting up zlib1g-dev:ppc64el (1:1.2.11.dfsg-2ubuntu7) ... Setting up libcifpp1 (1.0.1-3) ... Setting up libmd0:ppc64el (1.0.4-1) ... Setting up libuchardet0:ppc64el (0.0.7-1build1) ... Setting up libmpdec3:ppc64el (2.5.1-2build1) ... Setting up clustalw (2.1+lgpl-7) ... Setting up fonts-lmodern (2.004.5-6.1) ... Setting up libmbedcrypto3:ppc64el (2.16.9-0.1ubuntu1) ... Setting up libopenjp2-7:ppc64el (2.4.0-3) ... Setting up libsub-override-perl (0.09-2) ... Setting up libharfbuzz0b:ppc64el (2.7.4-1ubuntu2) ... Setting up fasttree (2.1.11-2) ... Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-7) ... Setting up python-matplotlib-data (3.3.4-2) ... Setting up libwebpmux3:ppc64el (0.6.1-2.1build1) ... Setting up libbsd0:ppc64el (0.11.3-1ubuntu3) ... Setting up mailcap (3.70ubuntu1) ... Setting up libelf1:ppc64el (0.185-2) ... Setting up dialign (2.2.1-11) ... Setting up libxml2:ppc64el (2.9.12+dfsg-5) ... Setting up xdg-utils (1.1.3-2ubuntu2) ... Setting up libsynctex2:ppc64el (2021.20210626.59705-1) ... Setting up libpython3.9-stdlib:ppc64el (3.9.7-4) ... Setting up libpython3-stdlib:ppc64el (3.9.4-1ubuntu2) ... Setting up prank (0.0.170427+dfsg-3) ... Setting up libargtable2-0 (13-1.1) ... Setting up libjs-underscore (1.9.1~dfsg-4) ... Setting up libjpeg8:ppc64el (8c-2ubuntu8) ... Setting up libgs9-common (9.54.0~dfsg1-0ubuntu2) ... Setting up libfile-stripnondeterminism-perl (1.12.0-2) ... Setting up libpaper1:ppc64el (1.1.28build1) ... Creating config file /etc/papersize with new version Setting up libice6:ppc64el (2:1.0.10-1build1) ... Setting up libdw1:ppc64el (0.185-2) ... Setting up libxdmcp6:ppc64el (1:1.1.3-0ubuntu4) ... Setting up liblapack3:ppc64el (3.9.0-3ubuntu3) ... update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode Setting up libxcb1:ppc64el (1.14-3ubuntu2) ... Setting up gettext (0.21-4ubuntu3) ... Setting up libpdfbox-java (1:1.8.16-2) ... Setting up mime-support (3.66) ... Setting up libtool (2.4.6-15build1) ... Setting up libxcb-render0:ppc64el (1.14-3ubuntu2) ... Setting up libmbedx509-0:ppc64el (2.16.9-0.1ubuntu1) ... Setting up fontconfig-config (2.13.1-4.2ubuntu4) ... Setting up wise (2.4.1-23) ... Setting up libwebpdemux2:ppc64el (0.6.1-2.1build1) ... Setting up libedit2:ppc64el (3.1-20210910-1) ... Setting up libcommons-parent-java (43-1) ... Setting up libmbedtls12:ppc64el (2.16.9-0.1ubuntu1) ... Setting up libavahi-common3:ppc64el (0.8-5ubuntu4) ... Setting up libcommons-logging-java (1.2-2) ... Setting up m4 (1.4.18-5ubuntu1) ... Setting up libxcb-shm0:ppc64el (1.14-3ubuntu2) ... Setting up libpaper-utils (1.1.28build1) ... Setting up clustalo (1.2.4-7) ... Setting up dssp (4.0.0-2) ... Setting up python3.10-minimal (3.10.0-3) ... Setting up libldap-2.5-0:ppc64el (2.5.6+dfsg-1~exp1ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libpython3.10-stdlib:ppc64el (3.10.0-3) ... Setting up tex-common (6.17) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libpython3.9:ppc64el (3.9.7-4) ... Setting up libjs-jquery-ui (1.12.1+dfsg-8) ... Setting up libptexenc1:ppc64el (2021.20210626.59705-1) ... Setting up libraqm0:ppc64el (0.7.0-4) ... Setting up libjs-sphinxdoc (4.2.0-4build1) ... Setting up autoconf (2.71-2) ... Setting up dh-strip-nondeterminism (1.12.0-2) ... Setting up dwz (0.14-1build1) ... Setting up groff-base (1.22.4-7) ... Setting up debugedit (1:5.0-0ubuntu2) ... Setting up libx11-6:ppc64el (2:1.7.2-2) ... Setting up libtiff5:ppc64el (4.3.0-2) ... Setting up libfontconfig1:ppc64el (2.13.1-4.2ubuntu4) ... Setting up libsm6:ppc64el (2:1.2.3-1build1) ... Setting up libavahi-client3:ppc64el (0.8-5ubuntu4) ... Setting up python3.9 (3.9.7-4) ... Setting up liblbfgsb0:ppc64el (3.0+dfsg.3-9) ... Setting up automake (1:1.16.4-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libpython3.10:ppc64el (3.10.0-3) ... Setting up flex (2.6.4-8build1) ... Setting up python3.10 (3.10.0-3) ... Setting up libxpm4:ppc64el (1:3.5.12-1build1) ... Setting up libxrender1:ppc64el (1:0.9.10-1build3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up preview-latex-style (12.2-1ubuntu1) ... Setting up libpq5:ppc64el (14.0-1) ... Setting up libxext6:ppc64el (2:1.3.4-0ubuntu4) ... Setting up libpython3.9-dev:ppc64el (3.9.7-4) ... Setting up libcurl3-gnutls:ppc64el (7.74.0-1.3ubuntu2) ... Setting up python3 (3.9.4-1ubuntu2) ... Setting up man-db (2.9.4-2build1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up libcairo2:ppc64el (1.16.0-5ubuntu2) ... Setting up ncbi-blast+ (2.11.0+ds-1) ... Setting up python3-mysqldb (1.4.4-2build5) ... Setting up python3-six (1.16.0-2) ... Setting up dh-autoreconf (20) ... Setting up python3-isodate (0.6.0-2) ... Setting up python3-pil:ppc64el (8.3.2-1) ... Setting up python3-decorator (4.4.2-0ubuntu1) ... Setting up python3-pyparsing (2.4.7-1) ... Setting up python3-linecache2 (1.0.0-4ubuntu2) ... Setting up python3-cycler (0.10.0-3) ... Setting up python3-reportlab-accel:ppc64el (3.6.1-1) ... Setting up libgd3:ppc64el (2.3.0-2ubuntu1) ... Setting up python3-kiwisolver (1.3.2-1) ... Setting up python3-psycopg2 (2.9.1-1) ... Setting up libpython3.10-dev:ppc64el (3.10.0-3) ... Setting up netpbm (2:10.0-15.4) ... Setting up libxt6:ppc64el (1:1.2.0-1build1) ... Setting up python3-reportlab (3.6.1-1) ... Setting up libcups2:ppc64el (2.3.3op2-7ubuntu2) ... Setting up python3.10-dev (3.10.0-3) ... Setting up python3.9-dev (3.9.7-4) ... Setting up python3-rdflib (5.0.0-1.1build1) ... Setting up python3-dateutil (2.8.1-6) ... Setting up emboss-lib (6.6.0+dfsg-9ubuntu1) ... Setting up python3-msgpack (1.0.2-2) ... Setting up python3-lib2to3 (3.9.7-1) ... Setting up python3-pkg-resources (58.2.0-1) ... Setting up python3-distutils (3.9.7-1) ... Setting up dh-python (5.20211021) ... Setting up libhts3:ppc64el (1.13+ds-2) ... Setting up libxmu6:ppc64el (2:1.1.3-0ubuntu2) ... Setting up libpython3-dev:ppc64el (3.9.4-1ubuntu2) ... Setting up python3-renderpm:ppc64el (3.6.1-1) ... Setting up emboss (6.6.0+dfsg-9ubuntu1) ... Setting up python3-setuptools (58.2.0-1) ... Setting up libgs9:ppc64el (9.54.0~dfsg1-0ubuntu2) ... Setting up libxi6:ppc64el (2:1.8-1) ... Setting up python3-traceback2 (1.4.0-6) ... Setting up python3-all (3.9.4-1ubuntu2) ... Setting up debhelper (13.3.4ubuntu2) ... Setting up libxaw7:ppc64el (2:1.0.13-1.1build1) ... Setting up ghostscript (9.54.0~dfsg1-0ubuntu2) ... Setting up python3-networkx (2.4-4ubuntu1) ... /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_graphml.py:933: SyntaxWarning: "is" with a literal. Did you mean "=="? assert H.nodes['n1']['special'] is 0 /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_graphml.py:935: SyntaxWarning: "is" with a literal. Did you mean "=="? assert H.edges['n0','n1',1]['special'] is 0 /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_graphml.py:933: SyntaxWarning: "is" with a literal. Did you mean "=="? assert H.nodes['n1']['special'] is 0 /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_graphml.py:935: SyntaxWarning: "is" with a literal. Did you mean "=="? assert H.edges['n0','n1',1]['special'] is 0 Setting up samtools (1.13-2) ... Setting up python3-pygments (2.7.1+dfsg-2.1) ... Setting up libpython3-all-dev:ppc64el (3.9.4-1ubuntu2) ... Setting up python3-dev (3.9.4-1ubuntu2) ... Setting up python3-unittest2 (1.1.0-7) ... update-alternatives: using /usr/bin/python3-unit2 to provide /usr/bin/unit2 (unit2) in auto mode Setting up python3-numpy (1:1.20.2-1ubuntu1) ... Setting up texlive-binaries (2021.20210626.59705-1) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up texlive-base (2021.20210921-1) ... /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up python3-all-dev (3.9.4-1ubuntu2) ... Setting up python3-matplotlib (3.3.4-2) ... Setting up python3-scipy (1.6.0-2) ... Setting up python3-mmtf (1.1.2-3) ... Setting up texlive-latex-base (2021.20210921-1) ... Setting up texlive-latex-recommended (2021.20210921-1) ... Setting up hevea (2.35-1) ... Setting up texlive-pictures (2021.20210921-1) ... Setting up texlive-fonts-recommended (2021.20210921-1) ... Setting up texlive-latex-extra (2021.20210921-1) ... Setting up sbuild-build-depends-python-biopython-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.34-0ubuntu3) ... Processing triggers for tex-common (6.17) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. 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pkgbinarymangler_148 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3 poppler-data_0.4.11-1 prank_0.0.170427+dfsg-3 preview-latex-style_12.2-1ubuntu1 probcons_1.12-14 procps_2:3.3.17-5ubuntu3 python-matplotlib-data_3.3.4-2 python3_3.9.4-1ubuntu2 python3-all_3.9.4-1ubuntu2 python3-all-dev_3.9.4-1ubuntu2 python3-cycler_0.10.0-3 python3-dateutil_2.8.1-6 python3-decorator_4.4.2-0ubuntu1 python3-dev_3.9.4-1ubuntu2 python3-distutils_3.9.7-1 python3-isodate_0.6.0-2 python3-kiwisolver_1.3.2-1 python3-lib2to3_3.9.7-1 python3-linecache2_1.0.0-4ubuntu2 python3-matplotlib_3.3.4-2 python3-minimal_3.9.4-1ubuntu2 python3-mmtf_1.1.2-3 python3-msgpack_1.0.2-2 python3-mysqldb_1.4.4-2build5 python3-networkx_2.4-4ubuntu1 python3-numpy_1:1.20.2-1ubuntu1 python3-pil_8.3.2-1 python3-pkg-resources_58.2.0-1 python3-psycopg2_2.9.1-1 python3-pygments_2.7.1+dfsg-2.1 python3-pyparsing_2.4.7-1 python3-rdflib_5.0.0-1.1build1 python3-renderpm_3.6.1-1 python3-reportlab_3.6.1-1 python3-reportlab-accel_3.6.1-1 python3-scipy_1.6.0-2 python3-setuptools_58.2.0-1 python3-six_1.16.0-2 python3-traceback2_1.4.0-6 python3-unittest2_1.1.0-7 python3.10_3.10.0-3 python3.10-dev_3.10.0-3 python3.10-minimal_3.10.0-3 python3.9_3.9.7-4 python3.9-dev_3.9.7-4 python3.9-minimal_3.9.7-4 readline-common_8.1-2build1 rpcsvc-proto_1.4.2-0ubuntu5 samtools_1.13-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-python-biopython-dummy_0.invalid.0 sed_4.7-1ubuntu2 sensible-utils_0.0.17 systemd_248.3-1ubuntu8 systemd-sysv_248.3-1ubuntu8 systemd-timesyncd_248.3-1ubuntu8 sysvinit-utils_2.96-7ubuntu2 t-coffee_13.41.0.28bdc39+dfsg-4 t1utils_1.41-4build1 tar_1.34+dfsg-1build2 tex-common_6.17 texlive-base_2021.20210921-1 texlive-binaries_2021.20210626.59705-1 texlive-fonts-recommended_2021.20210921-1 texlive-latex-base_2021.20210921-1 texlive-latex-extra_2021.20210921-1 texlive-latex-recommended_2021.20210921-1 texlive-pictures_2021.20210921-1 ttf-bitstream-vera_1.10-8.1 tzdata_2021a-2ubuntu1 ubuntu-keyring_2021.03.26 ucf_3.0043 usrmerge_25ubuntu1 util-linux_2.36.1-8ubuntu2 wise_2.4.1-23 wise-data_2.4.1-23 x11-common_1:7.7+23ubuntu1 xdg-utils_1.1.3-2ubuntu2 xz-utils_5.2.5-2build1 zlib1g_1:1.2.11.dfsg-2ubuntu7 zlib1g-dev_1:1.2.11.dfsg-2ubuntu7 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Sun Oct 17 22:23:14 2021 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_1.78+dfsg-5ubuntu2.dsc dpkg-source: info: extracting python-biopython in /<>/python-biopython-1.78+dfsg dpkg-source: info: unpacking python-biopython_1.78+dfsg.orig.tar.xz dpkg-source: info: unpacking python-biopython_1.78+dfsg-5ubuntu2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying remove_mathml-qname.patch dpkg-source: info: applying privacy_breach.patch dpkg-source: info: applying privacy_breach_ie9.patch dpkg-source: info: applying blastdbv4-impl.patch dpkg-source: info: applying fix-use-of-unversioned-python.patch dpkg-source: info: applying stabilize-phyml-test.patch dpkg-source: info: applying spelling-error-in-binaries.patch dpkg-source: info: applying reproduciblebuild.patch dpkg-source: info: applying mkdssp4.path Check disk 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-22291105 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-22291105 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-22291105 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 1.78+dfsg-5ubuntu2 dpkg-buildpackage: info: source distribution jammy dpkg-source --before-build . dpkg-buildpackage: info: host architecture ppc64el debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/python-biopython-1.78+dfsg' dh_auto_clean install -d /<>/python-biopython-1.78\+dfsg/debian/.debhelper/generated/_source/home pybuild --clean -i python{version} -p "3.10 3.9" I: pybuild base:232: python3.10 setup.py clean /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'build-lib' will not be supported in future versions. Please use the underscore name 'build_lib' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-layout' will not be supported in future versions. Please use the underscore name 'install_layout' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-scripts' will not be supported in future versions. Please use the underscore name 'install_scripts' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-lib' will not be supported in future versions. Please use the underscore name 'install_lib' instead warnings.warn( running clean removing '/<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build' (and everything under it) 'build/bdist.linux-ppc64el' does not exist -- can't clean it 'build/scripts-3.10' does not exist -- can't clean it I: pybuild base:232: python3.9 setup.py clean /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'build-lib' will not be supported in future versions. Please use the underscore name 'build_lib' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-layout' will not be supported in future versions. Please use the underscore name 'install_layout' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-scripts' will not be supported in future versions. Please use the underscore name 'install_scripts' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-lib' will not be supported in future versions. Please use the underscore name 'install_lib' instead warnings.warn( running clean removing '/<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build' (and everything under it) 'build/bdist.linux-ppc64el' does not exist -- can't clean it 'build/scripts-3.9' 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-1.78+dfsg/Doc' ( for f in ; do make clean -C $f ; done ) rm -f Tutorial.aux rm -f Tutorial.toc rm -f Tutorial.log rm -f Tutorial.out rm -f Tutorial.haux rm -f Tutorial.htoc rm -f biopdb_faq.aux rm -f biopdb_faq.log rm -f biopdb_faq.out rm -f Tutorial/*.aux ( for f in ; do make distclean -C $f ; done ) rm -f version.sh rm -f biopdb_faq.pdf rm -f Tutorial.pdf rm -f Tutorial.html rm -f Tutorial.txt rm -f *_motif.gif #output from hacha make[2]: Leaving directory '/<>/python-biopython-1.78+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 find Doc -name "*.pygtex" -o -name "*.pygstyle" -delete rm -rf biopython.egg-info rm -rf .pybuild if [ -d Tests_avoid ] ; then \ mv Tests_avoid/* Tests ; \ rmdir Tests_avoid ; \ fi rm -rf debian/tmp_tests make[1]: Leaving directory '/<>/python-biopython-1.78+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/python3-biopython.substvars debian/python-biopython-doc.substvars debian/python3-biopython-sql.substvars debian/files rm -fr -- debian/python3-biopython/ debian/tmp/ debian/python-biopython-doc/ debian/python3-biopython-sql/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules binary-arch dh binary-arch --with python3 --buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_autoreconf -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild install -d /<>/python-biopython-1.78\+dfsg/debian/.debhelper/generated/_source/home pybuild --configure -i python{version} -p "3.10 3.9" I: pybuild base:232: python3.10 setup.py config /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'build-lib' will not be supported in future versions. Please use the underscore name 'build_lib' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-layout' will not be supported in future versions. Please use the underscore name 'install_layout' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-scripts' will not be supported in future versions. Please use the underscore name 'install_scripts' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-lib' will not be supported in future versions. Please use the underscore name 'install_lib' instead warnings.warn( running config I: pybuild base:232: python3.9 setup.py config /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'build-lib' will not be supported in future versions. Please use the underscore name 'build_lib' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-layout' will not be supported in future versions. Please use the underscore name 'install_layout' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-scripts' will not be supported in future versions. Please use the underscore name 'install_scripts' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-lib' will not be supported in future versions. Please use the underscore name 'install_lib' instead warnings.warn( running config debian/rules override_dh_auto_build make[1]: Entering directory '/<>/python-biopython-1.78+dfsg' dh_auto_build pybuild --build -i python{version} -p "3.10 3.9" I: pybuild base:232: /usr/bin/python3.10 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'build-lib' will not be supported in future versions. Please use the underscore name 'build_lib' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-layout' will not be supported in future versions. Please use the underscore name 'install_layout' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-scripts' will not be supported in future versions. Please use the underscore name 'install_scripts' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-lib' will not be supported in future versions. Please use the underscore name 'install_lib' instead warnings.warn( running build running build_py creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio copying Bio/_utils.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio copying Bio/MarkovModel.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio copying Bio/LogisticRegression.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio copying Bio/Seq.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio copying Bio/NaiveBayes.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio copying Bio/MaxEntropy.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio copying Bio/File.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio copying Bio/bgzf.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio copying Bio/SeqFeature.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio copying Bio/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio copying Bio/kNN.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio copying Bio/SeqRecord.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio copying Bio/pairwise2.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Affy copying Bio/Affy/CelFile.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Affy copying Bio/Affy/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Affy creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align copying Bio/Align/AlignInfo.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align copying Bio/Align/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/Applications copying Bio/Align/Applications/_Probcons.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/Applications copying Bio/Align/Applications/_ClustalOmega.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/Applications copying Bio/Align/Applications/_Muscle.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/Applications copying Bio/Align/Applications/_Mafft.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/Applications copying Bio/Align/Applications/_MSAProbs.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/Applications copying Bio/Align/Applications/_Dialign.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/Applications copying Bio/Align/Applications/_Prank.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/Applications copying Bio/Align/Applications/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/Applications copying Bio/Align/Applications/_Clustalw.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/Applications copying Bio/Align/Applications/_TCoffee.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/Applications creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices copying Bio/Align/substitution_matrices/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/AlignIO copying Bio/AlignIO/ClustalIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/AlignIO copying Bio/AlignIO/NexusIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/AlignIO copying Bio/AlignIO/MauveIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/AlignIO copying Bio/AlignIO/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/AlignIO copying Bio/AlignIO/MsfIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/AlignIO copying Bio/AlignIO/MafIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/AlignIO copying Bio/AlignIO/FastaIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/AlignIO copying Bio/AlignIO/PhylipIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/AlignIO copying Bio/AlignIO/StockholmIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/AlignIO copying Bio/AlignIO/Interfaces.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/AlignIO copying Bio/AlignIO/EmbossIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/AlignIO creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Alphabet copying Bio/Alphabet/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Alphabet creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Application copying Bio/Application/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Application creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Blast copying Bio/Blast/Record.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Blast copying Bio/Blast/Applications.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Blast copying Bio/Blast/NCBIXML.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Blast copying Bio/Blast/ParseBlastTable.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Blast copying Bio/Blast/NCBIWWW.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Blast copying Bio/Blast/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Blast creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/CAPS copying Bio/CAPS/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/CAPS creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Cluster copying Bio/Cluster/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Cluster creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/codonalign copying Bio/codonalign/chisq.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/codonalign copying Bio/codonalign/codonseq.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/codonalign copying Bio/codonalign/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/codonalign copying Bio/codonalign/codonalignment.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/codonalign creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Compass copying Bio/Compass/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Compass creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Crystal copying Bio/Crystal/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Crystal creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Data copying Bio/Data/CodonTable.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Data copying Bio/Data/IUPACData.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Data copying Bio/Data/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Data copying Bio/Data/SCOPData.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Data creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Emboss copying Bio/Emboss/Applications.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Emboss copying Bio/Emboss/PrimerSearch.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Emboss copying Bio/Emboss/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Emboss copying Bio/Emboss/Primer3.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Emboss creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez copying Bio/Entrez/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez copying Bio/Entrez/Parser.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/ExPASy copying Bio/ExPASy/cellosaurus.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/ExPASy copying Bio/ExPASy/ScanProsite.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/ExPASy copying Bio/ExPASy/Prosite.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/ExPASy copying Bio/ExPASy/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/ExPASy copying Bio/ExPASy/Prodoc.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/ExPASy copying Bio/ExPASy/Enzyme.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/ExPASy creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/FSSP copying Bio/FSSP/fssp_rec.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/FSSP copying Bio/FSSP/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/FSSP copying Bio/FSSP/FSSPTools.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/FSSP creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/GenBank copying Bio/GenBank/Record.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/GenBank copying Bio/GenBank/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/GenBank copying Bio/GenBank/utils.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/GenBank copying Bio/GenBank/Scanner.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/GenBank creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Geo copying Bio/Geo/Record.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Geo copying Bio/Geo/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Geo creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics copying Bio/Graphics/Comparative.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics copying Bio/Graphics/ColorSpiral.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics copying Bio/Graphics/BasicChromosome.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics copying Bio/Graphics/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics copying Bio/Graphics/KGML_vis.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics copying Bio/Graphics/DisplayRepresentation.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics copying Bio/Graphics/Distribution.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Diagram.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_GraphSet.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CrossLink.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Feature.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Track.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Graph.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Colors.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics/GenomeDiagram creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/HMM copying Bio/HMM/Trainer.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/HMM copying Bio/HMM/Utilities.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/HMM copying Bio/HMM/MarkovModel.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/HMM copying Bio/HMM/DynamicProgramming.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/HMM copying Bio/HMM/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/HMM creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/KEGG copying Bio/KEGG/REST.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/KEGG copying Bio/KEGG/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/KEGG creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/KEGG/Compound copying Bio/KEGG/Compound/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/KEGG/Compound creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/KEGG/Enzyme copying Bio/KEGG/Enzyme/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/KEGG/Enzyme creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/KEGG/Gene copying Bio/KEGG/Gene/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/KEGG/Gene creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/KEGG/Map copying Bio/KEGG/Map/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/KEGG/Map creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB/mmtf copying Bio/PDB/mmtf/mmtfio.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB/mmtf copying Bio/PDB/mmtf/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB/mmtf copying Bio/PDB/mmtf/DefaultParser.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB/mmtf creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_pathway.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_parser.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/KEGG/KGML copying Bio/KEGG/KGML/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/KEGG/KGML creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Medline copying Bio/Medline/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Medline creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs copying Bio/motifs/alignace.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs copying Bio/motifs/xms.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs copying Bio/motifs/minimal.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs copying Bio/motifs/transfac.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs copying Bio/motifs/pfm.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs copying Bio/motifs/meme.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs copying Bio/motifs/matrix.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs copying Bio/motifs/clusterbuster.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs copying Bio/motifs/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs copying Bio/motifs/thresholds.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs copying Bio/motifs/mast.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs/applications copying Bio/motifs/applications/_xxmotif.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs/applications copying Bio/motifs/applications/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs/applications creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs/jaspar copying Bio/motifs/jaspar/db.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs/jaspar copying Bio/motifs/jaspar/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs/jaspar creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Nexus copying Bio/Nexus/StandardData.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Nexus copying Bio/Nexus/Nexus.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Nexus copying Bio/Nexus/Trees.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Nexus copying Bio/Nexus/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Nexus copying Bio/Nexus/Nodes.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Nexus creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/NMR copying Bio/NMR/NOEtools.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/NMR copying Bio/NMR/xpktools.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/NMR copying Bio/NMR/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/NMR creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Pathway copying Bio/Pathway/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Pathway creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Pathway/Rep copying Bio/Pathway/Rep/MultiGraph.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Pathway/Rep copying Bio/Pathway/Rep/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Pathway/Rep copying Bio/Pathway/Rep/Graph.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Pathway/Rep copying Bio/PDB/FragmentMapper.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB copying Bio/PDB/mmcifio.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB copying Bio/PDB/Chain.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB copying Bio/PDB/SCADIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB copying Bio/PDB/MMCIF2Dict.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB copying Bio/PDB/Dice.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB copying Bio/PDB/PDBList.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB copying Bio/PDB/HSExposure.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB copying Bio/PDB/StructureBuilder.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB copying Bio/PDB/AbstractPropertyMap.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB copying Bio/PDB/NeighborSearch.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB copying Bio/PDB/ic_rebuild.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB copying Bio/PDB/vectors.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB copying Bio/PDB/Selection.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB copying Bio/PDB/PDBIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB copying Bio/PDB/PDBExceptions.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB copying Bio/PDB/internal_coords.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB copying Bio/PDB/Atom.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB copying Bio/PDB/Residue.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB copying Bio/PDB/DSSP.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB copying Bio/PDB/PSEA.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB copying Bio/PDB/PICIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB copying Bio/PDB/Polypeptide.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB copying Bio/PDB/PDBParser.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB copying Bio/PDB/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB copying Bio/PDB/Model.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB copying Bio/PDB/ResidueDepth.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB copying Bio/PDB/Entity.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB copying Bio/PDB/NACCESS.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB copying Bio/PDB/parse_pdb_header.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB copying Bio/PDB/ic_data.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB copying Bio/PDB/StructureAlignment.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB copying Bio/PDB/MMCIFParser.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB copying Bio/PDB/Structure.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB copying Bio/PDB/Superimposer.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/phenotype copying Bio/phenotype/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/phenotype copying Bio/phenotype/pm_fitting.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/phenotype copying Bio/phenotype/phen_micro.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/phenotype creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PopGen copying Bio/PopGen/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PopGen creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/Controller.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/FileParser.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/LargeFileParser.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/EasyController.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PopGen/GenePop creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Restriction copying Bio/Restriction/PrintFormat.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Restriction copying Bio/Restriction/Restriction_Dictionary.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Restriction copying Bio/Restriction/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Restriction copying Bio/Restriction/Restriction.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Restriction creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SCOP copying Bio/SCOP/Des.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SCOP copying Bio/SCOP/Cla.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SCOP copying Bio/SCOP/Hie.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SCOP copying Bio/SCOP/Residues.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SCOP copying Bio/SCOP/Dom.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SCOP copying Bio/SCOP/Raf.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SCOP copying Bio/SCOP/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SCOP creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO copying Bio/SearchIO/_utils.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO copying Bio/SearchIO/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO copying Bio/SearchIO/_index.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO copying Bio/SearchIO/BlatIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO copying Bio/SearchIO/FastaIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/_legacy copying Bio/SearchIO/_legacy/ParserSupport.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/_legacy copying Bio/SearchIO/_legacy/NCBIStandalone.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/_legacy copying Bio/SearchIO/_legacy/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/_legacy creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/query.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/hsp.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/hit.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/_base.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/_model creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_xml.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_tab.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_text.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/BlastIO creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/HHsuiteIO copying Bio/SearchIO/HHsuiteIO/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/HHsuiteIO copying Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/HHsuiteIO creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_text.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/_base.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_tab.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/HmmerIO creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_text.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/_base.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/ExonerateIO creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/interproscan_xml.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/InterproscanIO creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO copying Bio/SeqIO/PdbIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO copying Bio/SeqIO/SeqXmlIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO copying Bio/SeqIO/AbiIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO copying Bio/SeqIO/IgIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO copying Bio/SeqIO/TabIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO copying Bio/SeqIO/UniprotIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO copying Bio/SeqIO/InsdcIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO copying Bio/SeqIO/AceIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO copying Bio/SeqIO/SwissIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO copying Bio/SeqIO/QualityIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO copying Bio/SeqIO/SffIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO copying Bio/SeqIO/PirIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO copying Bio/SeqIO/XdnaIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO copying Bio/SeqIO/SnapGeneIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO copying Bio/SeqIO/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO copying Bio/SeqIO/PhdIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO copying Bio/SeqIO/GckIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO copying Bio/SeqIO/_index.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO copying Bio/SeqIO/FastaIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO copying Bio/SeqIO/NibIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO copying Bio/SeqIO/Interfaces.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqUtils copying Bio/SeqUtils/ProtParamData.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqUtils copying Bio/SeqUtils/CodonUsageIndices.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqUtils copying Bio/SeqUtils/CodonUsage.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqUtils copying Bio/SeqUtils/MeltingTemp.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqUtils copying Bio/SeqUtils/lcc.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqUtils copying Bio/SeqUtils/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqUtils copying Bio/SeqUtils/CheckSum.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqUtils copying Bio/SeqUtils/IsoelectricPoint.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqUtils copying Bio/SeqUtils/ProtParam.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqUtils creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Sequencing copying Bio/Sequencing/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Sequencing copying Bio/Sequencing/Phd.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Sequencing copying Bio/Sequencing/Ace.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Sequencing creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_bwa.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_samtools.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_Novoalign.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Sequencing/Applications creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Statistics copying Bio/Statistics/lowess.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Statistics copying Bio/Statistics/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Statistics creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SubsMat copying Bio/SubsMat/MatrixInfo.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SubsMat copying Bio/SubsMat/FreqTable.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SubsMat copying Bio/SubsMat/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SubsMat creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SVDSuperimposer copying Bio/SVDSuperimposer/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SVDSuperimposer creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB/QCPSuperimposer copying Bio/PDB/QCPSuperimposer/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB/QCPSuperimposer creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SwissProt copying Bio/SwissProt/KeyWList.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SwissProt copying Bio/SwissProt/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SwissProt creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/TogoWS copying Bio/TogoWS/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/TogoWS creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo copying Bio/Phylo/CDAOIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo copying Bio/Phylo/NexusIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo copying Bio/Phylo/Consensus.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo copying Bio/Phylo/_utils.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo copying Bio/Phylo/PhyloXMLIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo copying Bio/Phylo/CDAO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo copying Bio/Phylo/BaseTree.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo copying Bio/Phylo/Newick.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo copying Bio/Phylo/_cdao_owl.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo copying Bio/Phylo/PhyloXML.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo copying Bio/Phylo/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo copying Bio/Phylo/NeXMLIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo copying Bio/Phylo/_io.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo copying Bio/Phylo/TreeConstruction.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo copying Bio/Phylo/NeXML.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo copying Bio/Phylo/NewickIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Fasttree.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Phyml.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Raxml.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo/Applications creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_yn00.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_baseml.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/chi2.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/yn00.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_codeml.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/codeml.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/baseml.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_paml.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo/PAML creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/UniGene copying Bio/UniGene/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/UniGene creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/UniProt copying Bio/UniProt/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/UniProt copying Bio/UniProt/GOA.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/UniProt creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Wise copying Bio/Wise/psw.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Wise copying Bio/Wise/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Wise copying Bio/Wise/dnal.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Wise creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/BioSQL copying BioSQL/DBUtils.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/BioSQL copying BioSQL/BioSeq.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/BioSQL copying BioSQL/Loader.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/BioSQL copying BioSQL/BioSeqDatabase.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/BioSQL copying BioSQL/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/BioSQL running egg_info creating biopython.egg-info writing biopython.egg-info/PKG-INFO writing dependency_links to biopython.egg-info/dependency_links.txt writing requirements to biopython.egg-info/requires.txt writing top-level names to biopython.egg-info/top_level.txt writing manifest file 'biopython.egg-info/SOURCES.txt' reading manifest file 'biopython.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.py{}' found anywhere in distribution warning: no previously-included files matching '*.py-e' found anywhere in distribution adding license file 'LICENSE' adding license file 'LICENSE.rst' writing manifest file 'biopython.egg-info/SOURCES.txt' copying Bio/cpairwise2module.c -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio copying Bio/Align/_aligners.c -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER22 -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER6 -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER74 -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM45 -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM50 -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM62 -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM80 -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM90 -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/DAYHOFF -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/FENG -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/GENETIC -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/GONNET1992 -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/HOXD70 -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/JOHNSON -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/JONES -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/LEVIN -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MCLACHLAN -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MDM78 -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/NUC.4.4 -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM250 -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM30 -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM70 -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/RAO -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/RISLER -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/SCHNEIDER -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/STR -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/TRANS -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data copying Bio/Cluster/cluster.c -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Cluster copying Bio/Cluster/cluster.h -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Cluster copying Bio/Cluster/clustermodule.c -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Cluster creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying 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/<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PDB_General.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PDB_General.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PIR_General.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PIR_General.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PRF_General.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PRF_General.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/SP_General.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/SP_General.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/XHTMLtablesetup.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivearticle.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-classes.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-mixes.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-models.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-modules.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/articlemeta.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/backmatter.ent -> 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/<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/default-classes.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/default-mixes.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/display.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eInfo_020511.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eLink_090910.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eLink_101123.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/ePost_020511.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSearch_020511.dtd -> 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copying Bio/Entrez/DTDs/isocyr1.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isocyr2.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isodia.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk1.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk2.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk3.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk4.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isolat1.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isolat2.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomfrk.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomopf.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomscr.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isonum.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isopub.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isotech.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/journalmeta.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/link.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/list.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/math.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml-in-pubmed.mod -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml2.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml3-qname1.mod -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml3.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathmlsetup.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mmlalias.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mmlextra.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/modules.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_011101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_080101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_090101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_011101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_080101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_090101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_080101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_100101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/notat.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/para.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/phrase.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pmc-1.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_020114.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_080101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_090101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100301.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_110101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_120101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130501.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_140101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_150101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180601.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_190101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/references.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/section.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/taxon.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xmlspecchars.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/XSDs copying Bio/Entrez/XSDs/IPGReportSet.xsd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/XSDs copying Bio/motifs/_pwm.c -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs copying Bio/Nexus/cnexus.c -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Nexus copying Bio/PDB/kdtrees.c -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB copying Bio/PDB/QCPSuperimposer/qcprotmodule.c -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB/QCPSuperimposer running build_ext building 'Bio.Align._aligners' extension creating build creating build/temp.linux-ppc64el-3.10 creating build/temp.linux-ppc64el-3.10/Bio creating build/temp.linux-ppc64el-3.10/Bio/Align powerpc64le-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -fexceptions -g -fwrapv -O2 -g -O3 -ffile-prefix-map=/<>/python-biopython-1.78+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c Bio/Align/_aligners.c -o build/temp.linux-ppc64el-3.10/Bio/Align/_aligners.o powerpc64le-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -g -O3 -ffile-prefix-map=/<>/python-biopython-1.78+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-3.10/Bio/Align/_aligners.o -o /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/_aligners.cpython-310-powerpc64le-linux-gnu.so building 'Bio.cpairwise2' extension powerpc64le-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -fexceptions -g -fwrapv -O2 -g -O3 -ffile-prefix-map=/<>/python-biopython-1.78+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c Bio/cpairwise2module.c -o build/temp.linux-ppc64el-3.10/Bio/cpairwise2module.o Bio/cpairwise2module.c: In function ‘_get_match_score’: Bio/cpairwise2module.c:60:5: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations] 60 | if(!(py_result = PyEval_CallObject(py_match_fn, py_arglist))) | ^~ In file included from /usr/include/python3.10/Python.h:131, from Bio/cpairwise2module.c:16: /usr/include/python3.10/ceval.h:17:43: note: declared here 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -g -O3 -ffile-prefix-map=/<>/python-biopython-1.78+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-3.10/Bio/cpairwise2module.o -o /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/cpairwise2.cpython-310-powerpc64le-linux-gnu.so building 'Bio.Nexus.cnexus' extension creating build/temp.linux-ppc64el-3.10/Bio/Nexus powerpc64le-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -fexceptions -g -fwrapv -O2 -g -O3 -ffile-prefix-map=/<>/python-biopython-1.78+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c Bio/Nexus/cnexus.c -o build/temp.linux-ppc64el-3.10/Bio/Nexus/cnexus.o powerpc64le-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -g -O3 -ffile-prefix-map=/<>/python-biopython-1.78+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-3.10/Bio/Nexus/cnexus.o -o /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Nexus/cnexus.cpython-310-powerpc64le-linux-gnu.so building 'Bio.PDB.QCPSuperimposer.qcprotmodule' extension creating build/temp.linux-ppc64el-3.10/Bio/PDB creating build/temp.linux-ppc64el-3.10/Bio/PDB/QCPSuperimposer powerpc64le-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -fexceptions -g -fwrapv -O2 -g -O3 -ffile-prefix-map=/<>/python-biopython-1.78+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c Bio/PDB/QCPSuperimposer/qcprotmodule.c -o build/temp.linux-ppc64el-3.10/Bio/PDB/QCPSuperimposer/qcprotmodule.o powerpc64le-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -g -O3 -ffile-prefix-map=/<>/python-biopython-1.78+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-3.10/Bio/PDB/QCPSuperimposer/qcprotmodule.o -o /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-310-powerpc64le-linux-gnu.so building 'Bio.motifs._pwm' extension creating build/temp.linux-ppc64el-3.10/Bio/motifs powerpc64le-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -fexceptions -g -fwrapv -O2 -g -O3 -ffile-prefix-map=/<>/python-biopython-1.78+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c Bio/motifs/_pwm.c -o build/temp.linux-ppc64el-3.10/Bio/motifs/_pwm.o powerpc64le-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -g -O3 -ffile-prefix-map=/<>/python-biopython-1.78+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-3.10/Bio/motifs/_pwm.o -o /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs/_pwm.cpython-310-powerpc64le-linux-gnu.so building 'Bio.Cluster._cluster' extension creating build/temp.linux-ppc64el-3.10/Bio/Cluster powerpc64le-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -fexceptions -g -fwrapv -O2 -g -O3 -ffile-prefix-map=/<>/python-biopython-1.78+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c Bio/Cluster/cluster.c -o build/temp.linux-ppc64el-3.10/Bio/Cluster/cluster.o powerpc64le-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -fexceptions -g -fwrapv -O2 -g -O3 -ffile-prefix-map=/<>/python-biopython-1.78+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c Bio/Cluster/clustermodule.c -o build/temp.linux-ppc64el-3.10/Bio/Cluster/clustermodule.o powerpc64le-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -g -O3 -ffile-prefix-map=/<>/python-biopython-1.78+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-3.10/Bio/Cluster/cluster.o build/temp.linux-ppc64el-3.10/Bio/Cluster/clustermodule.o -o /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Cluster/_cluster.cpython-310-powerpc64le-linux-gnu.so building 'Bio.PDB.kdtrees' extension powerpc64le-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -fexceptions -g -fwrapv -O2 -g -O3 -ffile-prefix-map=/<>/python-biopython-1.78+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c Bio/PDB/kdtrees.c -o build/temp.linux-ppc64el-3.10/Bio/PDB/kdtrees.o powerpc64le-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -g -O3 -ffile-prefix-map=/<>/python-biopython-1.78+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-3.10/Bio/PDB/kdtrees.o -o /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB/kdtrees.cpython-310-powerpc64le-linux-gnu.so I: pybuild base:232: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'build-lib' will not be supported in future versions. Please use the underscore name 'build_lib' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-layout' will not be supported in future versions. Please use the underscore name 'install_layout' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-scripts' will not be supported in future versions. Please use the underscore name 'install_scripts' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-lib' will not be supported in future versions. Please use the underscore name 'install_lib' instead warnings.warn( running build running build_py creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio copying Bio/_utils.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio copying Bio/MarkovModel.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio copying Bio/LogisticRegression.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio copying Bio/Seq.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio copying Bio/NaiveBayes.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio copying Bio/MaxEntropy.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio copying Bio/File.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio copying Bio/bgzf.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio copying Bio/SeqFeature.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio copying Bio/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio copying Bio/kNN.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio copying Bio/SeqRecord.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio copying Bio/pairwise2.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Affy copying Bio/Affy/CelFile.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Affy copying Bio/Affy/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Affy creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align copying Bio/Align/AlignInfo.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align copying Bio/Align/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/Applications copying Bio/Align/Applications/_Probcons.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/Applications copying Bio/Align/Applications/_ClustalOmega.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/Applications copying Bio/Align/Applications/_Muscle.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/Applications copying Bio/Align/Applications/_Mafft.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/Applications copying Bio/Align/Applications/_MSAProbs.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/Applications copying Bio/Align/Applications/_Dialign.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/Applications copying Bio/Align/Applications/_Prank.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/Applications copying Bio/Align/Applications/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/Applications copying Bio/Align/Applications/_Clustalw.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/Applications copying Bio/Align/Applications/_TCoffee.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/Applications creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices copying Bio/Align/substitution_matrices/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/AlignIO copying Bio/AlignIO/ClustalIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/AlignIO copying Bio/AlignIO/NexusIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/AlignIO copying Bio/AlignIO/MauveIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/AlignIO copying Bio/AlignIO/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/AlignIO copying Bio/AlignIO/MsfIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/AlignIO copying Bio/AlignIO/MafIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/AlignIO copying Bio/AlignIO/FastaIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/AlignIO copying Bio/AlignIO/PhylipIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/AlignIO copying Bio/AlignIO/StockholmIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/AlignIO copying Bio/AlignIO/Interfaces.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/AlignIO copying Bio/AlignIO/EmbossIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/AlignIO creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Alphabet copying Bio/Alphabet/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Alphabet creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Application copying Bio/Application/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Application creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Blast copying Bio/Blast/Record.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Blast copying Bio/Blast/Applications.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Blast copying Bio/Blast/NCBIXML.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Blast copying Bio/Blast/ParseBlastTable.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Blast copying Bio/Blast/NCBIWWW.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Blast copying Bio/Blast/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Blast creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/CAPS copying Bio/CAPS/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/CAPS creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Cluster copying Bio/Cluster/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Cluster creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/codonalign copying Bio/codonalign/chisq.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/codonalign copying Bio/codonalign/codonseq.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/codonalign copying Bio/codonalign/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/codonalign copying Bio/codonalign/codonalignment.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/codonalign creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Compass copying Bio/Compass/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Compass creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Crystal copying Bio/Crystal/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Crystal creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Data copying Bio/Data/CodonTable.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Data copying Bio/Data/IUPACData.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Data copying Bio/Data/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Data copying Bio/Data/SCOPData.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Data creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Emboss copying Bio/Emboss/Applications.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Emboss copying Bio/Emboss/PrimerSearch.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Emboss copying Bio/Emboss/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Emboss copying Bio/Emboss/Primer3.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Emboss creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez copying Bio/Entrez/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez copying Bio/Entrez/Parser.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/ExPASy copying Bio/ExPASy/cellosaurus.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/ExPASy copying Bio/ExPASy/ScanProsite.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/ExPASy copying Bio/ExPASy/Prosite.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/ExPASy copying Bio/ExPASy/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/ExPASy copying Bio/ExPASy/Prodoc.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/ExPASy copying Bio/ExPASy/Enzyme.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/ExPASy creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/FSSP copying Bio/FSSP/fssp_rec.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/FSSP copying Bio/FSSP/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/FSSP copying Bio/FSSP/FSSPTools.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/FSSP creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/GenBank copying Bio/GenBank/Record.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/GenBank copying Bio/GenBank/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/GenBank copying Bio/GenBank/utils.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/GenBank copying Bio/GenBank/Scanner.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/GenBank creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Geo copying Bio/Geo/Record.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Geo copying Bio/Geo/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Geo creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Graphics copying Bio/Graphics/Comparative.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Graphics copying Bio/Graphics/ColorSpiral.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Graphics copying Bio/Graphics/BasicChromosome.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Graphics copying Bio/Graphics/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Graphics copying Bio/Graphics/KGML_vis.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Graphics copying Bio/Graphics/DisplayRepresentation.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Graphics copying Bio/Graphics/Distribution.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Graphics creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Diagram.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_GraphSet.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CrossLink.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Feature.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Track.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Graph.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Colors.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/HMM copying Bio/HMM/Trainer.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/HMM copying Bio/HMM/Utilities.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/HMM copying Bio/HMM/MarkovModel.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/HMM copying Bio/HMM/DynamicProgramming.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/HMM copying Bio/HMM/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/HMM creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/KEGG copying Bio/KEGG/REST.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/KEGG copying Bio/KEGG/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/KEGG creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/KEGG/Compound copying Bio/KEGG/Compound/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/KEGG/Compound creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/KEGG/Enzyme copying Bio/KEGG/Enzyme/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/KEGG/Enzyme creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/KEGG/Gene copying Bio/KEGG/Gene/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/KEGG/Gene creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/KEGG/Map copying Bio/KEGG/Map/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/KEGG/Map creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB/mmtf copying Bio/PDB/mmtf/mmtfio.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB/mmtf copying Bio/PDB/mmtf/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB/mmtf copying Bio/PDB/mmtf/DefaultParser.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB/mmtf creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_pathway.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_parser.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/KEGG/KGML copying Bio/KEGG/KGML/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/KEGG/KGML creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Medline copying Bio/Medline/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Medline creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/motifs copying Bio/motifs/alignace.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/motifs copying Bio/motifs/xms.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/motifs copying Bio/motifs/minimal.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/motifs copying Bio/motifs/transfac.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/motifs copying Bio/motifs/pfm.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/motifs copying Bio/motifs/meme.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/motifs copying Bio/motifs/matrix.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/motifs copying Bio/motifs/clusterbuster.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/motifs copying Bio/motifs/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/motifs copying Bio/motifs/thresholds.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/motifs copying Bio/motifs/mast.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/motifs creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/motifs/applications copying Bio/motifs/applications/_xxmotif.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/motifs/applications copying Bio/motifs/applications/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/motifs/applications creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/motifs/jaspar copying Bio/motifs/jaspar/db.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/motifs/jaspar copying Bio/motifs/jaspar/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/motifs/jaspar creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Nexus copying Bio/Nexus/StandardData.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Nexus copying Bio/Nexus/Nexus.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Nexus copying Bio/Nexus/Trees.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Nexus copying Bio/Nexus/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Nexus copying Bio/Nexus/Nodes.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Nexus creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/NMR copying Bio/NMR/NOEtools.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/NMR copying Bio/NMR/xpktools.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/NMR copying Bio/NMR/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/NMR creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Pathway copying Bio/Pathway/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Pathway creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Pathway/Rep copying Bio/Pathway/Rep/MultiGraph.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Pathway/Rep copying Bio/Pathway/Rep/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Pathway/Rep copying Bio/Pathway/Rep/Graph.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Pathway/Rep copying Bio/PDB/FragmentMapper.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB copying Bio/PDB/mmcifio.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB copying Bio/PDB/Chain.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB copying Bio/PDB/SCADIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB copying Bio/PDB/MMCIF2Dict.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB copying Bio/PDB/Dice.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB copying Bio/PDB/PDBList.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB copying Bio/PDB/HSExposure.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB copying Bio/PDB/StructureBuilder.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB copying Bio/PDB/AbstractPropertyMap.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB copying Bio/PDB/NeighborSearch.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB copying Bio/PDB/ic_rebuild.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB copying Bio/PDB/vectors.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB copying Bio/PDB/Selection.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB copying Bio/PDB/PDBIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB copying Bio/PDB/PDBExceptions.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB copying Bio/PDB/internal_coords.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB copying Bio/PDB/Atom.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB copying Bio/PDB/Residue.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB copying Bio/PDB/DSSP.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB copying Bio/PDB/PSEA.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB copying Bio/PDB/PICIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB copying Bio/PDB/Polypeptide.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB copying Bio/PDB/PDBParser.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB copying Bio/PDB/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB copying Bio/PDB/Model.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB copying Bio/PDB/ResidueDepth.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB copying Bio/PDB/Entity.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB copying Bio/PDB/NACCESS.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB copying Bio/PDB/parse_pdb_header.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB copying Bio/PDB/ic_data.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB copying Bio/PDB/StructureAlignment.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB copying Bio/PDB/MMCIFParser.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB copying Bio/PDB/Structure.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB copying Bio/PDB/Superimposer.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/phenotype copying Bio/phenotype/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/phenotype copying Bio/phenotype/pm_fitting.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/phenotype copying Bio/phenotype/phen_micro.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/phenotype creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PopGen copying Bio/PopGen/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PopGen creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/Controller.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/FileParser.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/LargeFileParser.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/EasyController.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PopGen/GenePop creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Restriction copying Bio/Restriction/PrintFormat.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Restriction copying Bio/Restriction/Restriction_Dictionary.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Restriction copying Bio/Restriction/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Restriction copying Bio/Restriction/Restriction.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Restriction creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SCOP copying Bio/SCOP/Des.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SCOP copying Bio/SCOP/Cla.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SCOP copying Bio/SCOP/Hie.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SCOP copying Bio/SCOP/Residues.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SCOP copying Bio/SCOP/Dom.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SCOP copying Bio/SCOP/Raf.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SCOP copying Bio/SCOP/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SCOP creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO copying Bio/SearchIO/_utils.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO copying Bio/SearchIO/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO copying Bio/SearchIO/_index.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO copying Bio/SearchIO/BlatIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO copying Bio/SearchIO/FastaIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO/_legacy copying Bio/SearchIO/_legacy/ParserSupport.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO/_legacy copying Bio/SearchIO/_legacy/NCBIStandalone.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO/_legacy copying Bio/SearchIO/_legacy/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO/_legacy creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/query.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/hsp.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/hit.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/_base.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO/_model creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_xml.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_tab.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_text.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO/BlastIO creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO/HHsuiteIO copying Bio/SearchIO/HHsuiteIO/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO/HHsuiteIO copying Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO/HHsuiteIO creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_text.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/_base.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_tab.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO/HmmerIO creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_text.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/_base.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO/ExonerateIO creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/interproscan_xml.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SearchIO/InterproscanIO creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SeqIO copying Bio/SeqIO/PdbIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SeqIO copying Bio/SeqIO/SeqXmlIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SeqIO copying Bio/SeqIO/AbiIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SeqIO copying Bio/SeqIO/IgIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SeqIO copying Bio/SeqIO/TabIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SeqIO copying Bio/SeqIO/UniprotIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SeqIO copying Bio/SeqIO/InsdcIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SeqIO copying Bio/SeqIO/AceIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SeqIO copying Bio/SeqIO/SwissIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SeqIO copying Bio/SeqIO/QualityIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SeqIO copying Bio/SeqIO/SffIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SeqIO copying Bio/SeqIO/PirIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SeqIO copying Bio/SeqIO/XdnaIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SeqIO copying Bio/SeqIO/SnapGeneIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SeqIO copying Bio/SeqIO/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SeqIO copying Bio/SeqIO/PhdIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SeqIO copying Bio/SeqIO/GckIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SeqIO copying Bio/SeqIO/_index.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SeqIO copying Bio/SeqIO/FastaIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SeqIO copying Bio/SeqIO/NibIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SeqIO copying Bio/SeqIO/Interfaces.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SeqIO creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SeqUtils copying Bio/SeqUtils/ProtParamData.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SeqUtils copying Bio/SeqUtils/CodonUsageIndices.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SeqUtils copying Bio/SeqUtils/CodonUsage.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SeqUtils copying Bio/SeqUtils/MeltingTemp.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SeqUtils copying Bio/SeqUtils/lcc.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SeqUtils copying Bio/SeqUtils/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SeqUtils copying Bio/SeqUtils/CheckSum.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SeqUtils copying Bio/SeqUtils/IsoelectricPoint.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SeqUtils copying Bio/SeqUtils/ProtParam.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SeqUtils creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Sequencing copying Bio/Sequencing/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Sequencing copying Bio/Sequencing/Phd.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Sequencing copying Bio/Sequencing/Ace.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Sequencing creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_bwa.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_samtools.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_Novoalign.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Sequencing/Applications creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Statistics copying Bio/Statistics/lowess.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Statistics copying Bio/Statistics/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Statistics creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SubsMat copying Bio/SubsMat/MatrixInfo.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SubsMat copying Bio/SubsMat/FreqTable.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SubsMat copying Bio/SubsMat/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SubsMat creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SVDSuperimposer copying Bio/SVDSuperimposer/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SVDSuperimposer creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB/QCPSuperimposer copying Bio/PDB/QCPSuperimposer/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB/QCPSuperimposer creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SwissProt copying Bio/SwissProt/KeyWList.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SwissProt copying Bio/SwissProt/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SwissProt creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/TogoWS copying Bio/TogoWS/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/TogoWS creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Phylo copying Bio/Phylo/CDAOIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Phylo copying Bio/Phylo/NexusIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Phylo copying Bio/Phylo/Consensus.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Phylo copying Bio/Phylo/_utils.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Phylo copying Bio/Phylo/PhyloXMLIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Phylo copying Bio/Phylo/CDAO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Phylo copying Bio/Phylo/BaseTree.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Phylo copying Bio/Phylo/Newick.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Phylo copying Bio/Phylo/_cdao_owl.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Phylo copying Bio/Phylo/PhyloXML.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Phylo copying Bio/Phylo/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Phylo copying Bio/Phylo/NeXMLIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Phylo copying Bio/Phylo/_io.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Phylo copying Bio/Phylo/TreeConstruction.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Phylo copying Bio/Phylo/NeXML.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Phylo copying Bio/Phylo/NewickIO.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Phylo creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Fasttree.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Phyml.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Raxml.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Phylo/Applications creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_yn00.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_baseml.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/chi2.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/yn00.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_codeml.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/codeml.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/baseml.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_paml.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/UniGene copying Bio/UniGene/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/UniGene creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/UniProt copying Bio/UniProt/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/UniProt copying Bio/UniProt/GOA.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/UniProt creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Wise copying Bio/Wise/psw.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Wise copying Bio/Wise/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Wise copying Bio/Wise/dnal.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Wise creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/BioSQL copying BioSQL/DBUtils.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/BioSQL copying BioSQL/BioSeq.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/BioSQL copying BioSQL/Loader.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/BioSQL copying BioSQL/BioSeqDatabase.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/BioSQL copying BioSQL/__init__.py -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/BioSQL running egg_info writing biopython.egg-info/PKG-INFO writing dependency_links to biopython.egg-info/dependency_links.txt writing requirements to biopython.egg-info/requires.txt writing top-level names to biopython.egg-info/top_level.txt reading manifest file 'biopython.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.py{}' found anywhere in distribution warning: no previously-included files matching '*.py-e' found anywhere in distribution adding license file 'LICENSE' adding license file 'LICENSE.rst' writing manifest file 'biopython.egg-info/SOURCES.txt' copying Bio/cpairwise2module.c -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio copying Bio/Align/_aligners.c -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER22 -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER6 -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER74 -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM45 -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM50 -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM62 -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM80 -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM90 -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/DAYHOFF -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/FENG -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/GENETIC -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/GONNET1992 -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/HOXD70 -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/JOHNSON -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/JONES -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/LEVIN -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MCLACHLAN -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MDM78 -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/NUC.4.4 -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM250 -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM30 -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM70 -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/RAO -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/RISLER -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/SCHNEIDER -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/STR -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/TRANS -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data copying Bio/Cluster/cluster.c -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Cluster copying Bio/Cluster/cluster.h -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Cluster copying Bio/Cluster/clustermodule.c -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Cluster creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Gene.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_General.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_General.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medlars.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medline.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mim.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mime.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Organism.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Project.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Protein.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Pub.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PubMed.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_RNA.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Remap.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Rsite.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> 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Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_080101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_100101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/notat.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/para.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/phrase.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pmc-1.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_020114.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_080101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_090101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100301.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_110101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_120101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130501.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_140101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_150101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180601.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_190101.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/references.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/section.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/taxon.dtd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xmlspecchars.ent -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs creating /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/XSDs copying Bio/Entrez/XSDs/IPGReportSet.xsd -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Entrez/XSDs copying Bio/motifs/_pwm.c -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/motifs copying Bio/Nexus/cnexus.c -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Nexus copying Bio/PDB/kdtrees.c -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB copying Bio/PDB/QCPSuperimposer/qcprotmodule.c -> /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB/QCPSuperimposer running build_ext building 'Bio.Align._aligners' extension creating build/temp.linux-ppc64el-3.9 creating build/temp.linux-ppc64el-3.9/Bio creating build/temp.linux-ppc64el-3.9/Bio/Align powerpc64le-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -fexceptions -g -fwrapv -O2 -g -O3 -ffile-prefix-map=/<>/python-biopython-1.78+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.9 -c Bio/Align/_aligners.c -o build/temp.linux-ppc64el-3.9/Bio/Align/_aligners.o powerpc64le-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -g -O3 -ffile-prefix-map=/<>/python-biopython-1.78+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-3.9/Bio/Align/_aligners.o -o /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Align/_aligners.cpython-39-powerpc64le-linux-gnu.so building 'Bio.cpairwise2' extension powerpc64le-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -fexceptions -g -fwrapv -O2 -g -O3 -ffile-prefix-map=/<>/python-biopython-1.78+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.9 -c Bio/cpairwise2module.c -o build/temp.linux-ppc64el-3.9/Bio/cpairwise2module.o Bio/cpairwise2module.c: In function ‘_get_match_score’: Bio/cpairwise2module.c:60:5: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations] 60 | if(!(py_result = PyEval_CallObject(py_match_fn, py_arglist))) | ^~ In file included from /usr/include/python3.9/Python.h:154, from Bio/cpairwise2module.c:16: /usr/include/python3.9/ceval.h:17:43: note: declared here 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -g -O3 -ffile-prefix-map=/<>/python-biopython-1.78+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-3.9/Bio/cpairwise2module.o -o /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/cpairwise2.cpython-39-powerpc64le-linux-gnu.so building 'Bio.Nexus.cnexus' extension creating build/temp.linux-ppc64el-3.9/Bio/Nexus powerpc64le-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -fexceptions -g -fwrapv -O2 -g -O3 -ffile-prefix-map=/<>/python-biopython-1.78+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.9 -c Bio/Nexus/cnexus.c -o build/temp.linux-ppc64el-3.9/Bio/Nexus/cnexus.o powerpc64le-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -g -O3 -ffile-prefix-map=/<>/python-biopython-1.78+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-3.9/Bio/Nexus/cnexus.o -o /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Nexus/cnexus.cpython-39-powerpc64le-linux-gnu.so building 'Bio.PDB.QCPSuperimposer.qcprotmodule' extension creating build/temp.linux-ppc64el-3.9/Bio/PDB creating build/temp.linux-ppc64el-3.9/Bio/PDB/QCPSuperimposer powerpc64le-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -fexceptions -g -fwrapv -O2 -g -O3 -ffile-prefix-map=/<>/python-biopython-1.78+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.9 -c Bio/PDB/QCPSuperimposer/qcprotmodule.c -o build/temp.linux-ppc64el-3.9/Bio/PDB/QCPSuperimposer/qcprotmodule.o powerpc64le-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -g -O3 -ffile-prefix-map=/<>/python-biopython-1.78+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-3.9/Bio/PDB/QCPSuperimposer/qcprotmodule.o -o /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-39-powerpc64le-linux-gnu.so building 'Bio.motifs._pwm' extension creating build/temp.linux-ppc64el-3.9/Bio/motifs powerpc64le-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -fexceptions -g -fwrapv -O2 -g -O3 -ffile-prefix-map=/<>/python-biopython-1.78+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.9 -c Bio/motifs/_pwm.c -o build/temp.linux-ppc64el-3.9/Bio/motifs/_pwm.o powerpc64le-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -g -O3 -ffile-prefix-map=/<>/python-biopython-1.78+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-3.9/Bio/motifs/_pwm.o -o /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/motifs/_pwm.cpython-39-powerpc64le-linux-gnu.so building 'Bio.Cluster._cluster' extension creating build/temp.linux-ppc64el-3.9/Bio/Cluster powerpc64le-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -fexceptions -g -fwrapv -O2 -g -O3 -ffile-prefix-map=/<>/python-biopython-1.78+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.9 -c Bio/Cluster/cluster.c -o build/temp.linux-ppc64el-3.9/Bio/Cluster/cluster.o powerpc64le-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -fexceptions -g -fwrapv -O2 -g -O3 -ffile-prefix-map=/<>/python-biopython-1.78+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.9 -c Bio/Cluster/clustermodule.c -o build/temp.linux-ppc64el-3.9/Bio/Cluster/clustermodule.o powerpc64le-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -g -O3 -ffile-prefix-map=/<>/python-biopython-1.78+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-3.9/Bio/Cluster/cluster.o build/temp.linux-ppc64el-3.9/Bio/Cluster/clustermodule.o -o /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Cluster/_cluster.cpython-39-powerpc64le-linux-gnu.so building 'Bio.PDB.kdtrees' extension powerpc64le-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -fexceptions -g -fwrapv -O2 -g -O3 -ffile-prefix-map=/<>/python-biopython-1.78+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.9 -c Bio/PDB/kdtrees.c -o build/temp.linux-ppc64el-3.9/Bio/PDB/kdtrees.o powerpc64le-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -g -O3 -ffile-prefix-map=/<>/python-biopython-1.78+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-3.9/Bio/PDB/kdtrees.o -o /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB/kdtrees.cpython-39-powerpc64le-linux-gnu.so cd Doc && make make[2]: Entering directory '/<>/python-biopython-1.78+dfsg/Doc' sed "s/\@VERSION\@/1.78/g" version.in > version.sh chmod +x version.sh hevea -exec ./version.sh -exec xxdate.exe -fix Tutorial.tex Exclude comment 'comment' ./Tutorial/chapter_introduction.tex:91: Warning: Undefined citation: 'cock2009' ./Tutorial/chapter_introduction.tex:95: Warning: Undefined citation: 'chapman2000' ./Tutorial/chapter_introduction.tex:96: Warning: Undefined citation: 'hamelryck2003a' ./Tutorial/chapter_introduction.tex:97: Warning: Undefined citation: 'dehoon2004' ./Tutorial/chapter_introduction.tex:98: Warning: Undefined citation: 'pritchard2006' ./Tutorial/chapter_introduction.tex:99: Warning: Undefined citation: 'talevich2012' ./Tutorial/chapter_introduction.tex:100: Warning: Undefined citation: 'cock2010' ./Tutorial/chapter_introduction.tex:186: Warning: Undefined label: 'sec:seq-comparison' ./Tutorial/chapter_introduction.tex:192: Warning: Undefined label: 'sec:appendix-handles' ./Tutorial/chapter_quick_start.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:14: Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_quick_start.tex:14: Warning: Undefined label: 'chapter:advanced' ./Tutorial/chapter_quick_start.tex:19: Warning: Undefined label: 'chapter:seq_objects' ./Tutorial/chapter_quick_start.tex:45: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_quick_start.tex:65: Warning: Undefined label: 'sec:sequence-parsing' ./Tutorial/chapter_quick_start.tex:65: Warning: Undefined label: 'chapter:entrez' ./Tutorial/chapter_quick_start.tex:65: Warning: Undefined label: 'chapter:uniprot' ./Tutorial/chapter_quick_start.tex:65: Warning: Undefined label: 'sec:align_clustal' ./Tutorial/chapter_quick_start.tex:72: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_quick_start.tex:79: Warning: Undefined label: 'sec:connecting-with-biological-databases' ./Tutorial/chapter_quick_start.tex:145: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_quick_start.tex:145: Warning: Undefined label: 'chapter:align' ./Tutorial/chapter_quick_start.tex:150: Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_quick_start.tex:158: Warning: Undefined label: 'chapter:entrez' ./Tutorial/chapter_quick_start.tex:159: Warning: Undefined label: 'chapter:uniprot' ./Tutorial/chapter_quick_start.tex:169: Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_seq_objects.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined label: 'chapter:seq_annot' ./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_objects.tex:85: Warning: Undefined label: 'sec:mutable-seq' ./Tutorial/chapter_seq_objects.tex:154: Warning: Undefined label: 'sec:SeqRecord-format' ./Tutorial/chapter_seq_objects.tex:156: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_objects.tex:268: Warning: Undefined label: 'sec:SeqIO-reverse-complement' ./Tutorial/chapter_seq_objects.tex:343: Warning: Undefined label: 'sec:seq-module-functions' ./Tutorial/chapter_seq_objects.tex:457: Warning: Undefined label: 'sec:SeqIO-translate' ./Tutorial/chapter_seq_objects.tex:463: Warning: Undefined label: 'sec:seq-module-functions' ./Tutorial/chapter_seq_objects.tex:586: Warning: Undefined label: 'sec:seq-to-string' ./Tutorial/chapter_seq_objects.tex:655: Warning: Undefined label: 'sec:seq-to-string' ./Tutorial/chapter_seq_objects.tex:713: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_annot.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined label: 'chapter:seq_objects' ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_annot.tex:21: Warning: Undefined label: 'chapter:seq_objects' ./Tutorial/chapter_seq_annot.tex:21: Warning: Undefined label: 'chapter: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:seqio' ./Tutorial/chapter_seq_annot.tex:131: Warning: Undefined label: 'chapter:quick_start' ./Tutorial/chapter_seq_annot.tex:133: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_annot.tex:212: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_annot.tex:276: Warning: Undefined label: 'sec:seq_features' ./Tutorial/chapter_seq_annot.tex:279: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_annot.tex:285: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:293: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:525: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:627: Warning: Undefined label: 'sec:seq-comparison' ./Tutorial/chapter_seq_annot.tex:635: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:675: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_annot.tex:678: Warning: Undefined label: 'sec:Bio.SeqIO-and-StringIO' ./Tutorial/chapter_seq_annot.tex:809: Warning: Undefined label: 'sec:SeqRecord-format' ./Tutorial/chapter_seq_annot.tex:817: Warning: Undefined label: 'sec:FASTQ-slicing-off-primer' ./Tutorial/chapter_seq_annot.tex:818: Warning: Undefined label: 'sec:FASTQ-slicing-off-adaptor' ./Tutorial/chapter_seq_annot.tex:831: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seqio.tex:4: Warning: Undefined label: 'chapter:quick_start' ./Tutorial/chapter_seqio.tex:4: Warning: Undefined label: 'chapter:seq_annot' ./Tutorial/chapter_seqio.tex:13: Warning: Undefined label: 'chapter:seq_annot' ./Tutorial/chapter_seqio.tex:13: Warning: Undefined label: 'chapter:seq_objects' ./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:44: Warning: Undefined label: 'sec:sequence-parsing' ./Tutorial/chapter_seqio.tex:69: Warning: Undefined label: 'sec:sequence-parsing-plus-pylab' ./Tutorial/chapter_seqio.tex:151: Warning: Undefined label: 'chapter:seq_annot' ./Tutorial/chapter_seqio.tex:310: Warning: Undefined label: 'sec:writing-sequence-files' ./Tutorial/chapter_seqio.tex:330: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:333: Warning: Undefined label: 'sec:appendix-handles' ./Tutorial/chapter_seqio.tex:401: Warning: Undefined label: 'sec:SeqIO-index-bgzf' ./Tutorial/chapter_seqio.tex:404: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:416: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:416: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:417: Warning: Undefined label: 'sec:efetch' ./Tutorial/chapter_seqio.tex:507: Warning: Undefined label: 'chapter:entrez' ./Tutorial/chapter_seqio.tex:507: Warning: Undefined label: 'sec:entrez-guidelines' ./Tutorial/chapter_seqio.tex:510: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:510: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:510: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:512: Warning: Undefined label: 'chapter:uniprot' ./Tutorial/chapter_seqio.tex:548: Warning: Undefined label: 'sec:seqio_todict' ./Tutorial/chapter_seqio.tex:554: Warning: Undefined label: 'sec:SeqIO-index' ./Tutorial/chapter_seqio.tex:558: Warning: Undefined label: 'sec:SeqIO-index-db' ./Tutorial/chapter_seqio.tex:561: Warning: Undefined label: 'sec:SeqIO-indexing-discussion' ./Tutorial/chapter_seqio.tex:564: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:571: Warning: Undefined label: 'sec:SeqIO-index' ./Tutorial/chapter_seqio.tex:645: Warning: Undefined label: 'sec:fasta-parsing' ./Tutorial/chapter_seqio.tex:766: Warning: Undefined label: 'sec:fastq-indexing' ./Tutorial/chapter_seqio.tex:787: Warning: Undefined label: 'sec:seqio-todict-functionkey' ./Tutorial/chapter_seqio.tex:849: Warning: Undefined label: 'sec:SeqIO-sort' ./Tutorial/chapter_seqio.tex:931: Warning: Undefined label: 'sec:seqio-index-getraw' ./Tutorial/chapter_seqio.tex:1172: Warning: Undefined label: 'sec:seqio-index-getraw' ./Tutorial/chapter_seqio.tex:1216: Warning: Undefined label: 'sec:SeqIO-fastq-conversion' ./Tutorial/chapter_seqio.tex:1216: Warning: Undefined label: 'sec:SeqIO-fasta-qual-conversion' ./Tutorial/chapter_seqio.tex:1231: Warning: Undefined label: 'sec:seq-reverse-complement' ./Tutorial/chapter_seqio.tex:1241: Warning: Undefined label: 'sec:SeqRecord-reverse-complement' ./Tutorial/chapter_seqio.tex:1283: Warning: Undefined label: 'sec:SeqIO-translate' ./Tutorial/chapter_seqio.tex:1303: Warning: Undefined label: 'sec:SeqRecord-format' ./Tutorial/chapter_seqio.tex:1384: Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_align.tex:31: Warning: Undefined label: 'sec:appendix-handles' ./Tutorial/chapter_align.tex:35: Warning: Undefined label: 'sec:AlignIO-count-argument' ./Tutorial/chapter_align.tex:113: Warning: Undefined label: 'sec:alignment-format' ./Tutorial/chapter_align.tex:444: Warning: Undefined label: 'sec:SeqIO-conversion' ./Tutorial/chapter_align.tex:633: Warning: Undefined label: 'sec:SeqRecord-format' ./Tutorial/chapter_align.tex:813: Warning: Undefined label: 'sec:SeqRecord-addition' ./Tutorial/chapter_align.tex:892: Warning: Undefined label: 'sec:subs_mat_ex' ./Tutorial/chapter_align.tex:915: Warning: Undefined label: 'sec:pairwise' ./Tutorial/chapter_align.tex:919: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_align.tex:945: Warning: Undefined label: 'sec:emboss-needle-water' ./Tutorial/chapter_align.tex:953: Warning: '_' occurring outside math mode ./Tutorial/chapter_align.tex:1091: Warning: Undefined label: 'chapter:phylo' ./Tutorial/chapter_align.tex:1312: Warning: Undefined label: 'sec:appendix-handles' ./Tutorial/chapter_align.tex:1684: Warning: Undefined citation: 'durbin1998' ./Tutorial/chapter_align.tex:1697: Warning: Undefined label: 'sec:pairwise-aligner' ./Tutorial/chapter_align.tex:1770: Warning: Undefined citation: 'waterman1987' ./Tutorial/chapter_align.tex:1799: Warning: Undefined label: 'sec:pairwise-substitution-scores' ./Tutorial/chapter_align.tex:1799: Warning: Undefined label: 'sec:pairwise-affine-gapscores' ./Tutorial/chapter_align.tex:1799: Warning: Undefined label: 'sec:pairwise-general-gapscores' ./Tutorial/chapter_align.tex:1800: Warning: Undefined label: 'sec:pairwise-basic' ./Tutorial/chapter_align.tex:1803: Warning: Undefined label: 'sec:pairwise-affine-gapscores' ./Tutorial/chapter_align.tex:1804: Warning: Undefined label: 'sec:pairwise-general-gapscores' ./Tutorial/chapter_align.tex:1830: Warning: Undefined citation: 'altschul1990' ./Tutorial/chapter_align.tex:1830: Warning: Undefined label: 'sec:pairwise-affine-gapscores' ./Tutorial/chapter_align.tex:1858: Warning: Undefined citation: 'altschul1990' ./Tutorial/chapter_align.tex:1962: Warning: Undefined label: 'table:align-meta-attributes' ./Tutorial/chapter_align.tex:2052: Warning: Undefined label: 'sec:pairwise-examples' ./Tutorial/chapter_align.tex:2185: Warning: Undefined citation: 'kent2002' ./Tutorial/chapter_align.tex:2366: Warning: Undefined citation: 'schneider2005' ./Tutorial/chapter_align.tex:2366: Warning: Undefined label: 'sec:substitution_matrices' ./Tutorial/chapter_align.tex:2569: Warning: '_' occurring outside math mode ./Tutorial/chapter_align.tex:2919: Warning: Undefined citation: 'altschul1990' ./Tutorial/chapter_align.tex:2991: Warning: Undefined citation: 'henikoff1992' ./Tutorial/chapter_align.tex:2991: Warning: Undefined citation: 'dayhoff1978' ./Tutorial/chapter_align.tex:3015: Warning: Undefined citation: 'schneider2005' ./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: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:282: Warning: Undefined label: 'sec:running-www-blast' ./Tutorial/chapter_blast.tex:284: Warning: Undefined label: 'sec:running-local-blast' ./Tutorial/chapter_blast.tex:299: Warning: Undefined label: 'sec:appendix-handles' ./Tutorial/chapter_blast.tex:335: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_blast.tex:335: Warning: Undefined label: 'chapter:align' ./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:seq_annot' ./Tutorial/chapter_searchio.tex:1082: Warning: Undefined label: 'sec:SeqIO-index' ./Tutorial/chapter_entrez.tex:21: Warning: Undefined label: 'sec:entrez-specialized-parsers' ./Tutorial/chapter_entrez.tex:60: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:63: Warning: Undefined label: 'sec:BioSQL' ./Tutorial/chapter_entrez.tex:216: Warning: Undefined label: 'sec:efetch' ./Tutorial/chapter_entrez.tex:220: Warning: Undefined label: 'sec:entrez-einfo' ./Tutorial/chapter_entrez.tex:234: Warning: Undefined label: 'sec:efetch' ./Tutorial/chapter_entrez.tex:297: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:323: Warning: Undefined label: 'sec:SeqIO_GenBank_Online' ./Tutorial/chapter_entrez.tex:323: Warning: Undefined label: 'sec:efetch' ./Tutorial/chapter_entrez.tex:417: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_entrez.tex:479: Warning: Undefined label: 'sec:entrez-specialized-parsers' ./Tutorial/chapter_entrez.tex:481: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:562: Warning: Undefined label: 'sec:elink-citations' ./Tutorial/chapter_entrez.tex:568: Warning: Undefined label: 'sec:entrez_example_genbank' ./Tutorial/chapter_entrez.tex:777: Warning: Undefined label: 'sec:SeqIO_GenBank_Online' ./Tutorial/chapter_entrez.tex:777: Warning: Undefined label: 'sec:efetch' ./Tutorial/chapter_entrez.tex:897: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1058: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1061: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1065: Warning: Undefined label: 'sec:orchids' ./Tutorial/chapter_entrez.tex:1108: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1152: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1152: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1154: Warning: Undefined label: 'sec:orchids' ./Tutorial/chapter_entrez.tex:1206: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1241: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1248: Warning: Undefined label: 'sec:SeqIO_GenBank_Online' ./Tutorial/chapter_entrez.tex:1249: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1301: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_entrez.tex:1325: Warning: Undefined label: 'sec:entrez-guidelines' ./Tutorial/chapter_entrez.tex:1326: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1386: Warning: Undefined label: 'sec:entrez-search-fetch-genbank' ./Tutorial/chapter_entrez.tex:1417: Warning: Undefined label: 'sec:entrez_example_genbank' ./Tutorial/chapter_entrez.tex:1494: Warning: Undefined label: 'sec:entrez-and-medline' ./Tutorial/chapter_entrez.tex:1499: Warning: Undefined label: 'sec:elink' ./Tutorial/chapter_entrez.tex:1523: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_uniprot.tex:12: Warning: Undefined label: 'sec:SeqIO_ExPASy_and_SwissProt' ./Tutorial/chapter_uniprot.tex:37: Warning: Undefined label: 'sec:expasy_swissprot' ./Tutorial/chapter_uniprot.tex:45: Warning: Undefined label: 'sec:SeqIO_ExPASy_and_SwissProt' ./Tutorial/chapter_uniprot.tex:341: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:343: Warning: Undefined label: 'sec:orchids' ./Tutorial/chapter_pdb.tex:85: Warning: Undefined label: 'sec:problem_structures' ./Tutorial/chapter_pdb.tex:276: Warning: Undefined label: 'fig:smcra' ./Tutorial/chapter_pdb.tex:285: Warning: Undefined label: 'sec:problem_structures' ./Tutorial/chapter_pdb.tex:422: Warning: Undefined label: 'sec:hetero_problems' ./Tutorial/chapter_pdb.tex:467: Warning: Undefined label: 'sec:point_mutations' ./Tutorial/chapter_pdb.tex:484: Warning: Undefined label: 'sec:disordered_atoms' ./Tutorial/chapter_pdb.tex:593: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:607: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:611: Warning: Undefined label: 'fig:smcra' ./Tutorial/chapter_pdb.tex:647: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:658: Warning: Undefined label: 'fig:smcra' ./Tutorial/chapter_pdb.tex:684: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:970: Warning: Undefined label: 'table:ic-attribs' ./Tutorial/chapter_pdb.tex:1015: Warning: Undefined citation: 'golub1989' ./Tutorial/chapter_pdb.tex:1043: Warning: Undefined citation: 'hamelryck2005' ./Tutorial/chapter_pdb.tex:1078: Warning: Undefined label: 'table:DSSP-codes' ./Tutorial/chapter_pdb.tex:1118: Warning: Undefined label: 'sec:residue_depth' ./Tutorial/chapter_pdb.tex:1121: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:1169: Warning: Undefined citation: 'hamelryck2003a' ./Tutorial/chapter_pdb.tex:1183: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:1380: Warning: Undefined citation: 'hamelryck2003b' ./Tutorial/chapter_pdb.tex:1381: 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:711: Warning: Undefined label: 'sec:alignment-tools' ./Tutorial/chapter_phylo.tex:782: Warning: Undefined label: 'sec:PhyloXML' ./Tutorial/chapter_motifs.tex:8: Warning: Undefined label: 'sec:links' ./Tutorial/chapter_motifs.tex:164: Warning: Undefined citation: 'cornish1985' ./Tutorial/chapter_motifs.tex:165: Warning: Undefined citation: 'cavener1987' ./Tutorial/chapter_motifs.tex:541: Warning: Undefined citation: 'bailey1994' ./Tutorial/chapter_motifs.tex:687: Warning: Undefined citation: 'matys2003' ./Tutorial/chapter_motifs.tex:771: Warning: Undefined label: 'table:transfaccodes' ./Tutorial/chapter_cluster.tex:6: Warning: Undefined citation: 'dehoon2004' ./Tutorial/chapter_cluster.tex:30: Warning: Undefined citation: 'lecuyer1988' ./Tutorial/chapter_cluster.tex:30: Warning: Undefined citation: 'kachitvichyanukul1988' ./Tutorial/chapter_cluster.tex:154: Warning: Undefined citation: 'snedecor1989' ./Tutorial/chapter_cluster.tex:183: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:277: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:345: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:555: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:599: Warning: Undefined citation: 'kohonen1997' ./Tutorial/chapter_cluster.tex:599: Warning: Undefined citation: 'tamayo1999' ./Tutorial/chapter_cluster.tex:646: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:659: Warning: Undefined citation: 'yeung2001' ./Tutorial/chapter_cluster.tex:667: Warning: Undefined citation: 'golub1971' ./Tutorial/chapter_cluster.tex:800: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:803: Warning: Undefined label: 'sec:distancematrix' ./Tutorial/chapter_cluster.tex:821: Warning: Undefined label: 'sec:clustercentroids' ./Tutorial/chapter_cluster.tex:844: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:869: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:898: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:920: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:952: Warning: Undefined citation: 'hihara2001' ./Tutorial/chapter_learning.tex:40: Warning: Undefined label: 'eq:OP' ./Tutorial/chapter_learning.tex:40: Warning: Undefined label: 'eq:NOP' ./Tutorial/chapter_learning.tex:75: Warning: Undefined label: 'table:training' ./Tutorial/chapter_learning.tex:211: Warning: Undefined label: 'eq:OP' ./Tutorial/chapter_learning.tex:211: Warning: Undefined label: 'eq:NOP' ./Tutorial/chapter_learning.tex:273: Warning: Undefined label: 'eq:OP' ./Tutorial/chapter_learning.tex:273: Warning: Undefined label: 'eq:NOP' ./Tutorial/chapter_learning.tex:275: Warning: Undefined label: 'eq:OP' ./Tutorial/chapter_learning.tex:275: Warning: Undefined label: 'eq:NOP' ./Tutorial/chapter_learning.tex:285: Warning: Undefined label: 'sec:LogisticRegression' ./Tutorial/chapter_learning.tex:289: Warning: Undefined label: 'table:training' ./Tutorial/chapter_learning.tex:297: Warning: Undefined label: 'sec:LogisticRegressionTraining' ./Tutorial/chapter_graphics.tex:18: Warning: Undefined citation: 'pritchard2006' ./Tutorial/chapter_graphics.tex:28: Warning: Undefined citation: 'toth2006' ./Tutorial/chapter_graphics.tex:31: Warning: Undefined citation: 'vanderauwera2009' ./Tutorial/chapter_graphics.tex:36: Warning: Undefined label: 'chapter:seq_annot' ./Tutorial/chapter_graphics.tex:36: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:64: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:220: Warning: Undefined label: 'sec:seq_features' ./Tutorial/chapter_graphics.tex:268: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:268: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:326: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:326: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:345: Warning: Undefined label: 'sec:gd_nice_example' ./Tutorial/chapter_graphics.tex:352: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:409: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:409: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:485: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:485: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:488: Warning: Undefined label: 'sec:gd_top_down' ./Tutorial/chapter_graphics.tex:591: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:591: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:596: Warning: Undefined citation: 'proux2002' ./Tutorial/chapter_graphics.tex:605: Warning: Undefined label: 'sec:efetch' ./Tutorial/chapter_graphics.tex:608: Warning: Undefined label: 'sec:SeqRecord-slicing' ./Tutorial/chapter_graphics.tex:610: Warning: Undefined label: 'sec:SeqRecord-reverse-complement' ./Tutorial/chapter_graphics.tex:752: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:752: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:759: Warning: Undefined citation: 'proux2002' ./Tutorial/chapter_graphics.tex:1012: Warning: Undefined citation: 'jupe2012' ./Tutorial/chapter_phenotype.tex: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: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:199: Warning: Undefined label: 'sec:translation' ./Tutorial/chapter_cookbook.tex:204: Warning: Undefined label: 'sec:SeqIO-reverse-complement' ./Tutorial/chapter_cookbook.tex:336: Warning: Undefined label: 'sec:seqio-index-getraw' ./Tutorial/chapter_cookbook.tex:441: Warning: Undefined label: 'sec:low-level-fasta-fastq' ./Tutorial/chapter_cookbook.tex:455: Warning: Undefined label: 'sec:low-level-fasta-fastq' ./Tutorial/chapter_cookbook.tex:478: Warning: Undefined label: 'sec:SeqRecord-slicing' ./Tutorial/chapter_cookbook.tex:641: Warning: Undefined label: 'sec:SeqIO-conversion' ./Tutorial/chapter_cookbook.tex:644: Warning: Undefined citation: 'cock2010' ./Tutorial/chapter_cookbook.tex:800: Warning: Undefined label: 'sec:SeqIO-index' ./Tutorial/chapter_cookbook.tex:822: Warning: Undefined label: 'sec:SeqIO-index' ./Tutorial/chapter_cookbook.tex:824: Warning: Undefined label: 'sec:SeqIO-sort' ./Tutorial/chapter_cookbook.tex:838: Warning: Undefined label: 'sec:SeqIO-conversion' ./Tutorial/chapter_cookbook.tex:905: Warning: Undefined label: 'sec:translation' ./Tutorial/chapter_cookbook.tex:1021: Warning: Undefined label: 'sec:gd_nice_example' ./Tutorial/chapter_cookbook.tex:1038: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_cookbook.tex:1413: Warning: Undefined label: 'chapter:align' ./Tutorial/chapter_cookbook.tex:1416: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1420: Warning: Undefined label: 'chapter:align' ./Tutorial/chapter_cookbook.tex:1431: Warning: Undefined label: 'sec:consensus' ./Tutorial/chapter_cookbook.tex:1432: Warning: Undefined label: 'sec:pssm' ./Tutorial/chapter_cookbook.tex:1433: Warning: Undefined label: 'sec:getting_info_content' ./Tutorial/chapter_cookbook.tex:1434: Warning: Undefined label: 'sec:sub_matrix' ./Tutorial/chapter_cookbook.tex:1440: Warning: Undefined label: 'sec:summary_info' ./Tutorial/chapter_cookbook.tex:1533: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1533: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1560: Warning: Undefined label: 'sec:summary_info' ./Tutorial/chapter_cookbook.tex:1612: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1621: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1621: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1635: Warning: Undefined label: 'sec:align_clustal' ./Tutorial/chapter_cookbook.tex:1741: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_testing.tex:55: Warning: Undefined label: 'sec:doctest' ./Tutorial/chapter_testing.tex:282: Warning: Undefined label: 'sec:doctest' ./Tutorial/chapter_advanced.tex:36: Warning: Undefined label: 'sec:substitution_matrices' ./Tutorial/chapter_advanced.tex:162: Warning: Undefined label: 'sec:freq_table' ./Tutorial/chapter_advanced.tex:222: Warning: '_' occurring outside math mode ./Tutorial/chapter_contributing.tex:32: Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_contributing.tex:38: Warning: '_' occurring outside math mode ./Tutorial/chapter_contributing.tex:85: Warning: Undefined label: 'chapter:testing' ./Tutorial/chapter_contributing.tex:101: Warning: Undefined label: 'chapter:testing' ./Tutorial/chapter_appendix.tex:91: Warning: Undefined label: 'sec:SeqIO_compressed' HeVeA Warning: Label(s) may have changed. Rerun me to get cross-references right. Run, run, again... 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./Tutorial/chapter_align.tex:1997: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1997: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1997: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1997: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1998: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1998: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1998: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1998: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1998: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1998: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1999: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1999: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1999: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1999: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1999: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1999: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2000: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2000: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2000: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2000: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2000: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2000: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2001: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2001: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2001: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2001: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2001: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2001: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2002: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2002: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2002: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2002: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2002: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2002: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2003: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2003: Warning: Undefined 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Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2005: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2005: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2005: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2005: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2006: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2006: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2006: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2006: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2006: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2006: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2008: Warning: overfull line in array : array too wide ./Tutorial/chapter_align.tex:2008: Warning: line too long ./Tutorial/chapter_align.tex:2008: Warning: line too long ./Tutorial/chapter_align.tex:2008: Warning: line too long ./Tutorial/chapter_align.tex:2052: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2052: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2052: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2052: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2052: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2052: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2052: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2052: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2052: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2052: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2052: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2052: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2052: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2052: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2054: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2054: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2056: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2056: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2056: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2056: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2056: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2056: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2056: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2056: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2090: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2090: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2128: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2128: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2128: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2128: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2128: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2128: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2132: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2132: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2132: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2132: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2133: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2133: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2143: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2143: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2143: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2143: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2174: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2174: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2190: Warning: line too long ./Tutorial/chapter_align.tex:2193: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2193: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2247: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2247: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2274: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2274: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2274: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2274: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2298: Warning: line too long ./Tutorial/chapter_align.tex:2299: Warning: line too long ./Tutorial/chapter_align.tex:2300: Warning: line too long ./Tutorial/chapter_align.tex:2330: Warning: line too long ./Tutorial/chapter_align.tex:2331: Warning: line too long ./Tutorial/chapter_align.tex:2332: Warning: line too long ./Tutorial/chapter_align.tex:2339: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2339: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2339: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2339: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2362: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2362: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2362: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2362: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2362: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2362: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2399: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2399: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2399: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2399: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2414: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2414: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2414: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2414: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2414: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2414: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2414: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2414: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2414: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2414: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2414: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2414: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2504: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2504: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2569: Warning: '_' occurring outside math mode ./Tutorial/chapter_align.tex:2571: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2571: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2571: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2571: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2571: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2571: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2571: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2571: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2571: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2571: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2575: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2575: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2588: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2588: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2595: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2595: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2612: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2612: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2630: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2630: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2630: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2630: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2644: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2644: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2667: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2667: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2686: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2686: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2707: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2707: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2709: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2709: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2709: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2709: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2709: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2709: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2744: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2744: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2744: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2744: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2744: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2744: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2744: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2744: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2756: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2756: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2756: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2756: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2854: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2854: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2854: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2854: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2869: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2869: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2869: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2869: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2869: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2869: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2869: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2869: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2900: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2900: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2919: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2919: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2939: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2939: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2952: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2952: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2952: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2952: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2987: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2987: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2991: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2991: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2991: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2991: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2991: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2991: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3006: 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./Tutorial/chapter_cluster.tex:595: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:595: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:595: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:595: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:595: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:595: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:606: 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:615: Warning: Cannot output that numerical entity: U+00B7 ./Tutorial/chapter_cluster.tex:622: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:622: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:624: Warning: 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have changed. Rerun me to get cross-references right. Run, run, again... Exclude comment 'comment' ./Tutorial.tex:73: Warning: tt_mode is an empty style ./Tutorial.haux:545: Giving up command: \@hevea@cbrace ./Tutorial.tex:73: Giving up command: \input ./Tutorial.tex:73: Warning: Failure while reading .haux ./Tutorial.tex:100: Warning: Application of '\'' on 'n' failed ./Tutorial/chapter_introduction.tex:82: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:82: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:91: Warning: Undefined citation: 'cock2009' ./Tutorial/chapter_introduction.tex:95: Warning: Undefined citation: 'chapman2000' ./Tutorial/chapter_introduction.tex:96: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:96: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_introduction.tex:96: Warning: Undefined citation: 'hamelryck2003a' ./Tutorial/chapter_introduction.tex:97: Warning: Undefined block in text mode: 'CODE' [] 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./Tutorial/chapter_seq_annot.tex:531: Warning: line too long ./Tutorial/chapter_seq_annot.tex:545: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:545: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:545: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:545: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:554: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:554: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:567: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:567: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:569: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:569: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:574: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:574: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:593: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:593: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:593: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:593: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:594: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:594: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:595: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:595: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:595: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:595: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:604: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:604: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:604: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:604: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:627: Warning: Undefined label: 'sec:seq-comparison' ./Tutorial/chapter_seq_annot.tex:631: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:631: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:633: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:633: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:633: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:633: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:633: 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'CODE' [] ./Tutorial/chapter_seq_annot.tex:635: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:637: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:637: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:637: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:637: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:643: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:643: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:643: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:643: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:645: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:645: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:674: 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'CODE' [] ./Tutorial/chapter_seq_annot.tex:683: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:683: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:695: Warning: line too long ./Tutorial/chapter_seq_annot.tex:702: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:702: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:702: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:702: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:710: Warning: line too long ./Tutorial/chapter_seq_annot.tex:731: Warning: line too long ./Tutorial/chapter_seq_annot.tex:731: Warning: line too long ./Tutorial/chapter_seq_annot.tex:735: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:735: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:742: Warning: 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./Tutorial/chapter_seqio.tex:411: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:411: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:416: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:416: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:417: Warning: Undefined label: 'sec:efetch' ./Tutorial/chapter_seqio.tex:424: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:424: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:451: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:451: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:474: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:474: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:507: Warning: Undefined label: 'chapter:entrez' ./Tutorial/chapter_seqio.tex:507: 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./Tutorial/chapter_seqio.tex:1384: Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_align.tex:1: Warning: line too long ./Tutorial/chapter_align.tex:1: Warning: line too long ./Tutorial/chapter_align.tex:1: Warning: line too long ./Tutorial/chapter_align.tex:1: Warning: line too long ./Tutorial/chapter_align.tex:1: Warning: line too long ./Tutorial/chapter_align.tex:1: Warning: line too long ./Tutorial/chapter_align.tex:8: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:8: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:11: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:11: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:12: Warning: Undefined block in text mode: 'CODE' [] 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'CODE' [] ./Tutorial/chapter_align.tex:1682: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1682: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1684: Warning: Undefined citation: 'durbin1998' ./Tutorial/chapter_align.tex:1689: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1689: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1696: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1696: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1696: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1696: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1697: Warning: Undefined label: 'sec:pairwise-aligner' ./Tutorial/chapter_align.tex:1715: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1715: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1727: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1727: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1727: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1727: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1746: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1746: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1746: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1746: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1748: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1748: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1748: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1748: Warning: Undefined block in 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./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1800: Warning: Undefined label: 'sec:pairwise-basic' ./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1803: Warning: Undefined label: 'sec:pairwise-affine-gapscores' ./Tutorial/chapter_align.tex:1804: Warning: Undefined label: 'sec:pairwise-general-gapscores' ./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1814: Warning: Undefined block 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'CODE' [] ./Tutorial/chapter_align.tex:1919: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1919: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1919: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1919: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1920: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1920: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1920: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1920: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1921: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1921: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1921: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1921: Warning: Undefined block in 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'CODE' [] ./Tutorial/chapter_align.tex:1987: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1988: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1988: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1989: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1989: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1989: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1989: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1989: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1989: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1990: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1990: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1990: Warning: Undefined block in 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'CODE' [] ./Tutorial/chapter_align.tex:2001: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2001: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2002: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2002: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2002: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2002: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2002: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2002: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2003: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2003: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2003: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2003: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2003: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2003: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2004: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2004: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2004: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2004: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2004: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2004: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2005: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2005: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2005: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2005: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2005: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2005: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2006: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2006: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2006: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2006: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2006: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2006: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2008: Warning: overfull line in array : array too wide ./Tutorial/chapter_align.tex:2008: Warning: line too long ./Tutorial/chapter_align.tex:2008: Warning: line too long ./Tutorial/chapter_align.tex:2008: Warning: line too long ./Tutorial/chapter_align.tex:2052: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2052: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2052: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2052: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2052: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2052: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2052: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2052: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2052: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2052: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2052: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2052: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2052: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2052: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2052: Warning: Undefined label: 'sec:pairwise-examples' ./Tutorial/chapter_align.tex:2054: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2054: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2056: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2056: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2056: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2056: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2056: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2056: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2056: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2056: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2090: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2090: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2128: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2128: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2128: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2128: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2128: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2128: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2132: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2132: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2132: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2132: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2133: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2133: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2143: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2143: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2143: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2143: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2174: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2174: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2185: Warning: Undefined citation: 'kent2002' ./Tutorial/chapter_align.tex:2190: Warning: line too long ./Tutorial/chapter_align.tex:2193: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2193: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2247: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2247: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2274: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2274: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2274: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2274: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2298: Warning: line too long ./Tutorial/chapter_align.tex:2299: Warning: line too long ./Tutorial/chapter_align.tex:2300: Warning: line too long ./Tutorial/chapter_align.tex:2330: Warning: line too long ./Tutorial/chapter_align.tex:2331: Warning: line too long ./Tutorial/chapter_align.tex:2332: Warning: line too long ./Tutorial/chapter_align.tex:2339: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2339: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2339: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2339: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2362: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2362: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2362: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2362: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2362: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2362: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined citation: 'schneider2005' ./Tutorial/chapter_align.tex:2366: Warning: Undefined label: 'sec:substitution_matrices' ./Tutorial/chapter_align.tex:2399: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2399: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2399: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2399: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2414: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2414: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2414: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2414: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2414: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2414: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2414: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2414: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2414: Warning: 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'CODE' [] ./Tutorial/chapter_align.tex:2744: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2744: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2744: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2756: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2756: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2756: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2756: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2854: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2854: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2854: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2854: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2869: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2869: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2869: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2869: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2869: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2869: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2869: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2869: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2900: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2900: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2919: Warning: Undefined citation: 'altschul1990' ./Tutorial/chapter_align.tex:2919: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2919: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2939: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2939: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2952: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2952: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2952: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2952: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2987: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2987: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2991: Warning: Undefined citation: 'henikoff1992' ./Tutorial/chapter_align.tex:2991: Warning: Undefined citation: 'dayhoff1978' ./Tutorial/chapter_align.tex:2991: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2991: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2991: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2991: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2991: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2991: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3006: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3006: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3015: Warning: Undefined citation: 'schneider2005' ./Tutorial/chapter_blast.tex:1: Warning: line too long ./Tutorial/chapter_blast.tex:1: Warning: line too long ./Tutorial/chapter_blast.tex:18: Warning: Undefined label: 'chapter:searchio' ./Tutorial/chapter_blast.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:20: Warning: 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in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:50: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:53: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:53: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:54: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:54: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:55: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:55: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:56: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:56: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:56: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:56: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:56: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:56: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:56: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:56: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:57: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:57: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:58: Warning: Undefined label: 'sec:parsing-blast' ./Tutorial/chapter_blast.tex:59: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:59: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:95: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:95: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:107: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:107: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:118: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:118: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:119: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_blast.tex:121: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:121: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:124: Warning: Undefined label: 'sec:parsing-blast' ./Tutorial/chapter_blast.tex:132: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:132: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:133: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:133: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:143: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:143: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:145: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:145: Warning: Undefined block in text mode: 'CODE' [] ./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:212: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:212: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:231: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:231: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:233: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:233: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:235: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:235: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:236: Warning: Undefined label: 'sec:parsing-blast' ./Tutorial/chapter_blast.tex:243: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:243: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:254: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:254: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:254: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:254: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:255: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:255: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:268: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:268: Warning: Undefined block in text mode: 'CODE' [] ./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:298: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:298: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:298: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:298: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:299: Warning: Undefined label: 'sec:appendix-handles' ./Tutorial/chapter_blast.tex:302: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:302: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:311: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:311: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:334: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:334: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:334: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:334: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:335: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_blast.tex:335: Warning: Undefined label: 'chapter:align' ./Tutorial/chapter_blast.tex:336: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:336: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:336: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:336: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:337: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:337: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:337: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:337: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:339: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:339: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:339: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:339: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:343: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:343: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:364: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:364: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:382: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:382: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:433: Warning: line too long ./Tutorial/chapter_blast.tex:435: Warning: line too long ./Tutorial/chapter_blast.tex:443: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:443: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:443: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:443: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:443: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:443: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:443: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:443: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:445: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:445: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:445: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:445: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:445: Warning: Undefined label: 'fig:blastrecord' ./Tutorial/chapter_blast.tex:449: Warning: Image in text ./Tutorial/chapter_blast.tex:461: Warning: Undefined label: 'fig:psiblastrecord' ./Tutorial/chapter_blast.tex:465: Warning: Image in text ./Tutorial/chapter_blast.tex:481: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:481: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:481: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:481: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:482: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:482: 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block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:18: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:21: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:21: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:27: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:27: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:29: Warning: '_' occurring outside math mode ./Tutorial/chapter_searchio.tex:31: Warning: '_' occurring outside math mode ./Tutorial/chapter_searchio.tex:32: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:32: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:40: Warning: 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./Tutorial/chapter_searchio.tex:72: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:72: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:77: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:77: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:78: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:78: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:78: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:78: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:79: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:79: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:79: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:79: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:80: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:80: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:81: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:81: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:82: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:82: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:83: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:83: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:83: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:83: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:84: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:84: Warning: 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./Tutorial/chapter_entrez.tex:1061: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1065: Warning: Undefined label: 'sec:orchids' ./Tutorial/chapter_entrez.tex:1078: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1078: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1098: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1098: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1108: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1110: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1110: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1152: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1152: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1154: Warning: Undefined label: 'sec:orchids' ./Tutorial/chapter_entrez.tex:1169: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1169: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1180: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1180: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1191: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1191: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1192: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1192: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1204: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1204: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1206: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1241: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1248: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1248: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1248: Warning: Undefined label: 'sec:SeqIO_GenBank_Online' ./Tutorial/chapter_entrez.tex:1249: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1301: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1301: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1301: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1301: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1301: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1301: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1301: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_entrez.tex:1325: Warning: 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./Tutorial/chapter_pdb.tex:772: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:772: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_pdb.tex:970: Warning: Undefined label: 'table:ic-attribs' ./Tutorial/chapter_pdb.tex:992: Warning: overfull line in array : array too wide ./Tutorial/chapter_pdb.tex:992: Warning: line too long ./Tutorial/chapter_pdb.tex:992: Warning: line too long ./Tutorial/chapter_pdb.tex:992: Warning: line too long ./Tutorial/chapter_pdb.tex:992: Warning: line too long ./Tutorial/chapter_pdb.tex:992: Warning: line too long ./Tutorial/chapter_pdb.tex:992: Warning: line too long ./Tutorial/chapter_pdb.tex:992: Warning: line too long ./Tutorial/chapter_pdb.tex:992: Warning: line too long ./Tutorial/chapter_pdb.tex:1015: Warning: Undefined citation: 'golub1989' ./Tutorial/chapter_pdb.tex:1043: Warning: Undefined citation: 'hamelryck2005' ./Tutorial/chapter_pdb.tex:1078: Warning: Undefined label: 'table:DSSP-codes' ./Tutorial/chapter_pdb.tex:1118: Warning: Undefined label: 'sec:residue_depth' ./Tutorial/chapter_pdb.tex:1121: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:1169: Warning: Undefined citation: 'hamelryck2003a' ./Tutorial/chapter_pdb.tex:1183: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:1380: Warning: Undefined citation: 'hamelryck2003b' ./Tutorial/chapter_pdb.tex:1381: Warning: Undefined citation: 'majumdar2005' ./Tutorial/chapter_popgen.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_popgen.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_popgen.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_popgen.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:9: Warning: Undefined citation: 'talevich2012' ./Tutorial/chapter_phylo.tex:34: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phylo.tex:34: Warning: 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./Tutorial/chapter_cluster.tex:545: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:545: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:545: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:545: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:545: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:545: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:545: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:545: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:549: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:549: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:550: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:550: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:551: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:551: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:552: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:552: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:554: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:554: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:554: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:554: Warning: 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./Tutorial/chapter_cluster.tex:582: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:582: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:583: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:583: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:586: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:586: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:587: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:587: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:588: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:588: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:593: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:593: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:593: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:593: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:593: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:593: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:593: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:593: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:595: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:595: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:595: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:595: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:595: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:595: Warning: 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./Tutorial/chapter_cluster.tex:631: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:631: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:633: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:633: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:633: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:633: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:634: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:634: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:634: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:634: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:634: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:634: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:634: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:634: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:636: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:636: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:636: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:636: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:637: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:637: Warning: 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./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:641: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:641: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:641: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:641: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:642: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:642: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:643: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:643: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:643: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:643: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:645: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:645: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:645: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:645: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:646: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:649: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:649: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:651: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:651: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:653: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:653: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:654: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:654: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:654: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:654: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:654: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:654: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:654: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:654: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:654: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:654: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:654: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:654: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:659: Warning: Undefined citation: 'yeung2001' ./Tutorial/chapter_cluster.tex:667: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:667: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:667: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:667: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:667: Warning: Undefined citation: 'golub1971' ./Tutorial/chapter_cluster.tex:667: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:667: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:669: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:669: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:674: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:674: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:676: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:676: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:677: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:677: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:678: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:678: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:679: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:679: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:680: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:680: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:682: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:682: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:685: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:685: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:685: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:685: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:689: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:689: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:691: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:691: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:691: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:691: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:710: Warning: line too long ./Tutorial/chapter_cluster.tex:712: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:712: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:714: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:714: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:714: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:714: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:747: Warning: overfull line in array : array too wide ./Tutorial/chapter_cluster.tex:747: Warning: line too long ./Tutorial/chapter_cluster.tex:747: Warning: line too long ./Tutorial/chapter_cluster.tex:753: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:753: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:756: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:756: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:759: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:759: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:760: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:760: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:760: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:760: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:760: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:760: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:760: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:760: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:760: Warning: Undefined block in 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./Tutorial/chapter_graphics.tex:212: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:212: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:212: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:212: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:219: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:219: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:219: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:219: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:220: Warning: Undefined label: 'sec:seq_features' ./Tutorial/chapter_graphics.tex:221: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:221: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:223: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:223: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:268: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:268: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:271: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:271: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:277: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:277: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:279: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:279: Warning: 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./Tutorial/chapter_graphics.tex:485: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:485: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:488: Warning: Undefined label: 'sec:gd_top_down' ./Tutorial/chapter_graphics.tex:564: Warning: Image in text ./Tutorial/chapter_graphics.tex:564: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:564: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:566: Warning: Image in text ./Tutorial/chapter_graphics.tex:566: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:566: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:591: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:591: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:596: Warning: Undefined citation: 'proux2002' ./Tutorial/chapter_graphics.tex:599: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:599: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:600: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:600: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:601: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:601: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:605: Warning: Undefined label: 'sec:efetch' ./Tutorial/chapter_graphics.tex:608: Warning: Undefined label: 'sec:SeqRecord-slicing' ./Tutorial/chapter_graphics.tex:610: Warning: Undefined label: 'sec:SeqRecord-reverse-complement' ./Tutorial/chapter_graphics.tex:728: Warning: Image in text ./Tutorial/chapter_graphics.tex:728: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:728: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:752: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:752: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:759: Warning: Undefined citation: 'proux2002' ./Tutorial/chapter_graphics.tex:841: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:841: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:843: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:843: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:843: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:843: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:843: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:873: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:873: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:874: Warning: Undefined block in text mode: 'CODE' [] 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./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:923: Warning: Image in text ./Tutorial/chapter_graphics.tex:923: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:923: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:953: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:953: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:954: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:954: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:1004: Warning: 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[]\OT1/cmr/m/n/10 is also much quicker than mul-ti-ple calls to the [][]\OT1/cm tt/m/n/10 SeqRecord.format(...) (./_minted-Tutorial/2F337ECD1F936D416FF9C5C6F41A02D767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/3337CD054623BAC21B6021E996EE0DFD14FA033DCB1376922271CBD58A8 A4A36.pygtex) Overfull \hbox (21.32593pt too wide) in paragraph at lines 1365--1369 []\OT1/cmr/m/n/10 Likewise, when pars-ing FASTQ files, in-ter-nally [][]\OT1/cm tt/m/n/10 Bio.SeqIO.parse() []\OT1/cmr/m/n/10 calls the low-level [][]\OT1/cmtt /m/n/10 FastqGeneralIterator (./_minted-Tutorial/D3AF6542680CA390CDA8C8DF87C693D367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [60]) LaTeX Warning: Reference `chapter:cookbook' on page 61 undefined on input line 1384. (./_minted-Tutorial/D749A84299CF58E876E9A899069830DB14FA033DCB1376922271CBD58A8 A4A36.pygtex)) [61] (./Tutorial/chapter_align.tex Chapter 6. LaTeX Warning: Reference `sec:appendix-handles' on page 62 undefined on input l ine 31. 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There-fore the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write() LaTeX Warning: Reference `sec:SeqIO-conversion' on page 70 undefined on input l ine 444. 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LaTeX Warning: Float too large for page by 32.27644pt on input line 474. ) [117] [118 <./images/BlastRecord.png>] [119 <./images/PSIBlastRecord.png>] (./Tutorial/chapter_searchio.tex Chapter 8. (./_minted-Tutorial/6D0EADF658E662CBA394834EFAC7346E0C640781732628151051B15D85C 9070A.pygtex) [120] Overfull \hbox (2.9019pt too wide) in paragraph at lines 85--93 [][][]\OT1/cmtt/m/n/10 HSPFragment[]\OT1/cmr/m/n/10 , to rep-re-sent a sin-gle con-tigu-ous align-ment be-tween query and hit se-quences. [][]\OT1/cmtt/m/n/10 HSPFragment Overfull \hbox (8.43927pt too wide) in paragraph at lines 105--107 [][][]\OT1/cmtt/m/n/10 parse []\OT1/cmr/m/n/10 is used for search out-put files with mul-ti-ple queries and re-turns a gen-er-a-tor that yields [][]\OT1/cmtt/ m/n/10 QueryResult (./_minted-Tutorial/0EF47CD31A1F702FF10BD5C95E6D18FC67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [121]) (./_minted-Tutorial/BCDD1F95C8585B3C70DE9C1280B5195567B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [122]) (./_minted-Tutorial/5218313E7181C19A936D3F4347E1930A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/7BE69614D007F3BE3249A547A9661D0767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/40227DD719AAD22E8DC2923BF43CE32767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [123]) (./_minted-Tutorial/DC6D0E585B2AACAC1C88A760863B4E4E67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/130BC5013C07805E69A888444A0B34DB67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/CA24D00985B075C56E7C71A246E439FF67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/DE8A481953AA0F7BD7A99C0E281AD1A067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/E7AA701BE1D007CE77D402E8CBFC777A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/906546E8B6F7831A0E7C5FC93AA56A0367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [124] (./_minted-Tutorial/0E8B9F4E4323CB258CA049D41E4AB7F767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/DAA6FD197F3F78FDFB781210387FEC2667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [125]) (./_minted-Tutorial/67A62206561049F4B7E307FD79F028C967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/5E1CC554EC31697163DDD9D33E32A45667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [126]) (./_minted-Tutorial/0A806FC81D8F7F64321B4A6911027F0C67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [127] (./_minted-Tutorial/DC76D831C6E940E11ED2C9452F770E0C67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/A2EA3A12F7596A64ECEE374A9C53499A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/3A61EC24A4603554A3865574A6B7378067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [128] (./_minted-Tutorial/4D85AB21D9819B066A1C948098FDB54B67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/DAAFD2AAF126ED8D7284764B561B5E2B67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/4B4824DE2ED3215F02082987EE57357767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/4D9A79F8BB08FCA20BAEA3DFAAA08BA467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/62792AA2C0390B83FD6A91F3B267312A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [129]) (./_minted-Tutorial/CE618F26D70602D511E57E53CD88044467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/DE23F71CD74CF7717D38AD01C1E1C78767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) LaTeX Warning: Reference `chapter:seq_annot' on page 130 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 (./_minted-Tutorial/338C616C7128C3DB7FFD516F5C2BDA1267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/64A5027CB01EBC16D0BBBCFA493BDAE167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/31F43A46088F6D2E63B39857A353690967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/B35C581DC0102E618595FCC0BE2AFE9867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [130]) (./_minted-Tutorial/23A338D38E31EFFAE0C56C5A5AAB567A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/F1953B67CE735DCB6EDDECF134C333B967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/69130C6EA441D4D1DEB35E75101C9AB967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [131]) (./_minted-Tutorial/688EDDC69F177DE7868A4B0C32B1499267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/E295C926B8D61E45F6C5FA1C0767BFD467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [132] (./_minted-Tutorial/4CFB05EC7DD8FA77EFE275E81B5A1B9767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/B41343A9090DC4C41F9EC69AB6DEDE1B67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [133] (./_minted-Tutorial/7A63CB5E786CCE052981F7DD10653DA967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) 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. 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(./_minted-Tutorial/3C3B5BB472E9A4A7B3F5BFA41CA60C7867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) Overfull \hbox (24.29903pt too wide) in paragraph at lines 362--363 []\OT1/cmr/m/n/10 If the ac-ces-sion num-ber you pro-vided to [][]\OT1/cmtt/m/n /10 ExPASy.get_sprot_raw []\OT1/cmr/m/n/10 does not ex-ist, then [][]\OT1/cmtt/ m/n/10 SwissProt.read(handle) (./_minted-Tutorial/483E7285F7FA2A76D28505EE0DE792D467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [171]) (./_minted-Tutorial/950511DA0658C1A2824DF92F06F34BE867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/6A833CD3DDDD6A4CCF169D082C63D87D67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) Overfull \hbox (65.93893pt too wide) in paragraph at lines 405--406 []\OT1/cmr/m/n/10 The same func-tion can be used to re-trieve a Prosite doc-u-m en-ta-tion record and parse it into a [][]\OT1/cmtt/m/n/10 Bio.ExPASy.Prodoc.Re cord (./_minted-Tutorial/DF2DA17EFC0F6336210C74066809B75367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/9457A436D281E066D350873A88476E5967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [172]) (./_minted-Tutorial/5C1399E579A6AA8D432E509AE441C2AE67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/7528F52197E46B376DB12FB34672D7A80C640781732628151051B15D85C 9070A.pygtex) (./_minted-Tutorial/AB8625F199818648FAC2C5737C2D032067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/C8BC3187BF8F96BDF009A2CA8A95A3C367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/4323DBBD15E176599A70095217F377E767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [173]) (./_minted-Tutorial/0B895A7CD7770AD5152A902E24E8616967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex)) [174] (./Tutorial/chapter_pdb.tex Chapter 11. 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[204] Overfull \hbox (19.85507pt too wide) in paragraph at lines 438--445 \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"}) [205 <./images/phylo-draw-example.png>] Overfull \hbox (13.48741pt too wide) in paragraph at lines 493--496 []\OT1/cmr/m/n/10 Find each clade con-tain-ing a match-ing el-e-ment. 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LaTeX Warning: Citation `dehoon2004' on page 238 undefined on input line 6. LaTeX Warning: Citation `lecuyer1988' on page 238 undefined on input line 30. LaTeX Warning: Citation `kachitvichyanukul1988' on page 238 undefined on input line 30. [238] [239] [240] LaTeX Warning: Citation `snedecor1989' on page 241 undefined on input line 154. [241] (./_minted-Tutorial/C7B59059E3AE6CDE790EFE6EB0ED414067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) LaTeX Warning: Reference `sec:distancefunctions' on page 242 undefined on input line 183. 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(./_minted-Tutorial/A2465D4E8908256A31684D5DDE7DA11114FA033DCB1376922271CBD58A8 A4A36.pygtex [286 <./images/three_track_simple.png>]) (./_minted-Tutorial/347EB36A3001532221DDF6C29AA04AFB14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/F46F39DD7A8EC7B20CD42ACF6EFD184014FA033DCB1376922271CBD58A8 A4A36.pygtex [287]) (./_minted-Tutorial/2CF2D2FC7E96B3F426F22452724A4C2814FA033DCB1376922271CBD58A8 A4A36.pygtex) Overfull \hbox (2.65141pt too wide) in paragraph at lines 873--879 []\OT1/cmr/m/n/10 There are sev-eral im-por-tant pieces to this code. First the [][]\OT1/cmtt/m/n/10 GenomeDiagram []\OT1/cmr/m/n/10 ob-ject has a [][]\OT1/cm tt/m/n/10 cross_track_links Excluding 'htmlonly' comment. LaTeX Warning: Reference `fig:three_track_cl' on page 288 undefined on input li ne 894. LaTeX Warning: Reference `sec:gd_cross_links' on page 288 undefined on input li ne 901. LaTeX Warning: Reference `sec:gd_cross_links' on page 288 undefined on input li ne 901. Excluding 'htmlonly' comment. 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How-ever, for large FASTQ files it woul d be faster the low-level [][]\OT1/cmtt/m/n/10 FastqGeneralIterator (./_minted-Tutorial/AB16E58608A2F17CC79E69295572088714FA033DCB1376922271CBD58A8 A4A36.pygtex) Overfull \hbox (4.57849pt too wide) in paragraph at lines 473--475 \OT1/cmr/m/n/10 That should find $13819$ reads from \OT1/cmtt/m/n/10 SRR014849. fastq \OT1/cmr/m/n/10 and save them to a new FASTQ file, \OT1/cmtt/m/n/10 with[ ]primer.fastq\OT1/cmr/m/n/10 . LaTeX Warning: Reference `sec:SeqRecord-slicing' on page 310 undefined on input line 478. 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(./_minted-Tutorial/06CAA397021B5D0CD904B7CF0209DCA314FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/16711B0A63F93BBACAF3C86CFFB7BEFA0C640781732628151051B15D85C 9070A.pygtex) (./_minted-Tutorial/96EC77291C119EF69670ACDB1C35CE210C640781732628151051B15D85C 9070A.pygtex [326]) (./_minted-Tutorial/6C14F4F0692168BA7165351C706B643D14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/E686FC2D122CF1560FAF4512CD53777F14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/E09A8EBF1B7CB9F831FC2D9DA481453514FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/E598995EF885D7803642E8685DCB8F900C640781732628151051B15D85C 9070A.pygtex) Overfull \hbox (49.0755pt too wide) in paragraph at lines 1523--1524 []\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 . 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For ex-am-ple, [][]\OT1/cmtt/m/n/10 expec ted_frequencies[^^MD^^M, ^^ME^^M] (./_minted-Tutorial/63599FE26E47E2B5739BC250C642AA5067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [330]) (./_minted-Tutorial/618B9F1B5BFA1CE93B03A47D26F6F6E367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) LaTeX Warning: Reference `chapter:seqio' on page 331 undefined on input line 17 41. ) [331] (./Tutorial/chapter_testing.tex Chapter 21. (./_minted-Tutorial/867AD481B37AFD4F1A17FC0F2F42FCAE6EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/E8078015A2C53794A733DDC875BD06216EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/754EBE4BCCE307413E74F18728530D046EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/E40D6903CCE8EA230C75C80B7C2D90736EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) LaTeX Warning: Reference `sec:doctest' on page 332 undefined on input line 55. 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(./_minted-Tutorial/415024C641C8DA7A09117B3DFE240C7867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/487DCC9F44A2539C9B32C0122AEF406567B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/5098CD053449CEC3C9C30C90A007A36467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [58] (./_minted-Tutorial/EEEF4ABAD66CE989F67C9E27EEDE95CC67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/6209F8400B12665DC9E51BC20774DF7014FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/C4099CB0613585FCCD5EA7D8198704CE67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) Overfull \hbox (9.93459pt too wide) in paragraph at lines 831--836 \OT1/cmr/m/n/10 FTP site ([][]$\OT1/cmtt/m/n/10 ftp : / / ftp . uniprot . org / pub / databases / uniprot / current _ release / knowledgebase / complete / (./_minted-Tutorial/D52DA4EEEEE2BF0FBE89EE253714929D67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [59]) Overfull \hbox (4.48064pt too wide) in paragraph at lines 874--877 []\OT1/cmr/m/n/10 As of Gen-Bank re-lease $210$, there are $38$ files mak-ing u p the vi-ral se-quences, \OT1/cmtt/m/n/10 gbvrl1.seq\OT1/cmr/m/n/10 , ..., \OT1 /cmtt/m/n/10 gbvrl38.seq\OT1/cmr/m/n/10 , (./_minted-Tutorial/D41A88D88AB398F0C3B719A5C7D017C16EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/B4D970E8C81930851D8639D77EC3E4106EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/7C4E0944FB13EC4E75DD6FC64900395A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [60]) (./_minted-Tutorial/C68CC3C9B3A505FB972706356D7F336F67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/61AD507889ED86CFCEFC880BAF2A277767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/DC5117490176932EFB8A7F0E0DA450F667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/657D43328835FC01F9133F8BC964475D6EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/82CBCD9B9F23373D67D9D0D7D2CA363F67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/36F8D0FD2B4ADF57AC4203A0C80C647167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [61]) (./_minted-Tutorial/9CEF7BF9B2634ACBC930BA5EB6DD734214FA033DCB1376922271CBD58A8 A4A36.pygtex [62]) (./_minted-Tutorial/AC02E3950380715FC960C04EF317D69F14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/1C65F538FA7F22F7BB5183FC1553A0C60C640781732628151051B15D85C 9070A.pygtex [63]) (./_minted-Tutorial/935F773BF84C3BF326F4BA093FEC79D40C640781732628151051B15D85C 9070A.pygtex) [64] (./_minted-Tutorial/C194E2231D844AE7D0223173D2A8999114FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/10CB116B7358444BA68AFA046B5B84D514FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/67EFA0AEA2A7C63922644A13FBF91A3767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/F1D514FF0D281415CACA329B41D1275667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/218C0A230BCAE3B7E030880B471BA86367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [65]) (./_minted-Tutorial/AA1E8DC650125C8460BF37E380CAC1AB67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/1435F1CEA90A4D217A423340747F87F067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/CA5B97CA60402CA0078F215AFF31799567B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/D19467E367634413AE9EE17A62E5D9EA14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/EDF3737891061C33EDE0FBFD16CCC63B14FA033DCB1376922271CBD58A8 A4A36.pygtex [66]) (./_minted-Tutorial/D1EAD55A1F8AD3DEAB82383A4F020F5314FA033DCB1376922271CBD58A8 A4A36.pygtex) Overfull \hbox (19.46596pt too wide) in paragraph at lines 1321--1323 \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(...) (./_minted-Tutorial/2F337ECD1F936D416FF9C5C6F41A02D767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/3337CD054623BAC21B6021E996EE0DFD14FA033DCB1376922271CBD58A8 A4A36.pygtex) Overfull \hbox (21.32593pt too wide) in paragraph at lines 1365--1369 []\OT1/cmr/m/n/10 Likewise, when pars-ing FASTQ files, in-ter-nally [][]\OT1/cm tt/m/n/10 Bio.SeqIO.parse() []\OT1/cmr/m/n/10 calls the low-level [][]\OT1/cmtt /m/n/10 FastqGeneralIterator (./_minted-Tutorial/D3AF6542680CA390CDA8C8DF87C693D367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [67]) (./_minted-Tutorial/D749A84299CF58E876E9A899069830DB14FA033DCB1376922271CBD58A8 A4A36.pygtex)) [68] (./Tutorial/chapter_align.tex Chapter 6. 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There-fore the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write() Overfull \hbox (39.68698pt too wide) in paragraph at lines 442--447 [][]\OT1/cmtt/m/n/10 Bio.AlignIO.parse() []\OT1/cmr/m/n/10 and then save them u s-ing the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write() []\OT1/cmr/m/n/10 -- or just use the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.convert() (./_minted-Tutorial/9776F24C4F96F850E549BEF997E4D18C67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/D8256B42DA32121F3B83617DD03F402467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/DA108466F70572EEAE2D54AEA4C156A167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/8FD10ACD641F4427B35E96F33B44479F0C640781732628151051B15D85C 9070A.pygtex [77]) (./_minted-Tutorial/ACC9FF1F2F025F77815D96DC3115B7DF67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/7E530BB128C8AE6BCF7BCE91DD4AF1890C640781732628151051B15D85C 9070A.pygtex) (./_minted-Tutorial/C17F8CD5F33DB6EB328532E02ADD1FE667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/C02EB78C9555A4FEE4954D77162ACF990C640781732628151051B15D85C 9070A.pygtex [78]) (./_minted-Tutorial/74D8F602592BD3646F12A04951B2C44C67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/CB14E2060AF38515C129AB5808537F1614FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/E78F5A80C222A5B2777910FED4F43F560C640781732628151051B15D85C 9070A.pygtex [79]) (./_minted-Tutorial/4D0AF4A40C449D27FF181EC477C63CE667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/2590B11C695B984E246A0A91734F786C67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [80] (./_minted-Tutorial/508710FC1759BFFED598544DEC99BC0D67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/886094CE2C1CAC714387144709D5A47A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/6DC12DBE1D4FD44E7395C66258B5EAC967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/CAC16111FAD8C2E739F6D7C04A986BF067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/A4149E9BEF55B5853014A59A3CBBFBE567B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [81]) (./_minted-Tutorial/8327145320A3BCB412D977F6683B71A267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/1E096B06E33D157FFE18E045579F838C67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/C7331D522D75BB7830A1364BC3B7169267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/C45FE25766D82D1C4A245CBB9A77DB0067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/C0937EED558D842CEA8E3DB9514C6E5967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [82]) (./_minted-Tutorial/8EC03E9C8500D05C6439AC85123A925367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/34725A02F7895E565E5A29E2AC23E8B967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/E139611EBF30A11F71B774B00CB422D667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [83] (./_minted-Tutorial/1FE6956CA319233DB7A5C00C9BEC6D4367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/523928538FA511A925EC995B1803BD1667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [84] (./_minted-Tutorial/7D984F47D0B3A0329DBE2A791B527F5367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/E7AA94166BAA5F4CBB44EF4336F3E89367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/B49F47BF4F2EB4093BDE51E631C6306467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [85] (./_minted-Tutorial/230B4706E315BD2F2A44F2EBCB37A44267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/C11A66992B6C74B61F5A0BE7757AF3BC67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/EAE190D91CC491562308EE568F98636867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/6256254C5A7DFD21185291C77133BFDF67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [86]) (./_minted-Tutorial/FC96AF22EDD72BC4AC2EE47EBAA6B04567B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/544A0904C171F7ACED98D10D90A2BBA267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) Overfull \hbox (8.40039pt too wide) in paragraph at lines 1124--1128 []\OT1/cmr/m/n/10 By de-fault MUS-CLE will out-put the align-ment as a FASTA fi le (us-ing gapped se-quences). The [][]\OT1/cmtt/m/n/10 Bio.AlignIO (./_minted-Tutorial/008DB28D2F01F3F29F1F82EB0591003367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/AE24E0D965703AA4106AE5CF699F0A9A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [87] (./_minted-Tutorial/801A8AB951B5DA791C92C02EB6139DB567B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/14F1F3BAF80772F5999B0773C02432E767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/80957FF2744A858A2D626820D87665F167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [88]) (./_minted-Tutorial/E2B86D066966C8BA13EEEF614D3E745467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/C4AEB9BD8A76F10ACD8C01403E911E8C67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/512DFE88FFA610D4550AF5A23966733167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/F551ABCEBB0043257A807C76B9D81B5C67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/37B6E52C66902FA821D4B0E80172CE7467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [89]) (./_minted-Tutorial/0BA045AD7DFE0F0F3DD972F3E2C40BA167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/482576AF06E80D82290535FF7857A24067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [90] (./_minted-Tutorial/5D3CCD84BC2EC46BF5FD98E7A3FC72660C640781732628151051B15D85C 9070A.pygtex) (./_minted-Tutorial/D9565472E525C9F2B734FC37A70D258E0C640781732628151051B15D85C 9070A.pygtex) (./_minted-Tutorial/798933B773DD1AAF5C2DC54E06491DCF67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/44B6EBA222E5AE2CF0E223148840D8AE67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/DC6CF8B5CDDD2C32E2052C03AF38567467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/4988824A3CF97A3309EED328C1CB00D167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [91]) (./_minted-Tutorial/DF151703751D72BD556402B910190A8767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/004029547AAB1172AF2684D2CA89EA8867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (/usr/share/texlive/texmf-dist/tex/latex/base/omlcmr.fd) [92] (./_minted-Tutorial/A7706714F4982C826867A73C2B665ED067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/3B28841A01F9F481844677E14CA7D2A367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/2203C1F3E2BE8BEF505556D02F8F382C67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/9AC50DD22A56E4DC2B26465D89DE35EA67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/CFB7E0A19AF729834746B283E60F209167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [93]) (./_minted-Tutorial/7DA73F8FE9E6D95C2255220886791B5D67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/E9F207F5DA488246642864EBF9EA466D67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/15FD2886E49804AE97038F2733592C7167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [94]) (./_minted-Tutorial/1D1D98CF394058EA9EB8F6FA3B0DB75A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) Overfull \hbox (0.78606pt too wide) in paragraph at lines 1682--1685 \OT1/cmr/m/n/10 The new [][]\OT1/cmtt/m/n/10 Bio.Align.PairwiseAligner []\OT1/c mr/m/n/10 im-ple-ments the Needleman-Wunsch, Smith-Waterman, Go-toh (three- (./_minted-Tutorial/554024580088332FAF0EA9296BACE82E67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/419ECEB266819C8DCC38EB3E1DC3E36167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/143B9D317680E51D3A6E5641208720CA67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/0ED9274F8C36E3C47BA70FD5BADC364467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [95]) (./_minted-Tutorial/A6265A24C74E31AABCC4CBCDC431287F67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/71831DAF6DA69540332844566CA78C5D67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/827F8E23B39B02EEFF7FF938570EE26E67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [96]) (./_minted-Tutorial/52B42D5819C8EC5D57A21AE60D28F6CE67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/5F566D907B2F88621EC4175F1F17AE0467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/0EDAB1611DCCA854E910FF7DD9D639FA67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [97]) (./_minted-Tutorial/1759F78B85C00128FE82428859F9AAB267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/3DC3D3FA19AFC359663B271CAF187B4867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/17CE58BCB76575958EE7A76C89836E6967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [98]) Overfull \hbox (76.42714pt too wide) in paragraph at lines 1897--1901 []\OT1/cmr/m/n/10 By de-fault, [][]\OT1/cmtt/m/n/10 aligner.substitution_matrix []\OT1/cmr/m/n/10 is [][]\OT1/cmtt/m/n/10 None[]\OT1/cmr/m/n/10 . The at-tribu tes [][]\OT1/cmtt/m/n/10 aligner.match_score []\OT1/cmr/m/n/10 and [][]\OT1/cmt t/m/n/10 aligner.mismatch_score Overfull \hbox (47.73264pt too wide) in paragraph at lines 1897--1901 []\OT1/cmr/m/n/10 are ig-nored if [][]\OT1/cmtt/m/n/10 aligner.substitution_mat rix []\OT1/cmr/m/n/10 is not [][]\OT1/cmtt/m/n/10 None[]\OT1/cmr/m/n/10 . Set-t ing [][]\OT1/cmtt/m/n/10 aligner.match_score []\OT1/cmr/m/n/10 or [][]\OT1/cmtt /m/n/10 aligner.mismatch_score Overfull \hbox (32.852pt too wide) in paragraph at lines 1966--2010 [][] (./_minted-Tutorial/52E7DD48238DDBFB9DE1318A616EEA0467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [99] [100]) (./_minted-Tutorial/FBB2100548FA74FADE3EAE28A2DE191167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [101]) (./_minted-Tutorial/9EAAC9128F41783D91F19053824A0E3267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/B788F0FBC120E74A47922EA232EB867167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/8AC2E9641A86FDB767AE88F57311BBC267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [102]) (./_minted-Tutorial/DE91DA6F7C30BDD779CED0A91AB75DAF67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/A59C6CF4854355E98CC312686998A38B67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/9680AE27F087032C33AE5BA458DF8E9C67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) 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paragraph at lines 2274--2275 \OT1/cmr/m/n/10 In this ex-am-ple, the to-tal num-ber of op-ti-mal align-ments is huge (more than $4 \OMS/cmsy/m/n/10 ^^B \OT1/cmr/m/n/10 10[]$), and call-ing [][]\OT1/cmtt/m/n/10 len(alignments) (./_minted-Tutorial/F89522EF58FB067C6521C367C713471667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/76A8D90A1791A7B42DD5E6329FCCBE2067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/71A68A4BDF8B5654D3E2E0470AE163B467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/CE4E999FF33F9D09A2BB895447AA462967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [105]) (./_minted-Tutorial/3E4691AEB06522E457CDE497E3092DE867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/2E1DF2678D7C68CA2C465BCE6BBBBD6367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/C149B172A838F697839B85AE70CC6CDB67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [106]) (./_minted-Tutorial/467CA50C36874E405E988587FEC0768667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) 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Excluding 'htmlonly' comment. LaTeX Warning: Float too large for page by 32.27644pt on input line 474. ) [124] [125 <./images/BlastRecord.png>] [126 <./images/PSIBlastRecord.png>] (./Tutorial/chapter_searchio.tex Chapter 8. (./_minted-Tutorial/6D0EADF658E662CBA394834EFAC7346E0C640781732628151051B15D85C 9070A.pygtex) [127] Overfull \hbox (2.9019pt too wide) in paragraph at lines 85--93 [][][]\OT1/cmtt/m/n/10 HSPFragment[]\OT1/cmr/m/n/10 , to rep-re-sent a sin-gle con-tigu-ous align-ment be-tween query and hit se-quences. [][]\OT1/cmtt/m/n/10 HSPFragment Overfull \hbox (8.43927pt too wide) in paragraph at lines 105--107 [][][]\OT1/cmtt/m/n/10 parse []\OT1/cmr/m/n/10 is used for search out-put files with mul-ti-ple queries and re-turns a gen-er-a-tor that yields [][]\OT1/cmtt/ m/n/10 QueryResult (./_minted-Tutorial/0EF47CD31A1F702FF10BD5C95E6D18FC67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [128]) (./_minted-Tutorial/BCDD1F95C8585B3C70DE9C1280B5195567B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [129]) (./_minted-Tutorial/5218313E7181C19A936D3F4347E1930A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/7BE69614D007F3BE3249A547A9661D0767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/40227DD719AAD22E8DC2923BF43CE32767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [130]) (./_minted-Tutorial/DC6D0E585B2AACAC1C88A760863B4E4E67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/130BC5013C07805E69A888444A0B34DB67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/CA24D00985B075C56E7C71A246E439FF67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/DE8A481953AA0F7BD7A99C0E281AD1A067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/E7AA701BE1D007CE77D402E8CBFC777A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/906546E8B6F7831A0E7C5FC93AA56A0367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [131] (./_minted-Tutorial/0E8B9F4E4323CB258CA049D41E4AB7F767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/DAA6FD197F3F78FDFB781210387FEC2667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [132]) (./_minted-Tutorial/67A62206561049F4B7E307FD79F028C967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/5E1CC554EC31697163DDD9D33E32A45667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [133]) (./_minted-Tutorial/0A806FC81D8F7F64321B4A6911027F0C67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [134] (./_minted-Tutorial/DC76D831C6E940E11ED2C9452F770E0C67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/A2EA3A12F7596A64ECEE374A9C53499A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/3A61EC24A4603554A3865574A6B7378067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [135] (./_minted-Tutorial/4D85AB21D9819B066A1C948098FDB54B67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/DAAFD2AAF126ED8D7284764B561B5E2B67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/4B4824DE2ED3215F02082987EE57357767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/4D9A79F8BB08FCA20BAEA3DFAAA08BA467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/62792AA2C0390B83FD6A91F3B267312A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [136]) (./_minted-Tutorial/CE618F26D70602D511E57E53CD88044467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/DE23F71CD74CF7717D38AD01C1E1C78767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) 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 (./_minted-Tutorial/338C616C7128C3DB7FFD516F5C2BDA1267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/64A5027CB01EBC16D0BBBCFA493BDAE167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/31F43A46088F6D2E63B39857A353690967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/B35C581DC0102E618595FCC0BE2AFE9867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [137]) (./_minted-Tutorial/23A338D38E31EFFAE0C56C5A5AAB567A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/F1953B67CE735DCB6EDDECF134C333B967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/69130C6EA441D4D1DEB35E75101C9AB967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [138]) (./_minted-Tutorial/688EDDC69F177DE7868A4B0C32B1499267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/E295C926B8D61E45F6C5FA1C0767BFD467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [139] (./_minted-Tutorial/4CFB05EC7DD8FA77EFE275E81B5A1B9767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/B41343A9090DC4C41F9EC69AB6DEDE1B67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [140] (./_minted-Tutorial/7A63CB5E786CCE052981F7DD10653DA967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) 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 , (./_minted-Tutorial/B5F76D201899B345CB64AACD67C7346067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) 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 . (./_minted-Tutorial/0AB25750C7D89E832295045C60D6B8C467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [141]) (./_minted-Tutorial/DFACFE04880AE0CA2E8E32ABDC9E986867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/E4B312798560C8CE4ABF272A364D9E2F67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/35C0940CA4025285AAECA54EF82C993367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) 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 (./_minted-Tutorial/BDE985FA3ADA6B0D37013C3D5F37C17667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex)) [142] [143] (./Tutorial/chapter_entrez.tex Chapter 9. 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(./_minted-Tutorial/6C5156DAD460519324A5B7657B301B5D67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/1836031BC83AA94C8906762F613E6CBA67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [207] (./_minted-Tutorial/D0A75FB8C1C791E4AA80420B93F216A867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/FEC6C2CB5FA0AFCFE00D995BD3642FF267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/2B435DC3041611A5D6A663B437ADB1AD67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) 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 (./_minted-Tutorial/29624A9666C9430AABADF395148BBF2767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/D0F05D42BA0A9BC594EEDB16319A972D67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/87517FEF82BFE1AB8D89A83F4DC5E8B967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [208 <./images/phylo-simple-draw.png>]) Excluding 'htmlonly' comment. 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[211] Overfull \hbox (19.85507pt too wide) in paragraph at lines 438--445 \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"}) [212 <./images/phylo-draw-example.png>] Overfull \hbox (13.48741pt too wide) in paragraph at lines 493--496 []\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 , [213] (./_minted-Tutorial/6AAB725DBD2E5B7C5FD79A9A16536BF614FA033DCB1376922271CBD58A8 A4A36.pygtex) [214] (./_minted-Tutorial/5B477DBF8C94B1E6FDC020E6A741C0DC67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/A317CBB9F004B52870B25AB07ACF279167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) Overfull \hbox (4.04672pt too wide) in paragraph at lines 704--707 []\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- [215] (./_minted-Tutorial/4A4A0B08C37495B73842BFCD67A687D367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/C395044A3DB827E8D2E36BA5259475D267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [216]) [217] (./Tutorial/chapter_motifs.tex Chapter 14. 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[245] [246] [247] [248] (./_minted-Tutorial/C7B59059E3AE6CDE790EFE6EB0ED414067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/2CEA2595B9B8CEAD10513E8D15566D0167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/425EDAA643B5AA9589F3EEE60173582767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/50B5971EFCF22FCC4E1302DB2D0A250014FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/293084E63EA5C0E01F325A4DD59469C067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [249]) Overfull \hbox (78.60634pt too wide) in paragraph at lines 244--245 \OT1/cmr/m/n/10 men-sions of these ar-rays are $[]$ if [][]\OT1/cmtt/m/n/10 tra nspose []\OT1/cmr/m/n/10 is [][]\OT1/cmtt/m/n/10 0[]\OT1/cmr/m/n/10 , or $[]$ (./_minted-Tutorial/05DC01C08B8EDF71F86E3C3A9C28EB3467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [250] [251] (./_minted-Tutorial/A4A28B5A443208DEAB3B4D76AA3B762E67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [252] (./_minted-Tutorial/C286E2777B917B774560CBDC7CF9262667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/D04E097D8E8C4C039FEC20FA103CED1814FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/36EF8931044EF448BC70F722AFADB43D14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/805B33438269C932AC54C0DAB5A3D7AC14FA033DCB1376922271CBD58A8 A4A36.pygtex) [253] [254] Overfull \hbox (16.73593pt too wide) in paragraph at lines 422--423 [][]\OT1/cmtt/m/n/10 distance []\OT1/cmr/m/n/10 is the dis-tance be-tween them. 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How-ever, for large FASTQ files it woul d be faster the low-level [][]\OT1/cmtt/m/n/10 FastqGeneralIterator (./_minted-Tutorial/AB16E58608A2F17CC79E69295572088714FA033DCB1376922271CBD58A8 A4A36.pygtex) Overfull \hbox (4.57849pt too wide) in paragraph at lines 473--475 \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 . 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[326] Overfull \hbox (4.00363pt too wide) in paragraph at lines 1114--1117 []\OT1/cmr/m/it/10 Tip: \OT1/cmr/m/n/10 Rather than us-ing [][]\OT1/cmtt/m/n/10 pylab.show() []\OT1/cmr/m/n/10 to show the plot in a win-dow, you can also use [][]\OT1/cmtt/m/n/10 pylab.savefig(...) (./_minted-Tutorial/7C23BDB073E316E7093E4D3A77BD752E14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/CB78AD94DFE82ADBAF348C0EC1D261CD14FA033DCB1376922271CBD58A8 A4A36.pygtex [327 <./images/hist_plot.png>]) Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. (./_minted-Tutorial/6E0DA723E11A7B9CA8E2353A984B5DF714FA033DCB1376922271CBD58A8 A4A36.pygtex) [328 <./images/gc_plot.png>] (./_minted-Tutorial/219B67DCB31F2334EDD0B85471FABDEA14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/9574E55C4A182E2A0201DF18689F52F414FA033DCB1376922271CBD58A8 A4A36.pygtex [329 <./images/dot_plot.png>]) Excluding 'htmlonly' comment. (./_minted-Tutorial/ECC0A1626B0ABEA9CD4E0A0DA9142CD414FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/6D9EA8AD382A3B03E65A62B6462353A114FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/7727E7020AA1BDC4C2A426B7590C20AD14FA033DCB1376922271CBD58A8 A4A36.pygtex [330]) Excluding 'htmlonly' comment. (./_minted-Tutorial/601CCA4B782F1DA528DB81B02480319514FA033DCB1376922271CBD58A8 A4A36.pygtex [331 <./images/dot_plot_scatter.png>]) Excluding 'htmlonly' comment. [332 <./images/SRR001666.png>] (./_minted-Tutorial/9D2779E6D02C00C016A7A73A452EBC7314FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/06CAA397021B5D0CD904B7CF0209DCA314FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/16711B0A63F93BBACAF3C86CFFB7BEFA0C640781732628151051B15D85C 9070A.pygtex) (./_minted-Tutorial/96EC77291C119EF69670ACDB1C35CE210C640781732628151051B15D85C 9070A.pygtex [333]) (./_minted-Tutorial/6C14F4F0692168BA7165351C706B643D14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/E686FC2D122CF1560FAF4512CD53777F14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/E09A8EBF1B7CB9F831FC2D9DA481453514FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/E598995EF885D7803642E8685DCB8F900C640781732628151051B15D85C 9070A.pygtex) Overfull \hbox (49.0755pt too wide) in paragraph at lines 1523--1524 []\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 . 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For ex-am-ple, [][]\OT1/cmtt/m/n/10 expec ted_frequencies[^^MD^^M, ^^ME^^M] (./_minted-Tutorial/63599FE26E47E2B5739BC250C642AA5067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [337]) (./_minted-Tutorial/618B9F1B5BFA1CE93B03A47D26F6F6E367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex)) [338] (./Tutorial/chapter_testing.tex Chapter 21. (./_minted-Tutorial/867AD481B37AFD4F1A17FC0F2F42FCAE6EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/E8078015A2C53794A733DDC875BD06216EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/754EBE4BCCE307413E74F18728530D046EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/E40D6903CCE8EA230C75C80B7C2D90736EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/7A0DBB9735CDAA1699A6FA164701062F6EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/BC243371043473AEE20C23FF0FABFF0D6EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) Overfull \hbox (39.35472pt too wide) in paragraph at lines 73--77 []\OT1/cmr/m/n/10 Tests based on Python's stan-dard [][]\OT1/cmtt/m/n/10 unitte st []\OT1/cmr/m/n/10 frame-work will [][]\OT1/cmtt/m/n/10 import unittest []\OT 1/cmr/m/n/10 and then de-fine [][]\OT1/cmtt/m/n/10 unittest.TestCase [339] (./_minted-Tutorial/68D5F2D4CFDBBFF65405364F54DA0BCC0C640781732628151051B15D85C 9070A.pygtex) (./_minted-Tutorial/2A1F0B8D037B993D748BF652420448ED6EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex [340]) (./_minted-Tutorial/61465735FDB5BC7ADF12D7A4628FC9A714FA033DCB1376922271CBD58A8 A4A36.pygtex) [341] (./_minted-Tutorial/826F7B9143F73D7CFCAB00906377DAB914FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/B1E279D3993E4775FBE4555B6DD342AD6EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/313C740A73E814DA220EB71149FE706E14FA033DCB1376922271CBD58A8 A4A36.pygtex [342]) (./_minted-Tutorial/99DA0A53F2BD41D9D1BCE2B0332444F46EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/4916E014295B56C6CDDB3C287542DA2914FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/1B0AB11BDA71CF4763A5A4A8B829771114FA033DCB1376922271CBD58A8 A4A36.pygtex [343]) (./_minted-Tutorial/7A0DBB9735CDAA1699A6FA164701062F6EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) [344] (./_minted-Tutorial/3E57444149EF1ACC12DA2995F5B034566EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/DD3A1A642CB850F292FC934F9336EC436EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex)) [345] (./Tutorial/chapter_advanced.tex Chapter 22. Overfull \hbox (61.48412pt too wide) in paragraph at lines 42--44 []\OT1/cmr/m/n/10 The [][]\OT1/cmtt/m/n/10 SeqMat []\OT1/cmr/m/n/10 class de-ri ves from a dic-tio-nary. The dic-tio-nary is of the form [][]\OT1/cmtt/m/n/10 { (i1,j1):n1, (i1,j2):n2,...,(ik,jk):nk} [346] (./_minted-Tutorial/B9AA829C45C3718734961EED663138A314FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/C91962005319864FA8A80F7CE461D6C614FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/949D631F5CFAE16DADE8A9B46DC246FE14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/D57E65C15B8337B55081A0ABDE216E8B14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/30813B956DA3EC8A9CBD746D69F32D000C640781732628151051B15D85C 9070A.pygtex) (./_minted-Tutorial/758DB025D865DFC37AEBF0F3FB3EAF8D0C640781732628151051B15D85C 9070A.pygtex) (./_minted-Tutorial/0C3F6A07854D0D0ACBB80A71C6F047250C640781732628151051B15D85C 9070A.pygtex) [347] (./_minted-Tutorial/01598304B617194419D3D22E288DDBB414FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/2EE2B4E009A2AA257D683D54D33A379814FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/092222FC5487DB13D5744BF56515DC5767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/3FBCEA7E512BCF1A100675C665984F1E14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/F90C13646B17B56314C7FA6500465F7F14FA033DCB1376922271CBD58A8 A4A36.pygtex) Overfull \hbox (30.74179pt too wide) in paragraph at lines 196--197 [][][]\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 (./_minted-Tutorial/4C4AB8D87E6E7015C3AF4CC8FB7D06D214FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/73F214546259C26F0E69498480C6F5E414FA033DCB1376922271CBD58A8 A4A36.pygtex [348]) (./_minted-Tutorial/3C40FC62A59A2301A420D8E25D52D8FB0C640781732628151051B15D85C 9070A.pygtex) (./_minted-Tutorial/9AD3043016CF73EB0A57C6DFA985DB280C640781732628151051B15D85C 9070A.pygtex) (./_minted-Tutorial/D009E3834E447E34C2A0FF5922F938B814FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/4E08040CCAE3D812784651E566C1B38314FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/ACABC0B74314C452E389E9078BF83C3D67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex)) [349] (./Tutorial/chapter_contributing.tex Chapter 23. 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(./_minted-Tutorial/415024C641C8DA7A09117B3DFE240C7867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/487DCC9F44A2539C9B32C0122AEF406567B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/5098CD053449CEC3C9C30C90A007A36467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [58] (./_minted-Tutorial/EEEF4ABAD66CE989F67C9E27EEDE95CC67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/6209F8400B12665DC9E51BC20774DF7014FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/C4099CB0613585FCCD5EA7D8198704CE67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) Overfull \hbox (9.93459pt too wide) in paragraph at lines 831--836 \OT1/cmr/m/n/10 FTP site ([][]$\OT1/cmtt/m/n/10 ftp : / / ftp . uniprot . org / pub / databases / uniprot / current _ release / knowledgebase / complete / (./_minted-Tutorial/D52DA4EEEEE2BF0FBE89EE253714929D67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [59]) Overfull \hbox (4.48064pt too wide) in paragraph at lines 874--877 []\OT1/cmr/m/n/10 As of Gen-Bank re-lease $210$, there are $38$ files mak-ing u p the vi-ral se-quences, \OT1/cmtt/m/n/10 gbvrl1.seq\OT1/cmr/m/n/10 , ..., \OT1 /cmtt/m/n/10 gbvrl38.seq\OT1/cmr/m/n/10 , (./_minted-Tutorial/D41A88D88AB398F0C3B719A5C7D017C16EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/B4D970E8C81930851D8639D77EC3E4106EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/7C4E0944FB13EC4E75DD6FC64900395A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [60]) (./_minted-Tutorial/C68CC3C9B3A505FB972706356D7F336F67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/61AD507889ED86CFCEFC880BAF2A277767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/DC5117490176932EFB8A7F0E0DA450F667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/657D43328835FC01F9133F8BC964475D6EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/82CBCD9B9F23373D67D9D0D7D2CA363F67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/36F8D0FD2B4ADF57AC4203A0C80C647167B6D4EEEA70E83368C1BFCE3E2 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(./_minted-Tutorial/1435F1CEA90A4D217A423340747F87F067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/CA5B97CA60402CA0078F215AFF31799567B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/D19467E367634413AE9EE17A62E5D9EA14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/EDF3737891061C33EDE0FBFD16CCC63B14FA033DCB1376922271CBD58A8 A4A36.pygtex [66]) (./_minted-Tutorial/D1EAD55A1F8AD3DEAB82383A4F020F5314FA033DCB1376922271CBD58A8 A4A36.pygtex) Overfull \hbox (19.46596pt too wide) in paragraph at lines 1321--1323 \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(...) (./_minted-Tutorial/2F337ECD1F936D416FF9C5C6F41A02D767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/3337CD054623BAC21B6021E996EE0DFD14FA033DCB1376922271CBD58A8 A4A36.pygtex) Overfull \hbox (21.32593pt too wide) in paragraph at lines 1365--1369 []\OT1/cmr/m/n/10 Likewise, when pars-ing FASTQ files, in-ter-nally [][]\OT1/cm tt/m/n/10 Bio.SeqIO.parse() []\OT1/cmr/m/n/10 calls the low-level [][]\OT1/cmtt /m/n/10 FastqGeneralIterator (./_minted-Tutorial/D3AF6542680CA390CDA8C8DF87C693D367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [67]) (./_minted-Tutorial/D749A84299CF58E876E9A899069830DB14FA033DCB1376922271CBD58A8 A4A36.pygtex)) [68] (./Tutorial/chapter_align.tex Chapter 6. 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There-fore the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write() Overfull \hbox (39.68698pt too wide) in paragraph at lines 442--447 [][]\OT1/cmtt/m/n/10 Bio.AlignIO.parse() []\OT1/cmr/m/n/10 and then save them u s-ing the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write() []\OT1/cmr/m/n/10 -- or just use the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.convert() (./_minted-Tutorial/9776F24C4F96F850E549BEF997E4D18C67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/D8256B42DA32121F3B83617DD03F402467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/DA108466F70572EEAE2D54AEA4C156A167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/8FD10ACD641F4427B35E96F33B44479F0C640781732628151051B15D85C 9070A.pygtex [77]) (./_minted-Tutorial/ACC9FF1F2F025F77815D96DC3115B7DF67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/7E530BB128C8AE6BCF7BCE91DD4AF1890C640781732628151051B15D85C 9070A.pygtex) (./_minted-Tutorial/C17F8CD5F33DB6EB328532E02ADD1FE667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/C02EB78C9555A4FEE4954D77162ACF990C640781732628151051B15D85C 9070A.pygtex [78]) (./_minted-Tutorial/74D8F602592BD3646F12A04951B2C44C67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/CB14E2060AF38515C129AB5808537F1614FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/E78F5A80C222A5B2777910FED4F43F560C640781732628151051B15D85C 9070A.pygtex [79]) (./_minted-Tutorial/4D0AF4A40C449D27FF181EC477C63CE667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/2590B11C695B984E246A0A91734F786C67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [80] (./_minted-Tutorial/508710FC1759BFFED598544DEC99BC0D67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/886094CE2C1CAC714387144709D5A47A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/6DC12DBE1D4FD44E7395C66258B5EAC967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/CAC16111FAD8C2E739F6D7C04A986BF067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/A4149E9BEF55B5853014A59A3CBBFBE567B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [81]) (./_minted-Tutorial/8327145320A3BCB412D977F6683B71A267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/1E096B06E33D157FFE18E045579F838C67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/C7331D522D75BB7830A1364BC3B7169267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/C45FE25766D82D1C4A245CBB9A77DB0067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/C0937EED558D842CEA8E3DB9514C6E5967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [82]) (./_minted-Tutorial/8EC03E9C8500D05C6439AC85123A925367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/34725A02F7895E565E5A29E2AC23E8B967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/E139611EBF30A11F71B774B00CB422D667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [83] (./_minted-Tutorial/1FE6956CA319233DB7A5C00C9BEC6D4367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/523928538FA511A925EC995B1803BD1667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [84] (./_minted-Tutorial/7D984F47D0B3A0329DBE2A791B527F5367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/E7AA94166BAA5F4CBB44EF4336F3E89367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/B49F47BF4F2EB4093BDE51E631C6306467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [85] (./_minted-Tutorial/230B4706E315BD2F2A44F2EBCB37A44267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/C11A66992B6C74B61F5A0BE7757AF3BC67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/EAE190D91CC491562308EE568F98636867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/6256254C5A7DFD21185291C77133BFDF67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [86]) (./_minted-Tutorial/FC96AF22EDD72BC4AC2EE47EBAA6B04567B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/544A0904C171F7ACED98D10D90A2BBA267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) Overfull \hbox (8.40039pt too wide) in paragraph at lines 1124--1128 []\OT1/cmr/m/n/10 By de-fault MUS-CLE will out-put the align-ment as a FASTA fi le (us-ing gapped se-quences). The [][]\OT1/cmtt/m/n/10 Bio.AlignIO (./_minted-Tutorial/008DB28D2F01F3F29F1F82EB0591003367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/AE24E0D965703AA4106AE5CF699F0A9A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [87] (./_minted-Tutorial/801A8AB951B5DA791C92C02EB6139DB567B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/14F1F3BAF80772F5999B0773C02432E767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/80957FF2744A858A2D626820D87665F167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [88]) (./_minted-Tutorial/E2B86D066966C8BA13EEEF614D3E745467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/C4AEB9BD8A76F10ACD8C01403E911E8C67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/512DFE88FFA610D4550AF5A23966733167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/F551ABCEBB0043257A807C76B9D81B5C67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/37B6E52C66902FA821D4B0E80172CE7467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [89]) (./_minted-Tutorial/0BA045AD7DFE0F0F3DD972F3E2C40BA167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/482576AF06E80D82290535FF7857A24067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [90] (./_minted-Tutorial/5D3CCD84BC2EC46BF5FD98E7A3FC72660C640781732628151051B15D85C 9070A.pygtex) (./_minted-Tutorial/D9565472E525C9F2B734FC37A70D258E0C640781732628151051B15D85C 9070A.pygtex) (./_minted-Tutorial/798933B773DD1AAF5C2DC54E06491DCF67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/44B6EBA222E5AE2CF0E223148840D8AE67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/DC6CF8B5CDDD2C32E2052C03AF38567467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/4988824A3CF97A3309EED328C1CB00D167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [91]) (./_minted-Tutorial/DF151703751D72BD556402B910190A8767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/004029547AAB1172AF2684D2CA89EA8867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (/usr/share/texlive/texmf-dist/tex/latex/base/omlcmr.fd) [92] (./_minted-Tutorial/A7706714F4982C826867A73C2B665ED067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/3B28841A01F9F481844677E14CA7D2A367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/2203C1F3E2BE8BEF505556D02F8F382C67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/9AC50DD22A56E4DC2B26465D89DE35EA67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/CFB7E0A19AF729834746B283E60F209167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [93]) (./_minted-Tutorial/7DA73F8FE9E6D95C2255220886791B5D67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/E9F207F5DA488246642864EBF9EA466D67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/15FD2886E49804AE97038F2733592C7167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [94]) (./_minted-Tutorial/1D1D98CF394058EA9EB8F6FA3B0DB75A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) Overfull \hbox (0.78606pt too wide) in paragraph at lines 1682--1685 \OT1/cmr/m/n/10 The new [][]\OT1/cmtt/m/n/10 Bio.Align.PairwiseAligner []\OT1/c mr/m/n/10 im-ple-ments the Needleman-Wunsch, Smith-Waterman, Go-toh (three- (./_minted-Tutorial/554024580088332FAF0EA9296BACE82E67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/419ECEB266819C8DCC38EB3E1DC3E36167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/143B9D317680E51D3A6E5641208720CA67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/0ED9274F8C36E3C47BA70FD5BADC364467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [95]) (./_minted-Tutorial/A6265A24C74E31AABCC4CBCDC431287F67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/71831DAF6DA69540332844566CA78C5D67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/827F8E23B39B02EEFF7FF938570EE26E67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [96]) (./_minted-Tutorial/52B42D5819C8EC5D57A21AE60D28F6CE67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/5F566D907B2F88621EC4175F1F17AE0467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/0EDAB1611DCCA854E910FF7DD9D639FA67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [97]) (./_minted-Tutorial/1759F78B85C00128FE82428859F9AAB267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/3DC3D3FA19AFC359663B271CAF187B4867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/17CE58BCB76575958EE7A76C89836E6967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [98]) Overfull \hbox (76.42714pt too wide) in paragraph at lines 1897--1901 []\OT1/cmr/m/n/10 By de-fault, [][]\OT1/cmtt/m/n/10 aligner.substitution_matrix []\OT1/cmr/m/n/10 is [][]\OT1/cmtt/m/n/10 None[]\OT1/cmr/m/n/10 . The at-tribu tes [][]\OT1/cmtt/m/n/10 aligner.match_score []\OT1/cmr/m/n/10 and [][]\OT1/cmt t/m/n/10 aligner.mismatch_score Overfull \hbox (47.73264pt too wide) in paragraph at lines 1897--1901 []\OT1/cmr/m/n/10 are ig-nored if [][]\OT1/cmtt/m/n/10 aligner.substitution_mat rix []\OT1/cmr/m/n/10 is not [][]\OT1/cmtt/m/n/10 None[]\OT1/cmr/m/n/10 . Set-t ing [][]\OT1/cmtt/m/n/10 aligner.match_score []\OT1/cmr/m/n/10 or [][]\OT1/cmtt /m/n/10 aligner.mismatch_score Overfull \hbox (32.852pt too wide) in paragraph at lines 1966--2010 [][] (./_minted-Tutorial/52E7DD48238DDBFB9DE1318A616EEA0467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [99] [100]) (./_minted-Tutorial/FBB2100548FA74FADE3EAE28A2DE191167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [101]) (./_minted-Tutorial/9EAAC9128F41783D91F19053824A0E3267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/B788F0FBC120E74A47922EA232EB867167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/8AC2E9641A86FDB767AE88F57311BBC267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [102]) (./_minted-Tutorial/DE91DA6F7C30BDD779CED0A91AB75DAF67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/A59C6CF4854355E98CC312686998A38B67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/9680AE27F087032C33AE5BA458DF8E9C67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) 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paragraph at lines 2274--2275 \OT1/cmr/m/n/10 In this ex-am-ple, the to-tal num-ber of op-ti-mal align-ments is huge (more than $4 \OMS/cmsy/m/n/10 ^^B \OT1/cmr/m/n/10 10[]$), and call-ing [][]\OT1/cmtt/m/n/10 len(alignments) (./_minted-Tutorial/F89522EF58FB067C6521C367C713471667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/76A8D90A1791A7B42DD5E6329FCCBE2067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/71A68A4BDF8B5654D3E2E0470AE163B467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/CE4E999FF33F9D09A2BB895447AA462967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [105]) (./_minted-Tutorial/3E4691AEB06522E457CDE497E3092DE867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/2E1DF2678D7C68CA2C465BCE6BBBBD6367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/C149B172A838F697839B85AE70CC6CDB67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [106]) (./_minted-Tutorial/467CA50C36874E405E988587FEC0768667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) 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Excluding 'htmlonly' comment. LaTeX Warning: Float too large for page by 32.27644pt on input line 474. ) [124] [125 <./images/BlastRecord.png>] [126 <./images/PSIBlastRecord.png>] (./Tutorial/chapter_searchio.tex Chapter 8. (./_minted-Tutorial/6D0EADF658E662CBA394834EFAC7346E0C640781732628151051B15D85C 9070A.pygtex) [127] Overfull \hbox (2.9019pt too wide) in paragraph at lines 85--93 [][][]\OT1/cmtt/m/n/10 HSPFragment[]\OT1/cmr/m/n/10 , to rep-re-sent a sin-gle con-tigu-ous align-ment be-tween query and hit se-quences. [][]\OT1/cmtt/m/n/10 HSPFragment Overfull \hbox (8.43927pt too wide) in paragraph at lines 105--107 [][][]\OT1/cmtt/m/n/10 parse []\OT1/cmr/m/n/10 is used for search out-put files with mul-ti-ple queries and re-turns a gen-er-a-tor that yields [][]\OT1/cmtt/ m/n/10 QueryResult (./_minted-Tutorial/0EF47CD31A1F702FF10BD5C95E6D18FC67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [128]) (./_minted-Tutorial/BCDD1F95C8585B3C70DE9C1280B5195567B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [129]) (./_minted-Tutorial/5218313E7181C19A936D3F4347E1930A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/7BE69614D007F3BE3249A547A9661D0767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/40227DD719AAD22E8DC2923BF43CE32767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [130]) (./_minted-Tutorial/DC6D0E585B2AACAC1C88A760863B4E4E67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/130BC5013C07805E69A888444A0B34DB67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/CA24D00985B075C56E7C71A246E439FF67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/DE8A481953AA0F7BD7A99C0E281AD1A067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/E7AA701BE1D007CE77D402E8CBFC777A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/906546E8B6F7831A0E7C5FC93AA56A0367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [131] (./_minted-Tutorial/0E8B9F4E4323CB258CA049D41E4AB7F767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/DAA6FD197F3F78FDFB781210387FEC2667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [132]) (./_minted-Tutorial/67A62206561049F4B7E307FD79F028C967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/5E1CC554EC31697163DDD9D33E32A45667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [133]) (./_minted-Tutorial/0A806FC81D8F7F64321B4A6911027F0C67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [134] (./_minted-Tutorial/DC76D831C6E940E11ED2C9452F770E0C67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/A2EA3A12F7596A64ECEE374A9C53499A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/3A61EC24A4603554A3865574A6B7378067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [135] (./_minted-Tutorial/4D85AB21D9819B066A1C948098FDB54B67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/DAAFD2AAF126ED8D7284764B561B5E2B67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/4B4824DE2ED3215F02082987EE57357767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/4D9A79F8BB08FCA20BAEA3DFAAA08BA467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/62792AA2C0390B83FD6A91F3B267312A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [136]) (./_minted-Tutorial/CE618F26D70602D511E57E53CD88044467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/DE23F71CD74CF7717D38AD01C1E1C78767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) 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 (./_minted-Tutorial/338C616C7128C3DB7FFD516F5C2BDA1267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/64A5027CB01EBC16D0BBBCFA493BDAE167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/31F43A46088F6D2E63B39857A353690967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/B35C581DC0102E618595FCC0BE2AFE9867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [137]) (./_minted-Tutorial/23A338D38E31EFFAE0C56C5A5AAB567A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/F1953B67CE735DCB6EDDECF134C333B967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/69130C6EA441D4D1DEB35E75101C9AB967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [138]) (./_minted-Tutorial/688EDDC69F177DE7868A4B0C32B1499267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/E295C926B8D61E45F6C5FA1C0767BFD467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [139] (./_minted-Tutorial/4CFB05EC7DD8FA77EFE275E81B5A1B9767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/B41343A9090DC4C41F9EC69AB6DEDE1B67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [140] (./_minted-Tutorial/7A63CB5E786CCE052981F7DD10653DA967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) 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 , (./_minted-Tutorial/B5F76D201899B345CB64AACD67C7346067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) 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 . (./_minted-Tutorial/0AB25750C7D89E832295045C60D6B8C467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [141]) (./_minted-Tutorial/DFACFE04880AE0CA2E8E32ABDC9E986867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/E4B312798560C8CE4ABF272A364D9E2F67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/35C0940CA4025285AAECA54EF82C993367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) 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 (./_minted-Tutorial/BDE985FA3ADA6B0D37013C3D5F37C17667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex)) [142] [143] (./Tutorial/chapter_entrez.tex Chapter 9. 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(./_minted-Tutorial/6C5156DAD460519324A5B7657B301B5D67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/1836031BC83AA94C8906762F613E6CBA67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [207] (./_minted-Tutorial/D0A75FB8C1C791E4AA80420B93F216A867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/FEC6C2CB5FA0AFCFE00D995BD3642FF267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/2B435DC3041611A5D6A663B437ADB1AD67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) 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 (./_minted-Tutorial/29624A9666C9430AABADF395148BBF2767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/D0F05D42BA0A9BC594EEDB16319A972D67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/87517FEF82BFE1AB8D89A83F4DC5E8B967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [208 <./images/phylo-simple-draw.png>]) Excluding 'htmlonly' comment. 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[211] Overfull \hbox (19.85507pt too wide) in paragraph at lines 438--445 \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"}) [212 <./images/phylo-draw-example.png>] Overfull \hbox (13.48741pt too wide) in paragraph at lines 493--496 []\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 , [213] (./_minted-Tutorial/6AAB725DBD2E5B7C5FD79A9A16536BF614FA033DCB1376922271CBD58A8 A4A36.pygtex) [214] (./_minted-Tutorial/5B477DBF8C94B1E6FDC020E6A741C0DC67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/A317CBB9F004B52870B25AB07ACF279167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) Overfull \hbox (4.04672pt too wide) in paragraph at lines 704--707 []\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- [215] (./_minted-Tutorial/4A4A0B08C37495B73842BFCD67A687D367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/C395044A3DB827E8D2E36BA5259475D267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [216]) [217] (./Tutorial/chapter_motifs.tex Chapter 14. 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[245] [246] [247] [248] (./_minted-Tutorial/C7B59059E3AE6CDE790EFE6EB0ED414067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/2CEA2595B9B8CEAD10513E8D15566D0167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/425EDAA643B5AA9589F3EEE60173582767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/50B5971EFCF22FCC4E1302DB2D0A250014FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/293084E63EA5C0E01F325A4DD59469C067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [249]) Overfull \hbox (78.60634pt too wide) in paragraph at lines 244--245 \OT1/cmr/m/n/10 men-sions of these ar-rays are $[]$ if [][]\OT1/cmtt/m/n/10 tra nspose []\OT1/cmr/m/n/10 is [][]\OT1/cmtt/m/n/10 0[]\OT1/cmr/m/n/10 , or $[]$ (./_minted-Tutorial/05DC01C08B8EDF71F86E3C3A9C28EB3467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [250] [251] (./_minted-Tutorial/A4A28B5A443208DEAB3B4D76AA3B762E67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [252] (./_minted-Tutorial/C286E2777B917B774560CBDC7CF9262667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/D04E097D8E8C4C039FEC20FA103CED1814FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/36EF8931044EF448BC70F722AFADB43D14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/805B33438269C932AC54C0DAB5A3D7AC14FA033DCB1376922271CBD58A8 A4A36.pygtex) [253] [254] Overfull \hbox (16.73593pt too wide) in paragraph at lines 422--423 [][]\OT1/cmtt/m/n/10 distance []\OT1/cmr/m/n/10 is the dis-tance be-tween them. 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How-ever, for large FASTQ files it woul d be faster the low-level [][]\OT1/cmtt/m/n/10 FastqGeneralIterator (./_minted-Tutorial/AB16E58608A2F17CC79E69295572088714FA033DCB1376922271CBD58A8 A4A36.pygtex) Overfull \hbox (4.57849pt too wide) in paragraph at lines 473--475 \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 . 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[326] Overfull \hbox (4.00363pt too wide) in paragraph at lines 1114--1117 []\OT1/cmr/m/it/10 Tip: \OT1/cmr/m/n/10 Rather than us-ing [][]\OT1/cmtt/m/n/10 pylab.show() []\OT1/cmr/m/n/10 to show the plot in a win-dow, you can also use [][]\OT1/cmtt/m/n/10 pylab.savefig(...) (./_minted-Tutorial/7C23BDB073E316E7093E4D3A77BD752E14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/CB78AD94DFE82ADBAF348C0EC1D261CD14FA033DCB1376922271CBD58A8 A4A36.pygtex [327 <./images/hist_plot.png>]) Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. (./_minted-Tutorial/6E0DA723E11A7B9CA8E2353A984B5DF714FA033DCB1376922271CBD58A8 A4A36.pygtex) [328 <./images/gc_plot.png>] (./_minted-Tutorial/219B67DCB31F2334EDD0B85471FABDEA14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/9574E55C4A182E2A0201DF18689F52F414FA033DCB1376922271CBD58A8 A4A36.pygtex [329 <./images/dot_plot.png>]) Excluding 'htmlonly' comment. (./_minted-Tutorial/ECC0A1626B0ABEA9CD4E0A0DA9142CD414FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/6D9EA8AD382A3B03E65A62B6462353A114FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/7727E7020AA1BDC4C2A426B7590C20AD14FA033DCB1376922271CBD58A8 A4A36.pygtex [330]) Excluding 'htmlonly' comment. (./_minted-Tutorial/601CCA4B782F1DA528DB81B02480319514FA033DCB1376922271CBD58A8 A4A36.pygtex [331 <./images/dot_plot_scatter.png>]) Excluding 'htmlonly' comment. [332 <./images/SRR001666.png>] (./_minted-Tutorial/9D2779E6D02C00C016A7A73A452EBC7314FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/06CAA397021B5D0CD904B7CF0209DCA314FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/16711B0A63F93BBACAF3C86CFFB7BEFA0C640781732628151051B15D85C 9070A.pygtex) (./_minted-Tutorial/96EC77291C119EF69670ACDB1C35CE210C640781732628151051B15D85C 9070A.pygtex [333]) (./_minted-Tutorial/6C14F4F0692168BA7165351C706B643D14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/E686FC2D122CF1560FAF4512CD53777F14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/E09A8EBF1B7CB9F831FC2D9DA481453514FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/E598995EF885D7803642E8685DCB8F900C640781732628151051B15D85C 9070A.pygtex) Overfull \hbox (49.0755pt too wide) in paragraph at lines 1523--1524 []\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 . 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For ex-am-ple, [][]\OT1/cmtt/m/n/10 expec ted_frequencies[^^MD^^M, ^^ME^^M] (./_minted-Tutorial/63599FE26E47E2B5739BC250C642AA5067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [337]) (./_minted-Tutorial/618B9F1B5BFA1CE93B03A47D26F6F6E367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex)) [338] (./Tutorial/chapter_testing.tex Chapter 21. (./_minted-Tutorial/867AD481B37AFD4F1A17FC0F2F42FCAE6EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/E8078015A2C53794A733DDC875BD06216EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/754EBE4BCCE307413E74F18728530D046EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/E40D6903CCE8EA230C75C80B7C2D90736EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/7A0DBB9735CDAA1699A6FA164701062F6EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/BC243371043473AEE20C23FF0FABFF0D6EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) Overfull \hbox (39.35472pt too wide) in paragraph at lines 73--77 []\OT1/cmr/m/n/10 Tests based on Python's stan-dard [][]\OT1/cmtt/m/n/10 unitte st []\OT1/cmr/m/n/10 frame-work will [][]\OT1/cmtt/m/n/10 import unittest []\OT 1/cmr/m/n/10 and then de-fine [][]\OT1/cmtt/m/n/10 unittest.TestCase [339] (./_minted-Tutorial/68D5F2D4CFDBBFF65405364F54DA0BCC0C640781732628151051B15D85C 9070A.pygtex) (./_minted-Tutorial/2A1F0B8D037B993D748BF652420448ED6EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex [340]) (./_minted-Tutorial/61465735FDB5BC7ADF12D7A4628FC9A714FA033DCB1376922271CBD58A8 A4A36.pygtex) [341] (./_minted-Tutorial/826F7B9143F73D7CFCAB00906377DAB914FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/B1E279D3993E4775FBE4555B6DD342AD6EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/313C740A73E814DA220EB71149FE706E14FA033DCB1376922271CBD58A8 A4A36.pygtex [342]) (./_minted-Tutorial/99DA0A53F2BD41D9D1BCE2B0332444F46EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/4916E014295B56C6CDDB3C287542DA2914FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/1B0AB11BDA71CF4763A5A4A8B829771114FA033DCB1376922271CBD58A8 A4A36.pygtex [343]) (./_minted-Tutorial/7A0DBB9735CDAA1699A6FA164701062F6EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) [344] (./_minted-Tutorial/3E57444149EF1ACC12DA2995F5B034566EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/DD3A1A642CB850F292FC934F9336EC436EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex)) [345] (./Tutorial/chapter_advanced.tex Chapter 22. Overfull \hbox (61.48412pt too wide) in paragraph at lines 42--44 []\OT1/cmr/m/n/10 The [][]\OT1/cmtt/m/n/10 SeqMat []\OT1/cmr/m/n/10 class de-ri ves from a dic-tio-nary. The dic-tio-nary is of the form [][]\OT1/cmtt/m/n/10 { (i1,j1):n1, (i1,j2):n2,...,(ik,jk):nk} [346] (./_minted-Tutorial/B9AA829C45C3718734961EED663138A314FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/C91962005319864FA8A80F7CE461D6C614FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/949D631F5CFAE16DADE8A9B46DC246FE14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/D57E65C15B8337B55081A0ABDE216E8B14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/30813B956DA3EC8A9CBD746D69F32D000C640781732628151051B15D85C 9070A.pygtex) (./_minted-Tutorial/758DB025D865DFC37AEBF0F3FB3EAF8D0C640781732628151051B15D85C 9070A.pygtex) (./_minted-Tutorial/0C3F6A07854D0D0ACBB80A71C6F047250C640781732628151051B15D85C 9070A.pygtex) [347] (./_minted-Tutorial/01598304B617194419D3D22E288DDBB414FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/2EE2B4E009A2AA257D683D54D33A379814FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/092222FC5487DB13D5744BF56515DC5767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/3FBCEA7E512BCF1A100675C665984F1E14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/F90C13646B17B56314C7FA6500465F7F14FA033DCB1376922271CBD58A8 A4A36.pygtex) Overfull \hbox (30.74179pt too wide) in paragraph at lines 196--197 [][][]\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 (./_minted-Tutorial/4C4AB8D87E6E7015C3AF4CC8FB7D06D214FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/73F214546259C26F0E69498480C6F5E414FA033DCB1376922271CBD58A8 A4A36.pygtex [348]) (./_minted-Tutorial/3C40FC62A59A2301A420D8E25D52D8FB0C640781732628151051B15D85C 9070A.pygtex) (./_minted-Tutorial/9AD3043016CF73EB0A57C6DFA985DB280C640781732628151051B15D85C 9070A.pygtex) (./_minted-Tutorial/D009E3834E447E34C2A0FF5922F938B814FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/4E08040CCAE3D812784651E566C1B38314FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/ACABC0B74314C452E389E9078BF83C3D67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex)) [349] (./Tutorial/chapter_contributing.tex Chapter 23. [350] (./_minted-Tutorial/7713FA97EA16E9508BA3E6B9449449256EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/61D19A91BF1A1F95030292E40EF87A366EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) [351]) [352] (./Tutorial/chapter_appendix.tex Chapter 24. 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Transcript written on Tutorial.log. pdflatex biopdb_faq.tex This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./biopdb_faq.tex LaTeX2e <2021-06-01> patch level 1 L3 programming layer <2021-08-27> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2021/02/12 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/bookman.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pbk.fd)) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def)) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/generic/iftex/ifvtex.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty)) (/usr/share/texlive/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref-langpatches.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 56. (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def)) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf)) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) No file biopdb_faq.aux. *geometry* driver: auto-detecting *geometry* detected driver: pdftex *geometry* verbose mode - [ preamble ] result: * driver: pdftex * paper: a4paper * layout: * layoutoffset:(h,v)=(0.0pt,0.0pt) * modes: * h-part:(L,W,R)=(89.62709pt, 418.25368pt, 89.6271pt) * v-part:(T,H,B)=(56.9055pt, 731.23584pt, 56.9055pt) * \paperwidth=597.50787pt * \paperheight=845.04684pt * \textwidth=418.25368pt * \textheight=731.23584pt * \oddsidemargin=17.3571pt * \evensidemargin=17.3571pt * \topmargin=-52.36449pt * \headheight=12.0pt * \headsep=25.0pt * \topskip=10.0pt * \footskip=30.0pt * \marginparwidth=65.0pt * \marginparsep=11.0pt * \columnsep=10.0pt * \skip\footins=9.0pt plus 4.0pt minus 2.0pt * \hoffset=0.0pt * \voffset=0.0pt * \mag=1000 * \@twocolumnfalse * \@twosidefalse * \@mparswitchfalse * \@reversemarginfalse * (1in=72.27pt=25.4mm, 1cm=28.453pt) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) Overfull \hbox (40.90678pt too wide) in paragraph at lines 112--119 []\T1/pbk/l/n/10 However, the [][]\T1/pcr/m/n/10 Bio.PDB.mmCIF.MMCIFlex []\T1/p bk/l/n/10 mod-ule (used in-ter-nally by [][]\T1/pcr/m/n/10 Bio.PDB.MMCIFParser [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pbk.fd) [2] Overfull \hbox (21.75009pt too wide) in paragraph at lines 271--276 \T1/pbk/l/n/10 file to their val-ues. 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[9] LaTeX Warning: Reference `sub:Analysis' on page 10 undefined on input line 826. [10] Overfull \hbox (45.08351pt too wide) in paragraph at lines 1012--1016 \T1/pbk/l/n/10 Note that in the above case only model 0 of the struc-ture is co n-sid-ered by \T1/pcr/m/n/10 PolypeptideBuilder\T1/pbk/l/n/10 . Overfull \hbox (10.80998pt too wide) in paragraph at lines 1020--1024 \T1/pbk/l/n/10 try). The se-quence of each polypep-tide can then eas-ily be ob- tained from the \T1/pcr/m/n/10 Polypeptide [11] LaTeX Warning: Reference `cap:DSSP-codes' on page 12 undefined on input line 10 41. [12] Overfull \hbox (87.74638pt too wide) in paragraph at lines 1148--1149 []\T1/pcr/m/n/10 # Calculate classical coordination number exp_fs=hse.calc_fs_e xposure(model) Overfull \hbox (20.6135pt too wide) in paragraph at lines 1169--1174 \T1/pcr/m/n/10 Atom \T1/pbk/l/n/10 ob-jects re-turn a \T1/pcr/m/n/10 Vector \T1 /pbk/l/n/10 ob-ject rep-re-sen-ta-tion of the co-or-di-nates with the \T1/pcr/m /n/10 get_vector [13] [14] Overfull \hbox (1.21811pt too wide) in paragraph at lines 1350--1358 []\T1/pbk/l/n/10 THE CON-TRIB-U-TORS AND COPY-RIGHT HOLD-ERS OF THIS SOFT-WARE DIS-CLAIM [15] (./biopdb_faq.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. Package rerunfilecheck Warning: File `biopdb_faq.out' has changed. 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(/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def)) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf)) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./biopdb_faq.aux) *geometry* driver: auto-detecting *geometry* detected driver: pdftex *geometry* verbose mode - [ preamble ] result: * driver: pdftex * paper: a4paper * layout: * layoutoffset:(h,v)=(0.0pt,0.0pt) * modes: * h-part:(L,W,R)=(89.62709pt, 418.25368pt, 89.6271pt) * v-part:(T,H,B)=(56.9055pt, 731.23584pt, 56.9055pt) * \paperwidth=597.50787pt * \paperheight=845.04684pt * \textwidth=418.25368pt * \textheight=731.23584pt * \oddsidemargin=17.3571pt * \evensidemargin=17.3571pt * \topmargin=-52.36449pt * \headheight=12.0pt * \headsep=25.0pt * \topskip=10.0pt * \footskip=30.0pt * \marginparwidth=65.0pt * \marginparsep=11.0pt * \columnsep=10.0pt * \skip\footins=9.0pt plus 4.0pt minus 2.0pt * \hoffset=0.0pt * \voffset=0.0pt * \mag=1000 * \@twocolumnfalse * \@twosidefalse * \@mparswitchfalse * \@reversemarginfalse * (1in=72.27pt=25.4mm, 1cm=28.453pt) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/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/ts1pbk.fd) [2] Overfull \hbox (21.75009pt too wide) in paragraph at lines 271--276 \T1/pbk/l/n/10 file to their val-ues. If there are mul-ti-ple val-ues (like in the case of tag \T1/pcr/m/n/10 _atom_site.Cartn_y\T1/pbk/l/n/10 , [3] Overfull \hbox (13.9754pt too wide) in paragraph at lines 312--318 \T1/pbk/l/n/10 The avail-able keys are \T1/pcr/m/n/10 name, head, deposition_-d ate, release_-date, structure_- Overfull \hbox (11.71707pt too wide) in paragraph at lines 312--318 \T1/pcr/m/n/10 method, resolution, structure_-reference \T1/pbk/l/n/10 (maps to a list of ref-er-ences), \T1/pcr/m/n/10 journal_- [4] [5] [6] [7 <./images/smcra.png (PNG copy)>] [8] [9] [10] Overfull \hbox (45.08351pt too wide) in paragraph at lines 1012--1016 \T1/pbk/l/n/10 Note that in the above case only model 0 of the struc-ture is co n-sid-ered by \T1/pcr/m/n/10 PolypeptideBuilder\T1/pbk/l/n/10 . Overfull \hbox (10.80998pt too wide) in paragraph at lines 1020--1024 \T1/pbk/l/n/10 try). The se-quence of each polypep-tide can then eas-ily be ob- tained from the \T1/pcr/m/n/10 Polypeptide [11] [12] Overfull \hbox (87.74638pt too wide) in paragraph at lines 1148--1149 []\T1/pcr/m/n/10 # Calculate classical coordination number exp_fs=hse.calc_fs_e xposure(model) Overfull \hbox (20.6135pt too wide) in paragraph at lines 1169--1174 \T1/pcr/m/n/10 Atom \T1/pbk/l/n/10 ob-jects re-turn a \T1/pcr/m/n/10 Vector \T1 /pbk/l/n/10 ob-ject rep-re-sen-ta-tion of the co-or-di-nates with the \T1/pcr/m /n/10 get_vector [13] [14] Overfull \hbox (1.21811pt too wide) in paragraph at lines 1350--1358 []\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, 165360 bytes). Transcript written on biopdb_faq.log. pdflatex biopdb_faq.tex This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./biopdb_faq.tex LaTeX2e <2021-06-01> patch level 1 L3 programming layer <2021-08-27> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2021/02/12 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/bookman.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pbk.fd)) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def)) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/generic/iftex/ifvtex.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty)) (/usr/share/texlive/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref-langpatches.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 56. (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def)) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf)) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./biopdb_faq.aux) *geometry* driver: auto-detecting *geometry* detected driver: pdftex *geometry* verbose mode - [ preamble ] result: * driver: pdftex * paper: a4paper * layout: * layoutoffset:(h,v)=(0.0pt,0.0pt) * modes: * h-part:(L,W,R)=(89.62709pt, 418.25368pt, 89.6271pt) * v-part:(T,H,B)=(56.9055pt, 731.23584pt, 56.9055pt) * \paperwidth=597.50787pt * \paperheight=845.04684pt * \textwidth=418.25368pt * \textheight=731.23584pt * \oddsidemargin=17.3571pt * \evensidemargin=17.3571pt * \topmargin=-52.36449pt * \headheight=12.0pt * \headsep=25.0pt * \topskip=10.0pt * \footskip=30.0pt * \marginparwidth=65.0pt * \marginparsep=11.0pt * \columnsep=10.0pt * \skip\footins=9.0pt plus 4.0pt minus 2.0pt * \hoffset=0.0pt * \voffset=0.0pt * \mag=1000 * \@twocolumnfalse * \@twosidefalse * \@mparswitchfalse * \@reversemarginfalse * (1in=72.27pt=25.4mm, 1cm=28.453pt) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/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/ts1pbk.fd) [2] Overfull \hbox (21.75009pt too wide) in paragraph at lines 271--276 \T1/pbk/l/n/10 file to their val-ues. If there are mul-ti-ple val-ues (like in the case of tag \T1/pcr/m/n/10 _atom_site.Cartn_y\T1/pbk/l/n/10 , [3] Overfull \hbox (13.9754pt too wide) in paragraph at lines 312--318 \T1/pbk/l/n/10 The avail-able keys are \T1/pcr/m/n/10 name, head, deposition_-d ate, release_-date, structure_- Overfull \hbox (11.71707pt too wide) in paragraph at lines 312--318 \T1/pcr/m/n/10 method, resolution, structure_-reference \T1/pbk/l/n/10 (maps to a list of ref-er-ences), \T1/pcr/m/n/10 journal_- [4] [5] [6] [7 <./images/smcra.png (PNG copy)>] [8] [9] [10] Overfull \hbox (45.08351pt too wide) in paragraph at lines 1012--1016 \T1/pbk/l/n/10 Note that in the above case only model 0 of the struc-ture is co n-sid-ered by \T1/pcr/m/n/10 PolypeptideBuilder\T1/pbk/l/n/10 . Overfull \hbox (10.80998pt too wide) in paragraph at lines 1020--1024 \T1/pbk/l/n/10 try). The se-quence of each polypep-tide can then eas-ily be ob- tained from the \T1/pcr/m/n/10 Polypeptide [11] [12] Overfull \hbox (87.74638pt too wide) in paragraph at lines 1148--1149 []\T1/pcr/m/n/10 # Calculate classical coordination number exp_fs=hse.calc_fs_e xposure(model) Overfull \hbox (20.6135pt too wide) in paragraph at lines 1169--1174 \T1/pcr/m/n/10 Atom \T1/pbk/l/n/10 ob-jects re-turn a \T1/pcr/m/n/10 Vector \T1 /pbk/l/n/10 ob-ject rep-re-sen-ta-tion of the co-or-di-nates with the \T1/pcr/m /n/10 get_vector [13] [14] Overfull \hbox (1.21811pt too wide) in paragraph at lines 1350--1358 []\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, 165360 bytes). Transcript written on biopdb_faq.log. make[2]: Leaving directory '/<>/python-biopython-1.78+dfsg/Doc' make[1]: Leaving directory '/<>/python-biopython-1.78+dfsg' rm -f debian/python3-biopython.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/<>/python-biopython-1.78+dfsg' mkdir -p Tests_avoid for avoid in PAML_tools EmbossPhylipNew MSAProbs_tool NACCESS_tool PopGen_GenePop PopGen_GenePop_EasyController XXmotif_tool PDB_ResidueDepth mmtf mmtf_online raxml_tool BioSQL_MySQLdb BioSQL_psycopg2 \ ; do \ mv Tests/test_${avoid}.py Tests_avoid ; \ done mv: cannot stat 'Tests/test_NACCESS_tool.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 "3.10 3.9" --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:232: set -e; \ mkdir -p /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/home; \ mkdir -p /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Doc/examples; \ cp -a Doc/Tutorial.tex /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Doc; \ cp -a Doc/Tutorial /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Doc; \ cp -a Doc/examples /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Doc; \ cp -a Tests /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build; \ cd /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Tests; \ env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=/<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/home python3.10 run_tests.py --offline /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Tests/run_tests.py:33: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives import distutils.util 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_BWA_tool ... 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_Blast_Record ... ok test_CAPS ... ok test_Chi2 ... ok test_ClustalOmega_tool ... ok test_Clustalw_tool ... ok test_Cluster ... ok test_CodonTable ... ok test_ColorSpiral ... ok test_Compass ... ok test_Consensus ... ok test_Crystal ... 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_GenomeDiagram ... Warn: Can't find .pfb for face 'Times-Roman' ok test_GraphicsBitmaps ... ERROR test_GraphicsChromosome ... ok test_GraphicsDistribution ... ok test_GraphicsGeneral ... ok test_HMMCasino ... ok test_HMMGeneral ... 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_LogisticRegression ... ok test_MafIO_index ... ok test_Mafft_tool ... ok test_MarkovModel ... /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Tests/test_MarkovModel.py:403: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray. training_outputs = array( /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Tests/test_MarkovModel.py:411: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray. training_states = array( ok test_Medline ... ok test_Muscle_tool ... ok test_NCBITextParser ... ok test_NCBIXML ... ok test_NCBI_BLAST_tools ... /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Tests/test_NCBI_BLAST_tools.py:477: 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( /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Tests/test_NCBI_BLAST_tools.py:477: 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( /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Tests/test_NCBI_BLAST_tools.py:477: 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( /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Tests/test_NCBI_BLAST_tools.py:477: 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( /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Tests/test_NCBI_BLAST_tools.py:477: 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( /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Tests/test_NCBI_BLAST_tools.py:477: 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: -mt_mode,-sorthits,-sorthsps,-subject_besthit) warnings.warn( /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Tests/test_NCBI_BLAST_tools.py:477: 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: -mt_mode,-sorthits,-sorthsps) warnings.warn( /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Tests/test_NCBI_BLAST_tools.py:477: 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( /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Tests/test_NCBI_BLAST_tools.py:477: 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( ok test_NCBI_qblast ... ok test_NMR ... ok test_NaiveBayes ... ok test_Nexus ... ok test_PAML_baseml ... ok test_PAML_codeml ... ok test_PAML_yn00 ... ok test_PDBList ... skipping. internet not available test_PDB_DSSP ... /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB/DSSP.py:250: UserWarning: Unknown or untrusted program in REMARK 3, trying all parsers to see if there is a match warnings.warn(err) /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB/DSSP.py:250: UserWarning: Unknown or untrusted program in REMARK 3, trying all parsers to see if there is a match warnings.warn(err) /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB/DSSP.py:250: UserWarning: Invalid mmCIF file use --verbose option to see errors warnings.warn(err) /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB/DSSP.py:250: UserWarning: Invalid mmCIF file use --verbose option to see errors warnings.warn(err) /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB/DSSP.py:250: UserWarning: Invalid mmCIF file use --verbose option to see errors warnings.warn(err) /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB/DSSP.py:250: UserWarning: Invalid mmCIF file use --verbose option to see errors warnings.warn(err) ok test_PDB_Dice ... ok test_PDB_Disordered ... ok test_PDB_Exposure ... ok test_PDB_FragmentMapper ... ok test_PDB_KDTree ... ok test_PDB_MMCIF2Dict ... ok test_PDB_MMCIFIO ... ok test_PDB_MMCIFParser ... ok test_PDB_NACCESS ... ok test_PDB_PDBIO ... ok test_PDB_PDBParser ... ok test_PDB_Polypetide ... ok test_PDB_SMCRA ... ok test_PDB_StructureAlignment ... ok test_PDB_Superimposer ... ok test_PDB_internal_coords ... ok test_PDB_parse_pdb_header ... ok test_PDB_vectors ... ok test_PQR ... 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 ... ok 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_hhsuite2_text ... 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_Gck ... ok test_SeqIO_Insdc ... /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/GenBank/Scanner.py:303: BiopythonParserWarning: Non-standard feature line wrapping (didn't break on comma)? warnings.warn( ok test_SeqIO_NibIO ... ok test_SeqIO_PdbIO ... ok test_SeqIO_QualityIO ... ok test_SeqIO_SeqXML ... ok test_SeqIO_SnapGene ... ok test_SeqIO_Xdna ... 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 ... /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/SubsMat/__init__.py:126: BiopythonDeprecationWarning: Bio.SubsMat has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.substitution_matrices as a replacement, and contact the Biopython developers if you still need the Bio.SubsMat module. warnings.warn( ok test_SwissProt ... ok test_TCoffee_tool ... ok test_TogoWS ... skipping. internet not available test_TreeConstruction ... ok No entry for terminal type "unknown"; using dumb terminal settings. test_Tutorial ... FAIL test_UniGene ... ok test_UniProt_GOA ... ok test_Uniprot ... ok test_Wise ... ok test_align ... ok test_align_substitution_matrices ... ok test_bgzf ... ok test_cellosaurus ... ok test_codonalign ... /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/codonalign/codonalignment.py:113: BiopythonWarning: Please make sure the two CodonAlignment objects are sharing the same codon table. This is not checked by Biopython. warnings.warn( /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Seq.py:2309: 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( ok test_geo ... ok test_kNN ... ok test_lowess ... /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Statistics/__init__.py:11: BiopythonDeprecationWarning: Bio.Statistics has been deprecated, and we intend to remove it in a future release of Biopython. warnings.warn( ok test_motifs ... FAIL test_motifs_online ... skipping. internet not available test_pairwise2 ... ok test_pairwise2_no_C ... ok test_pairwise_aligner ... ok test_phenotype ... ok test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. test_phyml_tool ... skipping. Couldn't find the PhyML software. Install PhyML 3.0 or later if you want to use the Bio.Phylo.Applications wrapper. test_prodoc ... ok test_prosite1 ... ok test_prosite2 ... ok test_psw ... ok test_samtools_tool ... ok test_seq ... /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Seq.py:2334: 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( ok test_translate ... ok Bio docstring test ... ok Bio.Affy docstring test ... ok Bio.Affy.CelFile docstring test ... ok Bio.Align docstring test ... ok Bio.Align.AlignInfo docstring test ... ok Bio.Align.Applications docstring test ... ok Bio.Align.Applications._ClustalOmega docstring test ... ok Bio.Align.Applications._Clustalw 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._Prank docstring test ... ok Bio.Align.Applications._Probcons docstring test ... ok Bio.Align.Applications._TCoffee docstring test ... ok Bio.Align._aligners docstring test ... ok Bio.Align.substitution_matrices docstring test ... ok Bio.AlignIO docstring test ... ok Bio.AlignIO.ClustalIO docstring test ... ok Bio.AlignIO.EmbossIO docstring test ... ok Bio.AlignIO.FastaIO docstring test ... ok Bio.AlignIO.Interfaces docstring test ... ok Bio.AlignIO.MafIO docstring test ... ok Bio.AlignIO.MauveIO docstring test ... ok Bio.AlignIO.MsfIO docstring test ... ok Bio.AlignIO.NexusIO docstring test ... ok Bio.AlignIO.PhylipIO docstring test ... ok Bio.AlignIO.StockholmIO docstring test ... ok Bio.Application docstring test ... ok Bio.Blast docstring test ... ok Bio.Blast.Applications docstring test ... ok Bio.Blast.NCBIWWW docstring test ... ok Bio.Blast.NCBIXML docstring test ... ok Bio.Blast.ParseBlastTable docstring test ... ok Bio.Blast.Record docstring test ... ok Bio.CAPS docstring test ... ok Bio.Cluster docstring test ... ok Bio.Cluster._cluster docstring test ... ok Bio.Compass docstring test ... ok Bio.Crystal docstring test ... ok Bio.Data docstring test ... ok Bio.Data.CodonTable docstring test ... ok Bio.Data.IUPACData docstring test ... ok Bio.Data.SCOPData docstring test ... ok Bio.Emboss docstring test ... ok Bio.Emboss.Applications docstring test ... ok Bio.Emboss.Primer3 docstring test ... ok Bio.Emboss.PrimerSearch docstring test ... ok Bio.Entrez.Parser docstring test ... ok Bio.ExPASy.Enzyme docstring test ... ok Bio.ExPASy.Prodoc docstring test ... ok Bio.ExPASy.Prosite docstring test ... ok Bio.ExPASy.ScanProsite docstring test ... ok Bio.ExPASy.cellosaurus docstring test ... ok Bio.FSSP docstring test ... ok Bio.FSSP.FSSPTools docstring test ... ok Bio.FSSP.fssp_rec docstring test ... ok Bio.File docstring test ... ok Bio.GenBank docstring test ... ok Bio.GenBank.Record docstring test ... ok Bio.GenBank.Scanner docstring test ... ok Bio.GenBank.utils docstring test ... ok Bio.Geo docstring test ... ok Bio.Geo.Record docstring test ... ok Bio.Graphics docstring test ... ok Bio.Graphics.BasicChromosome docstring test ... ok Bio.Graphics.ColorSpiral docstring test ... ok Bio.Graphics.Comparative docstring test ... ok Bio.Graphics.DisplayRepresentation docstring test ... ok Bio.Graphics.Distribution docstring test ... ok Bio.Graphics.GenomeDiagram docstring test ... ok Bio.Graphics.GenomeDiagram._AbstractDrawer docstring test ... ok Bio.Graphics.GenomeDiagram._CircularDrawer docstring test ... ok Bio.Graphics.GenomeDiagram._Colors docstring test ... ok Bio.Graphics.GenomeDiagram._CrossLink docstring test ... ok Bio.Graphics.GenomeDiagram._Diagram docstring test ... ok Bio.Graphics.GenomeDiagram._Feature docstring test ... ok Bio.Graphics.GenomeDiagram._FeatureSet docstring test ... ok Bio.Graphics.GenomeDiagram._Graph docstring test ... ok Bio.Graphics.GenomeDiagram._GraphSet docstring test ... ok Bio.Graphics.GenomeDiagram._LinearDrawer docstring test ... ok Bio.Graphics.GenomeDiagram._Track docstring test ... ok Bio.Graphics.KGML_vis docstring test ... ok Bio.HMM docstring test ... ok Bio.HMM.DynamicProgramming docstring test ... ok Bio.HMM.MarkovModel docstring test ... ok Bio.HMM.Trainer docstring test ... ok Bio.HMM.Utilities docstring test ... ok Bio.KEGG docstring test ... ok Bio.KEGG.Compound docstring test ... ok Bio.KEGG.Enzyme docstring test ... ok Bio.KEGG.Gene docstring test ... ok Bio.KEGG.KGML docstring test ... ok Bio.KEGG.KGML.KGML_parser docstring test ... ok Bio.KEGG.KGML.KGML_pathway docstring test ... ok Bio.KEGG.Map docstring test ... ok Bio.KEGG.REST docstring test ... ok Bio.LogisticRegression docstring test ... ok Bio.MarkovModel docstring test ... ok Bio.MaxEntropy docstring test ... ok Bio.Medline docstring test ... ok Bio.NMR docstring test ... ok Bio.NMR.NOEtools docstring test ... ok Bio.NMR.xpktools docstring test ... ok Bio.NaiveBayes docstring test ... ok Bio.Nexus docstring test ... ok Bio.Nexus.Nexus docstring test ... ok Bio.Nexus.Nodes docstring test ... ok Bio.Nexus.StandardData docstring test ... ok Bio.Nexus.Trees docstring test ... ok Bio.Nexus.cnexus docstring test ... ok Bio.PDB docstring test ... ok Bio.PDB.AbstractPropertyMap docstring test ... ok Bio.PDB.Atom docstring test ... ok Bio.PDB.Chain docstring test ... ok Bio.PDB.DSSP docstring test ... ok Bio.PDB.Dice docstring test ... ok Bio.PDB.Entity docstring test ... ok Bio.PDB.FragmentMapper docstring test ... ok Bio.PDB.HSExposure docstring test ... ok Bio.PDB.MMCIF2Dict docstring test ... ok Bio.PDB.MMCIFParser docstring test ... ok Bio.PDB.Model docstring test ... ok Bio.PDB.NACCESS docstring test ... ok Bio.PDB.NeighborSearch docstring test ... ok Bio.PDB.PDBExceptions docstring test ... ok Bio.PDB.PDBIO docstring test ... ok Bio.PDB.PDBList docstring test ... ok Bio.PDB.PDBParser docstring test ... ok Bio.PDB.PICIO docstring test ... ok Bio.PDB.PSEA docstring test ... ok Bio.PDB.Polypeptide docstring test ... ok Bio.PDB.QCPSuperimposer docstring test ... ok Bio.PDB.QCPSuperimposer.qcprotmodule docstring test ... ok Bio.PDB.Residue docstring test ... ok Bio.PDB.ResidueDepth docstring test ... ok Bio.PDB.SCADIO docstring test ... ok Bio.PDB.Selection docstring test ... ok Bio.PDB.Structure docstring test ... ok Bio.PDB.StructureAlignment docstring test ... ok Bio.PDB.StructureBuilder docstring test ... ok Bio.PDB.Superimposer docstring test ... ok Bio.PDB.ic_data docstring test ... ok Bio.PDB.ic_rebuild docstring test ... ok Bio.PDB.internal_coords docstring test ... ok Bio.PDB.kdtrees docstring test ... ok Bio.PDB.mmcifio docstring test ... ok Bio.PDB.mmtf docstring test ... ok Bio.PDB.mmtf.DefaultParser docstring test ... ok Bio.PDB.mmtf.mmtfio docstring test ... ok Bio.PDB.parse_pdb_header docstring test ... ok Bio.PDB.vectors docstring test ... ok Bio.Pathway docstring test ... ok Bio.Pathway.Rep docstring test ... ok Bio.Pathway.Rep.Graph docstring test ... ok Bio.Pathway.Rep.MultiGraph docstring test ... ok Bio.Phylo docstring test ... ok Bio.Phylo.Applications docstring test ... ok Bio.Phylo.Applications._Fasttree docstring test ... ok Bio.Phylo.Applications._Phyml docstring test ... ok Bio.Phylo.Applications._Raxml docstring test ... ok Bio.Phylo.BaseTree docstring test ... ok Bio.Phylo.CDAO docstring test ... ok Bio.Phylo.CDAOIO docstring test ... ok Bio.Phylo.Consensus docstring test ... ok Bio.Phylo.NeXML docstring test ... ok Bio.Phylo.NeXMLIO docstring test ... ok Bio.Phylo.Newick docstring test ... ok Bio.Phylo.NewickIO docstring test ... ok Bio.Phylo.NexusIO docstring test ... ok Bio.Phylo.PAML docstring test ... ok Bio.Phylo.PAML._paml docstring test ... ok Bio.Phylo.PAML._parse_baseml docstring test ... ok Bio.Phylo.PAML._parse_codeml docstring test ... ok Bio.Phylo.PAML._parse_yn00 docstring test ... ok Bio.Phylo.PAML.baseml docstring test ... ok Bio.Phylo.PAML.chi2 docstring test ... ok Bio.Phylo.PAML.codeml docstring test ... ok Bio.Phylo.PAML.yn00 docstring test ... ok Bio.Phylo.PhyloXML docstring test ... ok Bio.Phylo.PhyloXMLIO docstring test ... ok Bio.Phylo.TreeConstruction docstring test ... ok Bio.Phylo._cdao_owl docstring test ... ok Bio.Phylo._io docstring test ... ok Bio.Phylo._utils docstring test ... ok Bio.PopGen docstring test ... ok Bio.PopGen.GenePop docstring test ... ok Bio.PopGen.GenePop.Controller docstring test ... ok Bio.PopGen.GenePop.EasyController docstring test ... ok Bio.PopGen.GenePop.FileParser docstring test ... ok Bio.PopGen.GenePop.LargeFileParser docstring test ... ok Bio.Restriction docstring test ... ok Bio.Restriction.PrintFormat docstring test ... ok Bio.Restriction.Restriction docstring test ... ok Bio.Restriction.Restriction_Dictionary docstring test ... ok Bio.SCOP docstring test ... ok Bio.SCOP.Cla docstring test ... ok Bio.SCOP.Des docstring test ... ok Bio.SCOP.Dom docstring test ... ok Bio.SCOP.Hie docstring test ... ok Bio.SCOP.Raf docstring test ... ok Bio.SCOP.Residues docstring test ... ok Bio.SVDSuperimposer docstring test ... ok Bio.SearchIO docstring test ... ok Bio.SearchIO.BlastIO docstring test ... ok Bio.SearchIO.BlastIO.blast_tab docstring test ... ok Bio.SearchIO.BlastIO.blast_text docstring test ... ok Bio.SearchIO.BlastIO.blast_xml docstring test ... ok Bio.SearchIO.BlatIO docstring test ... ok Bio.SearchIO.ExonerateIO docstring test ... ok Bio.SearchIO.ExonerateIO._base docstring test ... ok Bio.SearchIO.ExonerateIO.exonerate_cigar docstring test ... ok Bio.SearchIO.ExonerateIO.exonerate_text docstring test ... ok Bio.SearchIO.ExonerateIO.exonerate_vulgar docstring test ... ok Bio.SearchIO.FastaIO docstring test ... ok Bio.SearchIO.HHsuiteIO docstring test ... ok Bio.SearchIO.HHsuiteIO.hhsuite2_text docstring test ... ok Bio.SearchIO.HmmerIO docstring test ... ok Bio.SearchIO.HmmerIO._base docstring test ... ok Bio.SearchIO.HmmerIO.hmmer2_text docstring test ... ok Bio.SearchIO.HmmerIO.hmmer3_domtab docstring test ... ok Bio.SearchIO.HmmerIO.hmmer3_tab docstring test ... ok Bio.SearchIO.HmmerIO.hmmer3_text docstring test ... ok Bio.SearchIO.InterproscanIO docstring test ... ok Bio.SearchIO.InterproscanIO.interproscan_xml docstring test ... ok Bio.SearchIO._index docstring test ... ok Bio.SearchIO._legacy docstring test ... ok Bio.SearchIO._legacy.NCBIStandalone docstring test ... ok Bio.SearchIO._legacy.ParserSupport docstring test ... ok Bio.SearchIO._model docstring test ... ok Bio.SearchIO._model._base docstring test ... ok Bio.SearchIO._model.hit docstring test ... ok Bio.SearchIO._model.hsp docstring test ... ok Bio.SearchIO._model.query docstring test ... ok Bio.SearchIO._utils docstring test ... ok Bio.Seq docstring test ... ok Bio.SeqFeature docstring test ... ok Bio.SeqIO docstring test ... ok Bio.SeqIO.AbiIO docstring test ... ok Bio.SeqIO.AceIO docstring test ... ok Bio.SeqIO.FastaIO docstring test ... ok Bio.SeqIO.GckIO docstring test ... ok Bio.SeqIO.IgIO docstring test ... ok Bio.SeqIO.InsdcIO docstring test ... ok Bio.SeqIO.Interfaces docstring test ... ok Bio.SeqIO.NibIO docstring test ... ok Bio.SeqIO.PdbIO docstring test ... ok Bio.SeqIO.PhdIO docstring test ... ok Bio.SeqIO.PirIO docstring test ... ok Bio.SeqIO.QualityIO docstring test ... ok Bio.SeqIO.SeqXmlIO docstring test ... ok Bio.SeqIO.SffIO docstring test ... ok Bio.SeqIO.SnapGeneIO docstring test ... ok Bio.SeqIO.SwissIO docstring test ... ok Bio.SeqIO.TabIO docstring test ... ok Bio.SeqIO.UniprotIO docstring test ... ok Bio.SeqIO.XdnaIO docstring test ... ok Bio.SeqIO._index docstring test ... ok Bio.SeqRecord docstring test ... ok Bio.SeqUtils docstring test ... ok Bio.SeqUtils.CheckSum docstring test ... ok Bio.SeqUtils.CodonUsage docstring test ... ok Bio.SeqUtils.CodonUsageIndices docstring test ... ok Bio.SeqUtils.IsoelectricPoint docstring test ... ok Bio.SeqUtils.MeltingTemp docstring test ... ok Bio.SeqUtils.ProtParam docstring test ... ok Bio.SeqUtils.ProtParamData docstring test ... ok Bio.SeqUtils.lcc docstring test ... ok Bio.Sequencing docstring test ... ok Bio.Sequencing.Ace docstring test ... ok Bio.Sequencing.Applications 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.Sequencing.Phd docstring test ... ok Bio.Statistics docstring test ... ok Bio.Statistics.lowess docstring test ... ok Bio.SubsMat docstring test ... ok Bio.SubsMat.FreqTable docstring test ... ok Bio.SubsMat.MatrixInfo docstring test ... ok Bio.SwissProt docstring test ... ok Bio.SwissProt.KeyWList docstring test ... ok Bio.UniGene docstring test ... ok Bio.UniProt docstring test ... ok Bio.UniProt.GOA docstring test ... ok Bio.Wise docstring test ... ok Bio.Wise.dnal docstring test ... ok Bio.Wise.psw docstring test ... ok Bio._utils docstring test ... ok Bio.bgzf docstring test ... ok Bio.codonalign docstring test ... ok Bio.codonalign.chisq docstring test ... ok Bio.codonalign.codonalignment docstring test ... ok Bio.codonalign.codonseq docstring test ... ok Bio.cpairwise2 docstring test ... ok Bio.kNN docstring test ... ok Bio.motifs docstring test ... ok Bio.motifs._pwm docstring test ... ok Bio.motifs.alignace docstring test ... ok Bio.motifs.applications docstring test ... ok Bio.motifs.applications._xxmotif docstring test ... ok Bio.motifs.clusterbuster docstring test ... ok Bio.motifs.jaspar docstring test ... ok Bio.motifs.jaspar.db docstring test ... ok Bio.motifs.mast docstring test ... ok Bio.motifs.matrix docstring test ... ok Bio.motifs.meme docstring test ... ok Bio.motifs.minimal docstring test ... ok Bio.motifs.pfm docstring test ... ok Bio.motifs.thresholds docstring test ... ok Bio.motifs.transfac docstring test ... ok Bio.motifs.xms docstring test ... ok Bio.pairwise2 docstring test ... ok Bio.phenotype docstring test ... ok Bio.phenotype.phen_micro docstring test ... ok Bio.phenotype.pm_fitting docstring test ... skipped, missing Python dependency BioSQL docstring test ... ok BioSQL.BioSeq docstring test ... ok BioSQL.BioSeqDatabase docstring test ... ok BioSQL.DBUtils docstring test ... ok BioSQL.Loader docstring test ... ok ====================================================================== ERROR: test_GraphicsBitmaps ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Tests/run_tests.py", line 275, in runTest suite = loader.loadTestsFromName(name) File "/usr/lib/python3.10/unittest/loader.py", line 154, in loadTestsFromName module = __import__(module_name) File "/<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Tests/test_GraphicsBitmaps.py", line 119, in real_test() File "/<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Tests/test_GraphicsBitmaps.py", line 92, in real_test compare_plot.draw_to_file(output_file, "Testing Scatter Plots") File "/<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics/Comparative.py", line 96, in draw_to_file return _write(cur_drawing, output_file, self.output_format) File "/<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics/__init__.py", line 88, in _write return drawmethod.drawToFile(drawing, output_file, format, dpi=dpi) File "/usr/lib/python3/dist-packages/reportlab/graphics/renderPM.py", line 692, in drawToFile c = drawToPMCanvas(d, dpi=dpi, bg=bg, configPIL=configPIL, showBoundary=showBoundary,backend=backend) File "/usr/lib/python3/dist-packages/reportlab/graphics/renderPM.py", line 678, in drawToPMCanvas draw(d, c, 0, 0, showBoundary=showBoundary) File "/usr/lib/python3/dist-packages/reportlab/graphics/renderPM.py", line 49, in draw R.draw(renderScaledDrawing(drawing), canvas, x, y, showBoundary=showBoundary) File "/usr/lib/python3/dist-packages/reportlab/graphics/renderbase.py", line 185, in draw self.initState(x,y) #this is the push() File "/usr/lib/python3/dist-packages/reportlab/graphics/renderPM.py", line 96, in initState self.applyState() File "/usr/lib/python3/dist-packages/reportlab/graphics/renderPM.py", line 90, in applyState self._canvas.setFont(s['fontName'], s['fontSize']) File "/usr/lib/python3/dist-packages/reportlab/graphics/renderPM.py", line 406, in setFont _setFont(self._gs,fontName,fontSize) File "/usr/lib/python3/dist-packages/reportlab/graphics/utils.py", line 42, in setFont _errorDump(fontName,fontSize) File "/usr/lib/python3/dist-packages/reportlab/graphics/utils.py", line 29, in _errorDump rl_exec(code,dict(RenderPMError=RenderPMError)) File "", line 1, in reportlab.graphics.utils.RenderPMError: Error in setFont('Times-Roman',10) missing the T1 files? Originally : makeT1Font() argument 2 must be str, not None ====================================================================== ERROR: test_doctests (test_Tutorial.TutorialTestCase) Run tutorial doctests. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Tests/test_Tutorial.py", line 244, in test_doctests raise ValueError( ValueError: 1 Tutorial doctests failed: test_chapter_motifs_line_00030 ====================================================================== ERROR: test_simple (test_motifs.MotifTestPWM) Test if Bio.motifs PWM scoring works. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Tests/test_motifs.py", line 2222, in test_simple result = pssm.calculate(self.s) File "/<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs/matrix.py", line 364, in calculate scores = _calculate(self, sequence, m) File "/<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs/matrix.py", line 39, in _calculate _pwm.calculate(sequence, logodds, scores) SystemError: PY_SSIZE_T_CLEAN macro must be defined for '#' formats ====================================================================== ERROR: test_with_bad_char (test_motifs.MotifTestPWM) Test if Bio.motifs PWM scoring works with unexpected letters like N. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Tests/test_motifs.py", line 2255, in test_with_bad_char result = pssm.calculate(Seq("ACGTGTGCGTAGTGCGTN")) File "/<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs/matrix.py", line 364, in calculate scores = _calculate(self, sequence, m) File "/<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs/matrix.py", line 39, in _calculate _pwm.calculate(sequence, logodds, scores) SystemError: PY_SSIZE_T_CLEAN macro must be defined for '#' formats ====================================================================== ERROR: test_with_mixed_case (test_motifs.MotifTestPWM) Test if Bio.motifs PWM scoring works with mixed case. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Tests/test_motifs.py", line 2241, in test_with_mixed_case result = pssm.calculate(Seq("AcGTgTGCGtaGTGCGT")) File "/<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs/matrix.py", line 364, in calculate scores = _calculate(self, sequence, m) File "/<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs/matrix.py", line 39, in _calculate _pwm.calculate(sequence, logodds, scores) SystemError: PY_SSIZE_T_CLEAN macro must be defined for '#' formats ---------------------------------------------------------------------- Ran 516 tests in 445.678 seconds FAILED (failures = 3) Skipping any tests requiring internet access Python version: 3.10.0+ (default, Oct 17 2021, 09:10:32) [GCC 11.2.0] Operating system: posix linux E: pybuild pybuild:354: test: plugin custom failed with: exit code=1: set -e; \ mkdir -p /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/home; \ mkdir -p /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Doc/examples; \ cp -a Doc/Tutorial.tex /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Doc; \ cp -a Doc/Tutorial /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Doc; \ cp -a Doc/examples /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Doc; \ cp -a Tests /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build; \ cd /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/Tests; \ env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=/<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.10/build/home python3.10 run_tests.py --offline I: pybuild base:232: set -e; \ mkdir -p /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/home; \ mkdir -p /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Doc/examples; \ cp -a Doc/Tutorial.tex /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Doc; \ cp -a Doc/Tutorial /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Doc; \ cp -a Doc/examples /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Doc; \ cp -a Tests /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build; \ cd /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Tests; \ env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=/<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/home python3.9 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_BWA_tool ... 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_Blast_Record ... ok test_CAPS ... ok test_Chi2 ... ok test_ClustalOmega_tool ... ok test_Clustalw_tool ... ok test_Cluster ... ok test_CodonTable ... ok test_ColorSpiral ... ok test_Compass ... ok test_Consensus ... ok test_Crystal ... 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_GenomeDiagram ... Warn: Can't find .pfb for face 'Times-Roman' ok test_GraphicsBitmaps ... ERROR test_GraphicsChromosome ... ok test_GraphicsDistribution ... ok test_GraphicsGeneral ... ok test_HMMCasino ... ok test_HMMGeneral ... 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_LogisticRegression ... ok test_MafIO_index ... ok test_Mafft_tool ... ok test_MarkovModel ... /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Tests/test_MarkovModel.py:403: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray. training_outputs = array( /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Tests/test_MarkovModel.py:411: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray. training_states = array( ok test_Medline ... ok test_Muscle_tool ... ok test_NCBITextParser ... ok test_NCBIXML ... ok test_NCBI_BLAST_tools ... /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Tests/test_NCBI_BLAST_tools.py:477: 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( /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Tests/test_NCBI_BLAST_tools.py:477: 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( /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Tests/test_NCBI_BLAST_tools.py:477: 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( /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Tests/test_NCBI_BLAST_tools.py:477: 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( /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Tests/test_NCBI_BLAST_tools.py:477: 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( /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Tests/test_NCBI_BLAST_tools.py:477: 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: -mt_mode,-sorthits,-sorthsps,-subject_besthit) warnings.warn( /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Tests/test_NCBI_BLAST_tools.py:477: 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: -mt_mode,-sorthits,-sorthsps) warnings.warn( /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Tests/test_NCBI_BLAST_tools.py:477: 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( /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Tests/test_NCBI_BLAST_tools.py:477: 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( ok test_NCBI_qblast ... ok test_NMR ... ok test_NaiveBayes ... ok test_Nexus ... ok test_PAML_baseml ... ok test_PAML_codeml ... ok test_PAML_yn00 ... ok test_PDBList ... skipping. internet not available test_PDB_DSSP ... /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB/DSSP.py:250: UserWarning: Unknown or untrusted program in REMARK 3, trying all parsers to see if there is a match warnings.warn(err) /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB/DSSP.py:250: UserWarning: Unknown or untrusted program in REMARK 3, trying all parsers to see if there is a match warnings.warn(err) /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB/DSSP.py:250: UserWarning: Invalid mmCIF file use --verbose option to see errors warnings.warn(err) /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB/DSSP.py:250: UserWarning: Invalid mmCIF file use --verbose option to see errors warnings.warn(err) /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB/DSSP.py:250: UserWarning: Invalid mmCIF file use --verbose option to see errors warnings.warn(err) /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/PDB/DSSP.py:250: UserWarning: Invalid mmCIF file use --verbose option to see errors warnings.warn(err) ok test_PDB_Dice ... ok test_PDB_Disordered ... ok test_PDB_Exposure ... ok test_PDB_FragmentMapper ... ok test_PDB_KDTree ... ok test_PDB_MMCIF2Dict ... ok test_PDB_MMCIFIO ... ok test_PDB_MMCIFParser ... ok test_PDB_NACCESS ... ok test_PDB_PDBIO ... ok test_PDB_PDBParser ... ok test_PDB_Polypetide ... ok test_PDB_SMCRA ... ok test_PDB_StructureAlignment ... ok test_PDB_Superimposer ... ok test_PDB_internal_coords ... ok test_PDB_parse_pdb_header ... ok test_PDB_vectors ... ok test_PQR ... 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 ... ok 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_hhsuite2_text ... 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_Gck ... ok test_SeqIO_Insdc ... /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/GenBank/Scanner.py:303: BiopythonParserWarning: Non-standard feature line wrapping (didn't break on comma)? warnings.warn( ok test_SeqIO_NibIO ... ok test_SeqIO_PdbIO ... ok test_SeqIO_QualityIO ... ok test_SeqIO_SeqXML ... ok test_SeqIO_SnapGene ... ok test_SeqIO_Xdna ... 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 ... /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/SubsMat/__init__.py:126: BiopythonDeprecationWarning: Bio.SubsMat has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.substitution_matrices as a replacement, and contact the Biopython developers if you still need the Bio.SubsMat module. warnings.warn( 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_GOA ... ok test_Uniprot ... ok test_Wise ... ok test_align ... ok test_align_substitution_matrices ... ok test_bgzf ... ok test_cellosaurus ... ok test_codonalign ... /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/codonalign/codonalignment.py:113: BiopythonWarning: Please make sure the two CodonAlignment objects are sharing the same codon table. This is not checked by Biopython. warnings.warn( /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Seq.py:2309: 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( ok test_geo ... ok test_kNN ... ok test_lowess ... /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Statistics/__init__.py:11: BiopythonDeprecationWarning: Bio.Statistics has been deprecated, and we intend to remove it in a future release of Biopython. warnings.warn( ok test_motifs ... ok test_motifs_online ... skipping. internet not available test_pairwise2 ... ok test_pairwise2_no_C ... ok test_pairwise_aligner ... ok test_phenotype ... ok test_phenotype_fit ... ok test_phyml_tool ... skipping. Couldn't find the PhyML software. Install PhyML 3.0 or later if you want to use the Bio.Phylo.Applications wrapper. test_prodoc ... ok test_prosite1 ... ok test_prosite2 ... ok test_psw ... ok test_samtools_tool ... ok test_seq ... /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Seq.py:2334: 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( ok test_translate ... ok Bio docstring test ... ok Bio.Affy docstring test ... ok Bio.Affy.CelFile docstring test ... ok Bio.Align docstring test ... ok Bio.Align.AlignInfo docstring test ... ok Bio.Align.Applications docstring test ... ok Bio.Align.Applications._ClustalOmega docstring test ... ok Bio.Align.Applications._Clustalw 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._Prank docstring test ... ok Bio.Align.Applications._Probcons docstring test ... ok Bio.Align.Applications._TCoffee docstring test ... ok Bio.Align._aligners docstring test ... ok Bio.Align.substitution_matrices docstring test ... ok Bio.AlignIO docstring test ... ok Bio.AlignIO.ClustalIO docstring test ... ok Bio.AlignIO.EmbossIO docstring test ... ok Bio.AlignIO.FastaIO docstring test ... ok Bio.AlignIO.Interfaces docstring test ... ok Bio.AlignIO.MafIO docstring test ... ok Bio.AlignIO.MauveIO docstring test ... ok Bio.AlignIO.MsfIO docstring test ... ok Bio.AlignIO.NexusIO docstring test ... ok Bio.AlignIO.PhylipIO docstring test ... ok Bio.AlignIO.StockholmIO docstring test ... ok Bio.Application docstring test ... ok Bio.Blast docstring test ... ok Bio.Blast.Applications docstring test ... ok Bio.Blast.NCBIWWW docstring test ... ok Bio.Blast.NCBIXML docstring test ... ok Bio.Blast.ParseBlastTable docstring test ... ok Bio.Blast.Record docstring test ... ok Bio.CAPS docstring test ... ok Bio.Cluster docstring test ... ok Bio.Cluster._cluster docstring test ... ok Bio.Compass docstring test ... ok Bio.Crystal docstring test ... ok Bio.Data docstring test ... ok Bio.Data.CodonTable docstring test ... ok Bio.Data.IUPACData docstring test ... ok Bio.Data.SCOPData docstring test ... ok Bio.Emboss docstring test ... ok Bio.Emboss.Applications docstring test ... ok Bio.Emboss.Primer3 docstring test ... ok Bio.Emboss.PrimerSearch docstring test ... ok Bio.Entrez.Parser docstring test ... ok Bio.ExPASy.Enzyme docstring test ... ok Bio.ExPASy.Prodoc docstring test ... ok Bio.ExPASy.Prosite docstring test ... ok Bio.ExPASy.ScanProsite docstring test ... ok Bio.ExPASy.cellosaurus docstring test ... ok Bio.FSSP docstring test ... ok Bio.FSSP.FSSPTools docstring test ... ok Bio.FSSP.fssp_rec docstring test ... ok Bio.File docstring test ... ok Bio.GenBank docstring test ... ok Bio.GenBank.Record docstring test ... ok Bio.GenBank.Scanner docstring test ... ok Bio.GenBank.utils docstring test ... ok Bio.Geo docstring test ... ok Bio.Geo.Record docstring test ... ok Bio.Graphics docstring test ... ok Bio.Graphics.BasicChromosome docstring test ... ok Bio.Graphics.ColorSpiral docstring test ... ok Bio.Graphics.Comparative docstring test ... ok Bio.Graphics.DisplayRepresentation docstring test ... ok Bio.Graphics.Distribution docstring test ... ok Bio.Graphics.GenomeDiagram docstring test ... ok Bio.Graphics.GenomeDiagram._AbstractDrawer docstring test ... ok Bio.Graphics.GenomeDiagram._CircularDrawer docstring test ... ok Bio.Graphics.GenomeDiagram._Colors docstring test ... ok Bio.Graphics.GenomeDiagram._CrossLink docstring test ... ok Bio.Graphics.GenomeDiagram._Diagram docstring test ... ok Bio.Graphics.GenomeDiagram._Feature docstring test ... ok Bio.Graphics.GenomeDiagram._FeatureSet docstring test ... ok Bio.Graphics.GenomeDiagram._Graph docstring test ... ok Bio.Graphics.GenomeDiagram._GraphSet docstring test ... ok Bio.Graphics.GenomeDiagram._LinearDrawer docstring test ... ok Bio.Graphics.GenomeDiagram._Track docstring test ... ok Bio.Graphics.KGML_vis docstring test ... ok Bio.HMM docstring test ... ok Bio.HMM.DynamicProgramming docstring test ... ok Bio.HMM.MarkovModel docstring test ... ok Bio.HMM.Trainer docstring test ... ok Bio.HMM.Utilities docstring test ... ok Bio.KEGG docstring test ... ok Bio.KEGG.Compound docstring test ... ok Bio.KEGG.Enzyme docstring test ... ok Bio.KEGG.Gene docstring test ... ok Bio.KEGG.KGML docstring test ... ok Bio.KEGG.KGML.KGML_parser docstring test ... ok Bio.KEGG.KGML.KGML_pathway docstring test ... ok Bio.KEGG.Map docstring test ... ok Bio.KEGG.REST docstring test ... ok Bio.LogisticRegression docstring test ... ok Bio.MarkovModel docstring test ... ok Bio.MaxEntropy docstring test ... ok Bio.Medline docstring test ... ok Bio.NMR docstring test ... ok Bio.NMR.NOEtools docstring test ... ok Bio.NMR.xpktools docstring test ... ok Bio.NaiveBayes docstring test ... ok Bio.Nexus docstring test ... ok Bio.Nexus.Nexus docstring test ... ok Bio.Nexus.Nodes docstring test ... ok Bio.Nexus.StandardData docstring test ... ok Bio.Nexus.Trees docstring test ... ok Bio.Nexus.cnexus docstring test ... ok Bio.PDB docstring test ... ok Bio.PDB.AbstractPropertyMap docstring test ... ok Bio.PDB.Atom docstring test ... ok Bio.PDB.Chain docstring test ... ok Bio.PDB.DSSP docstring test ... ok Bio.PDB.Dice docstring test ... ok Bio.PDB.Entity docstring test ... ok Bio.PDB.FragmentMapper docstring test ... ok Bio.PDB.HSExposure docstring test ... ok Bio.PDB.MMCIF2Dict docstring test ... ok Bio.PDB.MMCIFParser docstring test ... ok Bio.PDB.Model docstring test ... ok Bio.PDB.NACCESS docstring test ... ok Bio.PDB.NeighborSearch docstring test ... ok Bio.PDB.PDBExceptions docstring test ... ok Bio.PDB.PDBIO docstring test ... ok Bio.PDB.PDBList docstring test ... ok Bio.PDB.PDBParser docstring test ... ok Bio.PDB.PICIO docstring test ... ok Bio.PDB.PSEA docstring test ... ok Bio.PDB.Polypeptide docstring test ... ok Bio.PDB.QCPSuperimposer docstring test ... ok Bio.PDB.QCPSuperimposer.qcprotmodule docstring test ... ok Bio.PDB.Residue docstring test ... ok Bio.PDB.ResidueDepth docstring test ... ok Bio.PDB.SCADIO docstring test ... ok Bio.PDB.Selection docstring test ... ok Bio.PDB.Structure docstring test ... ok Bio.PDB.StructureAlignment docstring test ... ok Bio.PDB.StructureBuilder docstring test ... ok Bio.PDB.Superimposer docstring test ... ok Bio.PDB.ic_data docstring test ... ok Bio.PDB.ic_rebuild docstring test ... ok Bio.PDB.internal_coords docstring test ... ok Bio.PDB.kdtrees docstring test ... ok Bio.PDB.mmcifio docstring test ... ok Bio.PDB.mmtf docstring test ... ok Bio.PDB.mmtf.DefaultParser docstring test ... ok Bio.PDB.mmtf.mmtfio docstring test ... ok Bio.PDB.parse_pdb_header docstring test ... ok Bio.PDB.vectors docstring test ... ok Bio.Pathway docstring test ... ok Bio.Pathway.Rep docstring test ... ok Bio.Pathway.Rep.Graph docstring test ... ok Bio.Pathway.Rep.MultiGraph docstring test ... ok Bio.Phylo docstring test ... ok Bio.Phylo.Applications docstring test ... ok Bio.Phylo.Applications._Fasttree docstring test ... ok Bio.Phylo.Applications._Phyml docstring test ... ok Bio.Phylo.Applications._Raxml docstring test ... ok Bio.Phylo.BaseTree docstring test ... ok Bio.Phylo.CDAO docstring test ... ok Bio.Phylo.CDAOIO docstring test ... ok Bio.Phylo.Consensus docstring test ... ok Bio.Phylo.NeXML docstring test ... ok Bio.Phylo.NeXMLIO docstring test ... ok Bio.Phylo.Newick docstring test ... ok Bio.Phylo.NewickIO docstring test ... ok Bio.Phylo.NexusIO docstring test ... ok Bio.Phylo.PAML docstring test ... ok Bio.Phylo.PAML._paml docstring test ... ok Bio.Phylo.PAML._parse_baseml docstring test ... ok Bio.Phylo.PAML._parse_codeml docstring test ... ok Bio.Phylo.PAML._parse_yn00 docstring test ... ok Bio.Phylo.PAML.baseml docstring test ... ok Bio.Phylo.PAML.chi2 docstring test ... ok Bio.Phylo.PAML.codeml docstring test ... ok Bio.Phylo.PAML.yn00 docstring test ... ok Bio.Phylo.PhyloXML docstring test ... ok Bio.Phylo.PhyloXMLIO docstring test ... ok Bio.Phylo.TreeConstruction docstring test ... ok Bio.Phylo._cdao_owl docstring test ... ok Bio.Phylo._io docstring test ... ok Bio.Phylo._utils docstring test ... ok Bio.PopGen docstring test ... ok Bio.PopGen.GenePop docstring test ... ok Bio.PopGen.GenePop.Controller docstring test ... ok Bio.PopGen.GenePop.EasyController docstring test ... ok Bio.PopGen.GenePop.FileParser docstring test ... ok Bio.PopGen.GenePop.LargeFileParser docstring test ... ok Bio.Restriction docstring test ... ok Bio.Restriction.PrintFormat docstring test ... ok Bio.Restriction.Restriction docstring test ... ok Bio.Restriction.Restriction_Dictionary docstring test ... ok Bio.SCOP docstring test ... ok Bio.SCOP.Cla docstring test ... ok Bio.SCOP.Des docstring test ... ok Bio.SCOP.Dom docstring test ... ok Bio.SCOP.Hie docstring test ... ok Bio.SCOP.Raf docstring test ... ok Bio.SCOP.Residues docstring test ... ok Bio.SVDSuperimposer docstring test ... ok Bio.SearchIO docstring test ... ok Bio.SearchIO.BlastIO docstring test ... ok Bio.SearchIO.BlastIO.blast_tab docstring test ... ok Bio.SearchIO.BlastIO.blast_text docstring test ... ok Bio.SearchIO.BlastIO.blast_xml docstring test ... ok Bio.SearchIO.BlatIO docstring test ... ok Bio.SearchIO.ExonerateIO docstring test ... ok Bio.SearchIO.ExonerateIO._base docstring test ... ok Bio.SearchIO.ExonerateIO.exonerate_cigar docstring test ... ok Bio.SearchIO.ExonerateIO.exonerate_text docstring test ... ok Bio.SearchIO.ExonerateIO.exonerate_vulgar docstring test ... ok Bio.SearchIO.FastaIO docstring test ... ok Bio.SearchIO.HHsuiteIO docstring test ... ok Bio.SearchIO.HHsuiteIO.hhsuite2_text docstring test ... ok Bio.SearchIO.HmmerIO docstring test ... ok Bio.SearchIO.HmmerIO._base docstring test ... ok Bio.SearchIO.HmmerIO.hmmer2_text docstring test ... ok Bio.SearchIO.HmmerIO.hmmer3_domtab docstring test ... ok Bio.SearchIO.HmmerIO.hmmer3_tab docstring test ... ok Bio.SearchIO.HmmerIO.hmmer3_text docstring test ... ok Bio.SearchIO.InterproscanIO docstring test ... ok Bio.SearchIO.InterproscanIO.interproscan_xml docstring test ... ok Bio.SearchIO._index docstring test ... ok Bio.SearchIO._legacy docstring test ... ok Bio.SearchIO._legacy.NCBIStandalone docstring test ... ok Bio.SearchIO._legacy.ParserSupport docstring test ... ok Bio.SearchIO._model docstring test ... ok Bio.SearchIO._model._base docstring test ... ok Bio.SearchIO._model.hit docstring test ... ok Bio.SearchIO._model.hsp docstring test ... ok Bio.SearchIO._model.query docstring test ... ok Bio.SearchIO._utils docstring test ... ok Bio.Seq docstring test ... ok Bio.SeqFeature docstring test ... ok Bio.SeqIO docstring test ... ok Bio.SeqIO.AbiIO docstring test ... ok Bio.SeqIO.AceIO docstring test ... ok Bio.SeqIO.FastaIO docstring test ... ok Bio.SeqIO.GckIO docstring test ... ok Bio.SeqIO.IgIO docstring test ... ok Bio.SeqIO.InsdcIO docstring test ... ok Bio.SeqIO.Interfaces docstring test ... ok Bio.SeqIO.NibIO docstring test ... ok Bio.SeqIO.PdbIO docstring test ... ok Bio.SeqIO.PhdIO docstring test ... ok Bio.SeqIO.PirIO docstring test ... ok Bio.SeqIO.QualityIO docstring test ... ok Bio.SeqIO.SeqXmlIO docstring test ... ok Bio.SeqIO.SffIO docstring test ... ok Bio.SeqIO.SnapGeneIO docstring test ... ok Bio.SeqIO.SwissIO docstring test ... ok Bio.SeqIO.TabIO docstring test ... ok Bio.SeqIO.UniprotIO docstring test ... ok Bio.SeqIO.XdnaIO docstring test ... ok Bio.SeqIO._index docstring test ... ok Bio.SeqRecord docstring test ... ok Bio.SeqUtils docstring test ... ok Bio.SeqUtils.CheckSum docstring test ... ok Bio.SeqUtils.CodonUsage docstring test ... ok Bio.SeqUtils.CodonUsageIndices docstring test ... ok Bio.SeqUtils.IsoelectricPoint docstring test ... ok Bio.SeqUtils.MeltingTemp docstring test ... ok Bio.SeqUtils.ProtParam docstring test ... ok Bio.SeqUtils.ProtParamData docstring test ... ok Bio.SeqUtils.lcc docstring test ... ok Bio.Sequencing docstring test ... ok Bio.Sequencing.Ace docstring test ... ok Bio.Sequencing.Applications 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.Sequencing.Phd docstring test ... ok Bio.Statistics docstring test ... ok Bio.Statistics.lowess docstring test ... ok Bio.SubsMat docstring test ... ok Bio.SubsMat.FreqTable docstring test ... ok Bio.SubsMat.MatrixInfo docstring test ... ok Bio.SwissProt docstring test ... ok Bio.SwissProt.KeyWList docstring test ... ok Bio.UniGene docstring test ... ok Bio.UniProt docstring test ... ok Bio.UniProt.GOA docstring test ... ok Bio.Wise docstring test ... ok Bio.Wise.dnal docstring test ... ok Bio.Wise.psw docstring test ... ok Bio._utils docstring test ... ok Bio.bgzf docstring test ... ok Bio.codonalign docstring test ... ok Bio.codonalign.chisq docstring test ... ok Bio.codonalign.codonalignment docstring test ... ok Bio.codonalign.codonseq docstring test ... ok Bio.cpairwise2 docstring test ... ok Bio.kNN docstring test ... ok Bio.motifs docstring test ... ok Bio.motifs._pwm docstring test ... ok Bio.motifs.alignace docstring test ... ok Bio.motifs.applications docstring test ... ok Bio.motifs.applications._xxmotif docstring test ... ok Bio.motifs.clusterbuster docstring test ... ok Bio.motifs.jaspar docstring test ... ok Bio.motifs.jaspar.db docstring test ... ok Bio.motifs.mast docstring test ... ok Bio.motifs.matrix docstring test ... ok Bio.motifs.meme docstring test ... ok Bio.motifs.minimal docstring test ... ok Bio.motifs.pfm docstring test ... ok Bio.motifs.thresholds docstring test ... ok Bio.motifs.transfac docstring test ... ok Bio.motifs.xms docstring test ... ok Bio.pairwise2 docstring test ... ok Bio.phenotype docstring test ... ok Bio.phenotype.phen_micro docstring test ... ok Bio.phenotype.pm_fitting docstring test ... ok BioSQL docstring test ... ok BioSQL.BioSeq docstring test ... ok BioSQL.BioSeqDatabase docstring test ... ok BioSQL.DBUtils docstring test ... ok BioSQL.Loader docstring test ... ok ====================================================================== ERROR: test_GraphicsBitmaps ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Tests/run_tests.py", line 275, in runTest suite = loader.loadTestsFromName(name) File "/usr/lib/python3.9/unittest/loader.py", line 154, in loadTestsFromName module = __import__(module_name) File "/<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Tests/test_GraphicsBitmaps.py", line 119, in real_test() File "/<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Tests/test_GraphicsBitmaps.py", line 92, in real_test compare_plot.draw_to_file(output_file, "Testing Scatter Plots") File "/<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Graphics/Comparative.py", line 96, in draw_to_file return _write(cur_drawing, output_file, self.output_format) File "/<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Bio/Graphics/__init__.py", line 88, in _write return drawmethod.drawToFile(drawing, output_file, format, dpi=dpi) File "/usr/lib/python3/dist-packages/reportlab/graphics/renderPM.py", line 692, in drawToFile c = drawToPMCanvas(d, dpi=dpi, bg=bg, configPIL=configPIL, showBoundary=showBoundary,backend=backend) File "/usr/lib/python3/dist-packages/reportlab/graphics/renderPM.py", line 678, in drawToPMCanvas draw(d, c, 0, 0, showBoundary=showBoundary) File "/usr/lib/python3/dist-packages/reportlab/graphics/renderPM.py", line 49, in draw R.draw(renderScaledDrawing(drawing), canvas, x, y, showBoundary=showBoundary) File "/usr/lib/python3/dist-packages/reportlab/graphics/renderbase.py", line 185, in draw self.initState(x,y) #this is the push() File "/usr/lib/python3/dist-packages/reportlab/graphics/renderPM.py", line 96, in initState self.applyState() File "/usr/lib/python3/dist-packages/reportlab/graphics/renderPM.py", line 90, in applyState self._canvas.setFont(s['fontName'], s['fontSize']) File "/usr/lib/python3/dist-packages/reportlab/graphics/renderPM.py", line 406, in setFont _setFont(self._gs,fontName,fontSize) File "/usr/lib/python3/dist-packages/reportlab/graphics/utils.py", line 42, in setFont _errorDump(fontName,fontSize) File "/usr/lib/python3/dist-packages/reportlab/graphics/utils.py", line 29, in _errorDump rl_exec(code,dict(RenderPMError=RenderPMError)) File "", line 1, in reportlab.graphics.utils.RenderPMError: Error in setFont('Times-Roman',10) missing the T1 files? Originally : makeT1Font() argument 2 must be str, not None ---------------------------------------------------------------------- Ran 516 tests in 484.350 seconds FAILED (failures = 1) Skipping any tests requiring internet access Python version: 3.9.7 (default, Sep 24 2021, 09:43:00) [GCC 11.2.0] Operating system: posix linux E: pybuild pybuild:354: test: plugin custom failed with: exit code=1: set -e; \ mkdir -p /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/home; \ mkdir -p /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Doc/examples; \ cp -a Doc/Tutorial.tex /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Doc; \ cp -a Doc/Tutorial /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Doc; \ cp -a Doc/examples /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Doc; \ cp -a Tests /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build; \ cd /<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/Tests; \ env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=/<>/python-biopython-1.78+dfsg/.pybuild/cpython3_3.9/build/home python3.9 run_tests.py --offline rm -fr -- /tmp/dh-xdg-rundir-5iNodC_z dh_auto_test: error: pybuild --test -i python{version} -p "3.10 3.9" --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:84: override_dh_auto_test] Error 25 make[1]: Leaving directory '/<>/python-biopython-1.78+dfsg' make: *** [debian/rules:42: binary-arch] Error 2 dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2021-10-22T10:58:01Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: ppc64el Build Type: any Build-Space: n/a Build-Time: 1186 Distribution: jammy-proposed Fail-Stage: build Host Architecture: ppc64el Install-Time: 101 Job: python-biopython_1.78+dfsg-5ubuntu2.dsc Machine Architecture: ppc64el Package: python-biopython Package-Time: 1289 Source-Version: 1.78+dfsg-5ubuntu2 Space: n/a Status: attempted Version: 1.78+dfsg-5ubuntu2 -------------------------------------------------------------------------------- Finished at 2021-10-22T10:58:01Z Build needed 00:21:29, no disk space E: Build failure (dpkg-buildpackage died) Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=jammy --arch=ppc64el PACKAGEBUILD-22291105 Scanning for processes to kill in build PACKAGEBUILD-22291105