https://launchpad.net/ubuntu/+source/python-biopython/1.81+dfsg-1build1/+build/26951322 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos01-arm64-017 5.4.0-164-generic #181-Ubuntu SMP Fri Sep 1 13:42:23 UTC 2023 aarch64 Buildd toolchain package versions: launchpad-buildd_235~645~ubuntu20.04.1 python3-lpbuildd_235~645~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.11 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1.1. Syncing the system clock with the buildd NTP service... 7 Nov 11:17:41 ntpdate[1870]: adjust time server 10.211.37.1 offset -0.000400 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-26951322 --image-type chroot /home/buildd/filecache-default/59612f0fc5bae33f6226b6e60c2e882b82c04bd0 Creating target for build PACKAGEBUILD-26951322 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-26951322 Starting target for build PACKAGEBUILD-26951322 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-26951322 'deb http://ftpmaster.internal/ubuntu noble main universe' 'deb http://ftpmaster.internal/ubuntu noble-security main universe' 'deb http://ftpmaster.internal/ubuntu noble-updates main universe' 'deb http://ftpmaster.internal/ubuntu noble-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-26951322 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-26951322 Updating target for build PACKAGEBUILD-26951322 Get:1 http://ftpmaster.internal/ubuntu noble InRelease [240 kB] Get:2 http://ftpmaster.internal/ubuntu noble-security InRelease [74.9 kB] Get:3 http://ftpmaster.internal/ubuntu noble-updates InRelease [74.9 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease [102 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main armhf Packages [1336 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main Translation-en [517 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe armhf Packages [14.4 MB] Get:8 http://ftpmaster.internal/ubuntu noble/universe Translation-en [6003 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main armhf Packages [138 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [54.1 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf Packages [1221 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [464 kB] Fetched 24.6 MB in 6s (4048 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following package was automatically installed and is no longer required: libunistring2 Use 'sudo apt autoremove' to remove it. The following NEW packages will be installed: libunistring5 The following packages will be upgraded: apt apt-utils base-files base-passwd bash-completion binutils binutils-arm-linux-gnueabihf binutils-common cpp-13 debianutils diffutils dpkg dpkg-dev fakeroot g++-13 gcc-13 gcc-13-base grep libapparmor1 libapt-pkg6.0 libargon2-1 libasan8 libatomic1 libaudit-common libaudit1 libbinutils libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcc1-0 libctf-nobfd0 libctf0 libdb5.3 libdpkg-perl libfakeroot libgcc-13-dev libgcc-s1 libgnutls30 libgomp1 libidn2-0 liblzma5 libncursesw6 libnsl-dev libnsl2 libpng16-16 libselinux1 libsemanage-common libsemanage2 libsframe1 libsqlite3-0 libssl3 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtinfo6 libubsan1 libudev1 libxxhash0 libzstd1 mawk ncurses-base ncurses-bin openssl optipng systemd systemd-dev systemd-sysv xz-utils 71 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 69.8 MB of archives. After this operation, 1747 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble/main armhf libnsl-dev armhf 1.3.0-3 [65.8 kB] Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libc6-dev armhf 2.38-3ubuntu1 [1347 kB] Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libc-dev-bin armhf 2.38-3ubuntu1 [18.9 kB] Get:4 http://ftpmaster.internal/ubuntu noble/main armhf libnsl2 armhf 1.3.0-3 [35.9 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main armhf libcc1-0 armhf 13.2.0-6ubuntu1 [43.7 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main armhf gcc-13-base armhf 13.2.0-6ubuntu1 [44.3 kB] Get:7 http://ftpmaster.internal/ubuntu noble/main armhf libgcc-s1 armhf 13.2.0-6ubuntu1 [41.4 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main armhf libgomp1 armhf 13.2.0-6ubuntu1 [120 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main armhf libatomic1 armhf 13.2.0-6ubuntu1 [7766 B] Get:10 http://ftpmaster.internal/ubuntu noble/main armhf libasan8 armhf 13.2.0-6ubuntu1 [2749 kB] Get:11 http://ftpmaster.internal/ubuntu noble/main armhf libubsan1 armhf 13.2.0-6ubuntu1 [1072 kB] Get:12 http://ftpmaster.internal/ubuntu noble/main armhf g++-13 armhf 13.2.0-6ubuntu1 [9436 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main armhf libstdc++-13-dev armhf 13.2.0-6ubuntu1 [2447 kB] Get:14 http://ftpmaster.internal/ubuntu noble/main armhf libgcc-13-dev armhf 13.2.0-6ubuntu1 [901 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main armhf gcc-13 armhf 13.2.0-6ubuntu1 [16.5 MB] Get:16 http://ftpmaster.internal/ubuntu noble/main armhf cpp-13 armhf 13.2.0-6ubuntu1 [8246 kB] Get:17 http://ftpmaster.internal/ubuntu noble/main armhf libstdc++6 armhf 13.2.0-6ubuntu1 [697 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main armhf libzstd1 armhf 1.5.5+dfsg2-2 [265 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main armhf libctf0 armhf 2.41-6ubuntu1 [86.8 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main armhf libctf-nobfd0 armhf 2.41-6ubuntu1 [87.2 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main armhf libsframe1 armhf 2.41-6ubuntu1 [12.9 kB] Get:22 http://ftpmaster.internal/ubuntu noble/main armhf libbinutils armhf 2.41-6ubuntu1 [457 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main armhf binutils-common armhf 2.41-6ubuntu1 [228 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main armhf binutils armhf 2.41-6ubuntu1 [3080 B] Get:25 http://ftpmaster.internal/ubuntu noble/main armhf binutils-arm-linux-gnueabihf armhf 2.41-6ubuntu1 [2934 kB] Get:26 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libc6 armhf 2.38-3ubuntu1 [2818 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main armhf base-files armhf 13ubuntu4 [73.4 kB] Get:28 http://ftpmaster.internal/ubuntu noble/main armhf debianutils armhf 5.14 [88.0 kB] Get:29 http://ftpmaster.internal/ubuntu noble/main armhf diffutils armhf 1:3.10-1 [167 kB] Get:30 http://ftpmaster.internal/ubuntu noble-proposed/main armhf liblzma5 armhf 5.4.4-0.1 [110 kB] Get:31 http://ftpmaster.internal/ubuntu noble/main armhf libapparmor1 armhf 4.0.0~alpha2-0ubuntu6 [43.6 kB] Get:32 http://ftpmaster.internal/ubuntu noble/main armhf libaudit-common all 1:3.1.1-1build1 [5510 B] Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcap-ng0 armhf 0.8.3-1build3 [13.7 kB] Get:34 http://ftpmaster.internal/ubuntu noble/main armhf libaudit1 armhf 1:3.1.1-1build1 [44.0 kB] Get:35 http://ftpmaster.internal/ubuntu noble/main armhf libselinux1 armhf 3.5-1build1 [70.1 kB] Get:36 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libssl3 armhf 3.0.10-1ubuntu2.1 [1572 kB] Get:37 http://ftpmaster.internal/ubuntu noble/main armhf systemd-sysv armhf 253.5-1ubuntu7 [11.5 kB] Get:38 http://ftpmaster.internal/ubuntu noble/main armhf systemd-dev all 253.5-1ubuntu7 [78.5 kB] Get:39 http://ftpmaster.internal/ubuntu noble/main armhf systemd armhf 253.5-1ubuntu7 [3043 kB] Get:40 http://ftpmaster.internal/ubuntu noble/main armhf libsystemd-shared armhf 253.5-1ubuntu7 [1781 kB] Get:41 http://ftpmaster.internal/ubuntu noble/main armhf libsystemd0 armhf 253.5-1ubuntu7 [379 kB] Get:42 http://ftpmaster.internal/ubuntu noble/main armhf libudev1 armhf 253.5-1ubuntu7 [151 kB] Get:43 http://ftpmaster.internal/ubuntu noble/main armhf libxxhash0 armhf 0.8.2-2 [31.3 kB] Get:44 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libapt-pkg6.0 armhf 2.7.6 [960 kB] Get:45 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dpkg armhf 1.22.1ubuntu2 [1348 kB] Get:46 http://ftpmaster.internal/ubuntu noble/main armhf grep armhf 3.11-3 [157 kB] Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ncurses-bin armhf 6.4+20231016-1 [176 kB] Get:48 http://ftpmaster.internal/ubuntu noble/main armhf base-passwd armhf 3.6.2 [51.0 kB] Get:49 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libc-bin armhf 2.38-3ubuntu1 [532 kB] Get:50 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ncurses-base all 6.4+20231016-1 [24.7 kB] Get:51 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdb5.3 armhf 5.3.28+dfsg2-3 [652 kB] Get:52 http://ftpmaster.internal/ubuntu noble-proposed/main armhf apt armhf 2.7.6 [1360 kB] Get:53 http://ftpmaster.internal/ubuntu noble-proposed/main armhf apt-utils armhf 2.7.6 [212 kB] Get:54 http://ftpmaster.internal/ubuntu noble/main armhf libunistring5 armhf 1.1-2 [512 kB] Get:55 http://ftpmaster.internal/ubuntu noble/main armhf libidn2-0 armhf 2.3.4-1build1 [94.2 kB] Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgnutls30 armhf 3.8.1-4ubuntu3 [942 kB] Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsemanage-common all 3.5-1build1 [9982 B] Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsemanage2 armhf 3.5-1build1 [84.1 kB] Get:59 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libncursesw6 armhf 6.4+20231016-1 [117 kB] Get:60 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtinfo6 armhf 6.4+20231016-1 [91.0 kB] Get:61 http://ftpmaster.internal/ubuntu noble/main armhf mawk armhf 1.3.4.20230808-1 [114 kB] Get:62 http://ftpmaster.internal/ubuntu noble/main armhf libargon2-1 armhf 0~20190702+dfsg-4 [22.3 kB] Get:63 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsqlite3-0 armhf 3.44.0-1 [586 kB] Get:64 http://ftpmaster.internal/ubuntu noble-proposed/main armhf openssl armhf 3.0.10-1ubuntu2.1 [1158 kB] Get:65 http://ftpmaster.internal/ubuntu noble/main armhf bash-completion all 1:2.11-8 [180 kB] Get:66 http://ftpmaster.internal/ubuntu noble/main armhf libpng16-16 armhf 1.6.40-2 [166 kB] Get:67 http://ftpmaster.internal/ubuntu noble-proposed/main armhf xz-utils armhf 5.4.4-0.1 [266 kB] Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dpkg-dev all 1.22.1ubuntu2 [1148 kB] Get:69 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdpkg-perl all 1.22.1ubuntu2 [285 kB] Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libfakeroot armhf 1.32.2-1 [28.0 kB] Get:71 http://ftpmaster.internal/ubuntu noble-proposed/main armhf fakeroot armhf 1.32.2-1 [68.8 kB] Get:72 http://ftpmaster.internal/ubuntu noble/main armhf optipng armhf 0.7.7-3 [82.2 kB] Preconfiguring packages ... 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Initializing machine ID from random generator. Setting up optipng (0.7.7-3) ... Setting up libgcc-13-dev:armhf (13.2.0-6ubuntu1) ... Setting up libnsl-dev:armhf (1.3.0-3) ... Setting up libc6-dev:armhf (2.38-3ubuntu1) ... Setting up binutils-arm-linux-gnueabihf (2.41-6ubuntu1) ... Setting up libstdc++-13-dev:armhf (13.2.0-6ubuntu1) ... Setting up systemd-sysv (253.5-1ubuntu7) ... Setting up binutils (2.41-6ubuntu1) ... Setting up dpkg-dev (1.22.1ubuntu2) ... Setting up gcc-13 (13.2.0-6ubuntu1) ... Setting up g++-13 (13.2.0-6ubuntu1) ... Processing triggers for libc-bin (2.38-3ubuntu1) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-26951322 armhf noble-proposed -c chroot:build-PACKAGEBUILD-26951322 --arch=armhf --dist=noble-proposed --nolog python-biopython_1.81+dfsg-1build1.dsc Initiating build PACKAGEBUILD-26951322 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-164-generic #181-Ubuntu SMP Fri Sep 1 13:42:23 UTC 2023 armv7l sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos01-arm64-017.buildd +==============================================================================+ | python-biopython 1.81+dfsg-1build1 (armhf) Tue, 07 Nov 2023 11:18:06 +0000 | +==============================================================================+ Package: python-biopython Version: 1.81+dfsg-1build1 Source Version: 1.81+dfsg-1build1 Distribution: noble-proposed Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-26951322/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/python-biopython-ys1VpR/resolver-6XrwtX' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- python-biopython_1.81+dfsg-1build1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/python-biopython-ys1VpR/python-biopython-1.81+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/python-biopython-ys1VpR' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-python, python3-all-dev, python3-numpy, flex, python3-reportlab (>= 4.0.4-1~), hevea, texlive-latex-base, texlive-latex-extra, texlive-fonts-recommended, bwa, clustalo, clustalw, dialign, dssp, emboss, fasttree, mafft, ncbi-blast+, phylip, prank, probcons, python3-networkx, python3-mysqldb, python3-matplotlib, python3-mmtf, python3-pil, python3-rdflib, python3-psycopg2, python3-pygments, python3-scipy, python3-setuptools, python3-unittest2, samtools, t-coffee, wise, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), dh-python, python3-all-dev, python3-numpy, flex, python3-reportlab (>= 4.0.4-1~), hevea, texlive-latex-base, texlive-latex-extra, texlive-fonts-recommended, bwa, clustalo, clustalw, dialign, dssp, emboss, fasttree, mafft, ncbi-blast+, phylip, prank, probcons, python3-networkx, python3-mysqldb, python3-matplotlib, python3-mmtf, python3-pil, python3-rdflib, python3-psycopg2, python3-pygments, python3-scipy, python3-setuptools, python3-unittest2, samtools, t-coffee, wise, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [963 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [658 B] Get:5 copy:/<>/apt_archive ./ Packages [678 B] Fetched 2299 B in 0s (156 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: apt-utils bash-completion ca-certificates debconf-i18n krb5-locales libgpg-error-l10n libgpm2 liblocale-gettext-perl libnss-nis libnss-nisplus libtext-charwidth-perl libtext-iconv-perl libtext-wrapi18n-perl libunistring2 openssl psmisc uuid-runtime Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev blt bwa clustalo clustalw debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dialign dssp dwz emboss emboss-data emboss-lib fasttree file flex fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono fonts-lmodern fonts-lyx fonts-noto-core fonts-noto-mono fonts-urw-base35 gettext gettext-base ghostscript groff-base hevea hicolor-icon-theme imagemagick imagemagick-6-common imagemagick-6.q16 intltool-debian libapache-pom-java libarchive-zip-perl libargtable2-0 libavahi-client3 libavahi-common-data libavahi-common3 libblas3 libboost-regex1.74.0 libbrotli1 libbsd0 libcairo2 libcifpp-data libcifpp5 libcommons-logging-java libcommons-parent-java libcups2 libcurl3-gnutls libdav1d7 libdbus-1-3 libde265-0 libdebhelper-perl libdeflate0 libdw1 libelf1 libexpat1 libexpat1-dev libfftw3-double3 libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgd3 libgfortran5 libglib2.0-0 libgraphite2-3 libgs-common libgs10 libgs10-common libharfbuzz0b libheif-plugin-dav1d libheif-plugin-libde265 libheif1 libhpdf-2.3.0 libhts3 libhtscodecs2 libice6 libicu72 libidn12 libijs-0.35 libimagequant0 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libkpathsea6 liblapack3 liblbfgsb0 liblcms2-2 libldap2 liblerc4 liblmdb0 liblqr-1-0 libltdl7 libmagic-mgc libmagic1 libmagickcore-6.q16-6 libmagickwand-6.q16-6 libmbedcrypto7 libmbedtls14 libmbedx509-1 libmysqlclient21 libncurses6 libnetpbm11 libnghttp2-14 libopenjp2-7 libpaper-utils libpaper1 libpdfbox-java libpipeline1 libpixman-1-0 libpotrace0 libpq5 libpsl5 libptexenc1 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.11 libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib libpython3.12 libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib libqhull-r8.0 libraqm0 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libssh-4 libsub-override-perl libsynctex2 libtcl8.6 libteckit0 libtexlua53-5 libtiff6 libtk8.6 libtool libuchardet0 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxslt1.1 libxss1 libxt6 libzzip-0-13 m4 mafft man-db media-types mysql-common ncbi-blast+ ncbi-data netpbm phylip po-debconf poppler-data prank preview-latex-style probcons python-matplotlib-data python3 python3-all python3-all-dev python3-appdirs python3-attr python3-brotli python3-cairo python3-contourpy python3-cycler python3-dateutil python3-decorator python3-dev python3-distutils python3-fonttools python3-freetype python3-fs python3-isodate python3-kiwisolver python3-lib2to3 python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-mmtf python3-mpmath python3-msgpack python3-mysqldb python3-networkx python3-numpy python3-packaging python3-pil python3-pil.imagetk python3-pkg-resources python3-psycopg2 python3-pygments python3-pyparsing python3-rdflib python3-reportlab python3-rlpycairo python3-scipy python3-setuptools python3-six python3-sympy python3-tk python3-tz python3-ufolib2 python3-unittest2 python3.11 python3.11-dev python3.11-minimal python3.12 python3.12-dev python3.12-minimal samtools t-coffee t1utils tex-common texlive-base texlive-binaries texlive-fonts-recommended texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures tk8.6-blt2.5 ucf unicode-data wise wise-data x11-common xdg-utils xfonts-encodings xfonts-utils zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc blt-demo clustalx seaview dh-make flit python3-build python3-installer python3-wheel emboss-doc emboss-test embassy bison flex-doc fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre gettext-doc libasprintf-dev libgettextpo-dev groff hevea-doc imagemagick-doc autotrace cups-bsd | lpr | lprng curl enscript ffmpeg gimp gnuplot grads graphviz hp2xx html2ps libwmf-bin mplayer povray radiance sane-utils transfig ufraw-batch libavalon-framework-java libcommons-logging-java-doc libexcalibur-logkit-java liblog4j1.2-java cups-common libfftw3-bin libfftw3-dev libgd-tools low-memory-monitor libheif-plugin-ffmpegdec libheif-plugin-jpegdec libheif-plugin-jpegenc libheif-plugin-j2kdec libheif-plugin-j2kenc libheif-plugin-rav1e libheif-plugin-svtenc libjs-jquery-ui-docs liblcms2-utils libmagickcore-6.q16-6-extra tcl8.6 tk8.6 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-venv python-attr-doc python-cycler-doc python-lxml-doc cm-super-minimal dvipng fonts-staypuft gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip python3-tornado texlive-extra-utils python-mpmath-doc python3-gmpy2 default-mysql-server | virtual-mysql-server python-networkx-doc python3-gdal python3-pydot python3-pygraphviz gfortran python3-pytest python-pil-doc python-psycopg2-doc python-pygments-doc ttf-bitstream-vera python-pyparsing-doc python-rdflib-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc python-scipy-doc python-setuptools-doc texlive-fonts-extra python-sympy-doc tix python3-tk-dbg python3.11-venv python3.11-doc binfmt-support python3.12-venv python3.12-doc cwltool boxshade t-coffee-examples perl-tk xpdf | pdf-viewer xzdec texlive-binaries-sse2 texlive-fonts-recommended-doc texlive-latex-base-doc wp2latex icc-profiles libfile-which-perl texlive-latex-extra-doc texlive-science texlive-latex-recommended-doc texlive-luatex texlive-pstricks dot2tex prerex texlive-pictures-doc vprerex wise-doc Recommended packages: primer3 libfl-dev curl | wget | lynx libmagickcore-6.q16-6-extra dbus libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs fonts-droid-fallback libheif-plugin-aomenc libheif-plugin-x265 javascript-common libldap-common gsfonts publicsuffix libsasl2-modules libltdl-dev blast2 libwww-perl lynx ruby libmail-sendmail-perl python3-bs4 python3-html5lib python3-yaml python3-olefile python3-sparqlwrapper isympy-common amap-align dialign-tx fsa kalign libsoap-lite-perl libxml-simple-perl muscle mustang poa proda tm-align lmodern dvisvgm tex-gyre tipa default-jre libspreadsheet-parseexcel-perl texlive-plain-generic tk libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: autoconf automake autopoint autotools-dev blt bwa clustalo clustalw debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dialign dssp dwz emboss emboss-data emboss-lib fasttree file flex fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono fonts-lmodern fonts-lyx fonts-noto-core fonts-noto-mono fonts-urw-base35 gettext gettext-base ghostscript groff-base hevea hicolor-icon-theme imagemagick imagemagick-6-common imagemagick-6.q16 intltool-debian libapache-pom-java libarchive-zip-perl libargtable2-0 libavahi-client3 libavahi-common-data libavahi-common3 libblas3 libboost-regex1.74.0 libbrotli1 libbsd0 libcairo2 libcifpp-data libcifpp5 libcommons-logging-java libcommons-parent-java libcups2 libcurl3-gnutls libdav1d7 libdbus-1-3 libde265-0 libdebhelper-perl libdeflate0 libdw1 libelf1 libexpat1 libexpat1-dev libfftw3-double3 libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgd3 libgfortran5 libglib2.0-0 libgraphite2-3 libgs-common libgs10 libgs10-common libharfbuzz0b libheif-plugin-dav1d libheif-plugin-libde265 libheif1 libhpdf-2.3.0 libhts3 libhtscodecs2 libice6 libicu72 libidn12 libijs-0.35 libimagequant0 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libkpathsea6 liblapack3 liblbfgsb0 liblcms2-2 libldap2 liblerc4 liblmdb0 liblqr-1-0 libltdl7 libmagic-mgc libmagic1 libmagickcore-6.q16-6 libmagickwand-6.q16-6 libmbedcrypto7 libmbedtls14 libmbedx509-1 libmysqlclient21 libncurses6 libnetpbm11 libnghttp2-14 libopenjp2-7 libpaper-utils libpaper1 libpdfbox-java libpipeline1 libpixman-1-0 libpotrace0 libpq5 libpsl5 libptexenc1 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.11 libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib libpython3.12 libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib libqhull-r8.0 libraqm0 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libssh-4 libsub-override-perl libsynctex2 libtcl8.6 libteckit0 libtexlua53-5 libtiff6 libtk8.6 libtool libuchardet0 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxslt1.1 libxss1 libxt6 libzzip-0-13 m4 mafft man-db media-types mysql-common ncbi-blast+ ncbi-data netpbm phylip po-debconf poppler-data prank preview-latex-style probcons python-matplotlib-data python3 python3-all python3-all-dev python3-appdirs python3-attr python3-brotli python3-cairo python3-contourpy python3-cycler python3-dateutil python3-decorator python3-dev python3-distutils python3-fonttools python3-freetype python3-fs python3-isodate python3-kiwisolver python3-lib2to3 python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-mmtf python3-mpmath python3-msgpack python3-mysqldb python3-networkx python3-numpy python3-packaging python3-pil python3-pil.imagetk python3-pkg-resources python3-psycopg2 python3-pygments python3-pyparsing python3-rdflib python3-reportlab python3-rlpycairo python3-scipy python3-setuptools python3-six python3-sympy python3-tk python3-tz python3-ufolib2 python3-unittest2 python3.11 python3.11-dev python3.11-minimal python3.12 python3.12-dev python3.12-minimal samtools sbuild-build-depends-main-dummy t-coffee t1utils tex-common texlive-base texlive-binaries texlive-fonts-recommended texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures tk8.6-blt2.5 ucf unicode-data wise wise-data x11-common xdg-utils xfonts-encodings xfonts-utils zlib1g-dev 0 upgraded, 271 newly installed, 0 to remove and 0 not upgraded. Need to get 338 MB of archives. After this operation, 1500 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [896 B] Get:2 http://ftpmaster.internal/ubuntu noble/main armhf libpython3.11-minimal armhf 3.11.6-3 [824 kB] Get:3 http://ftpmaster.internal/ubuntu noble/main armhf libexpat1 armhf 2.5.0-2 [63.7 kB] Get:4 http://ftpmaster.internal/ubuntu noble/main armhf python3.11-minimal armhf 3.11.6-3 [1896 kB] Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-minimal armhf 3.11.4-5ubuntu1 [26.9 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main armhf media-types all 10.1.0 [27.5 kB] Get:7 http://ftpmaster.internal/ubuntu noble/main armhf libpython3.11-stdlib armhf 3.11.6-3 [1804 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main armhf python3.11 armhf 3.11.6-3 [579 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3-stdlib armhf 3.11.4-5ubuntu1 [9568 B] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3 armhf 3.11.4-5ubuntu1 [22.9 kB] Get:11 http://ftpmaster.internal/ubuntu noble/main armhf m4 armhf 1.4.19-4 [235 kB] Get:12 http://ftpmaster.internal/ubuntu noble/main armhf flex armhf 2.6.4-8.2 [291 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main armhf libfftw3-double3 armhf 3.3.10-1ubuntu1 [363 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libbrotli1 armhf 1.1.0-1 [318 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main armhf libfreetype6 armhf 2.13.2+dfsg-1 [331 kB] Get:16 http://ftpmaster.internal/ubuntu noble/main armhf fonts-noto-mono all 20201225-2 [435 kB] Get:17 http://ftpmaster.internal/ubuntu noble/main armhf fonts-noto-core all 20201225-2 [13.3 MB] Get:18 http://ftpmaster.internal/ubuntu noble/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main armhf fonts-dejavu-core all 2.37-8 [835 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main armhf libfontenc1 armhf 1:1.1.4-1build3 [12.2 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main armhf x11-common all 1:7.7+23ubuntu2 [23.4 kB] Get:22 http://ftpmaster.internal/ubuntu noble/main armhf xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main armhf xfonts-utils armhf 1:7.7+6build2 [89.8 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main armhf fonts-urw-base35 all 20200910-7 [11.0 MB] Get:25 http://ftpmaster.internal/ubuntu noble/main armhf fontconfig-config armhf 2.14.2-4ubuntu1 [35.8 kB] Get:26 http://ftpmaster.internal/ubuntu noble/main armhf libfontconfig1 armhf 2.14.2-4ubuntu1 [112 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main armhf libsharpyuv0 armhf 1.3.2-0.3 [13.3 kB] Get:28 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libdav1d7 armhf 1.3.0-2 [299 kB] Get:29 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libheif-plugin-dav1d armhf 1.17.1-1ubuntu3 [9850 B] Get:30 http://ftpmaster.internal/ubuntu noble/universe armhf libde265-0 armhf 1.0.12-2 [157 kB] Get:31 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libheif-plugin-libde265 armhf 1.17.1-1ubuntu3 [10.4 kB] Get:32 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libheif1 armhf 1.17.1-1ubuntu3 [265 kB] Get:33 http://ftpmaster.internal/ubuntu noble/main armhf libjbig0 armhf 2.1-6.1ubuntu1 [24.9 kB] Get:34 http://ftpmaster.internal/ubuntu noble/main armhf libjpeg-turbo8 armhf 2.1.5-2ubuntu1 [123 kB] Get:35 http://ftpmaster.internal/ubuntu noble/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] Get:36 http://ftpmaster.internal/ubuntu noble/main armhf liblcms2-2 armhf 2.14-2 [134 kB] Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libglib2.0-0 armhf 2.78.1-2 [1403 kB] Get:38 http://ftpmaster.internal/ubuntu noble/universe armhf liblqr-1-0 armhf 0.4.2-2.1 [22.2 kB] Get:39 http://ftpmaster.internal/ubuntu noble/main armhf libltdl7 armhf 2.4.7-7 [37.9 kB] Get:40 http://ftpmaster.internal/ubuntu noble/main armhf libopenjp2-7 armhf 2.5.0-2 [160 kB] Get:41 http://ftpmaster.internal/ubuntu noble/main armhf libdeflate0 armhf 1.18-1 [40.7 kB] Get:42 http://ftpmaster.internal/ubuntu noble/main armhf liblerc4 armhf 4.0.0+ds-2ubuntu2 [151 kB] Get:43 http://ftpmaster.internal/ubuntu noble/main armhf libwebp7 armhf 1.3.2-0.3 [183 kB] Get:44 http://ftpmaster.internal/ubuntu noble/main armhf libtiff6 armhf 4.5.1+git230720-1ubuntu1 [177 kB] Get:45 http://ftpmaster.internal/ubuntu noble/main armhf libwebpdemux2 armhf 1.3.2-0.3 [11.8 kB] Get:46 http://ftpmaster.internal/ubuntu noble/main armhf libwebpmux3 armhf 1.3.2-0.3 [22.4 kB] Get:47 http://ftpmaster.internal/ubuntu noble/main armhf libxau6 armhf 1:1.0.9-1build5 [6622 B] Get:48 http://ftpmaster.internal/ubuntu noble/main armhf libbsd0 armhf 0.11.7-4 [36.9 kB] Get:49 http://ftpmaster.internal/ubuntu noble/main armhf libxdmcp6 armhf 1:1.1.3-0ubuntu5 [9452 B] Get:50 http://ftpmaster.internal/ubuntu noble/main armhf libxcb1 armhf 1.15-1 [45.4 kB] Get:51 http://ftpmaster.internal/ubuntu noble/main armhf libx11-data all 2:1.8.7-1 [115 kB] Get:52 http://ftpmaster.internal/ubuntu noble/main armhf libx11-6 armhf 2:1.8.7-1 [585 kB] Get:53 http://ftpmaster.internal/ubuntu noble/main armhf libxext6 armhf 2:1.3.4-1build1 [26.4 kB] Get:54 http://ftpmaster.internal/ubuntu noble/main armhf libicu72 armhf 72.1-3ubuntu3 [10.5 MB] Get:55 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libxml2 armhf 2.9.14+dfsg-1.3build1 [599 kB] Get:56 http://ftpmaster.internal/ubuntu noble/universe armhf imagemagick-6-common all 8:6.9.11.60+dfsg-1.6ubuntu1 [64.8 kB] Get:57 http://ftpmaster.internal/ubuntu noble/universe armhf libmagickcore-6.q16-6 armhf 8:6.9.11.60+dfsg-1.6ubuntu1 [1703 kB] Get:58 http://ftpmaster.internal/ubuntu noble/universe armhf libmagickwand-6.q16-6 armhf 8:6.9.11.60+dfsg-1.6ubuntu1 [342 kB] Get:59 http://ftpmaster.internal/ubuntu noble/main armhf poppler-data all 0.4.12-1 [2060 kB] Get:60 http://ftpmaster.internal/ubuntu noble/main armhf libpython3.12-minimal armhf 3.12.0-1 [811 kB] Get:61 http://ftpmaster.internal/ubuntu noble/main armhf python3.12-minimal armhf 3.12.0-1 [2038 kB] Get:62 http://ftpmaster.internal/ubuntu noble/main armhf libdbus-1-3 armhf 1.14.10-1ubuntu1 [188 kB] Get:63 http://ftpmaster.internal/ubuntu noble/main armhf libelf1 armhf 0.189-4 [48.7 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main armhf libfribidi0 armhf 1.0.13-3 [24.0 kB] Get:65 http://ftpmaster.internal/ubuntu noble/main armhf python3-pkg-resources all 68.1.2-2 [167 kB] Get:66 http://ftpmaster.internal/ubuntu noble/main armhf python3-pygments all 2.15.1+dfsg-1 [820 kB] Get:67 http://ftpmaster.internal/ubuntu noble/main armhf ucf all 3.0043+nmu1 [56.5 kB] Get:68 http://ftpmaster.internal/ubuntu noble/main armhf libmagic-mgc armhf 1:5.45-2 [307 kB] Get:69 http://ftpmaster.internal/ubuntu noble/main armhf libmagic1 armhf 1:5.45-2 [80.9 kB] Get:70 http://ftpmaster.internal/ubuntu noble/main armhf file armhf 1:5.45-2 [21.1 kB] Get:71 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gettext-base armhf 0.21-13build1 [37.7 kB] Get:72 http://ftpmaster.internal/ubuntu noble/main armhf libuchardet0 armhf 0.0.7-1build2 [75.7 kB] Get:73 http://ftpmaster.internal/ubuntu noble/main armhf groff-base armhf 1.23.0-3 [948 kB] Get:74 http://ftpmaster.internal/ubuntu noble/main armhf liblmdb0 armhf 0.9.31-1 [39.8 kB] Get:75 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libncurses6 armhf 6.4+20231016-1 [87.8 kB] Get:76 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnghttp2-14 armhf 1.58.0-1 [68.2 kB] Get:77 http://ftpmaster.internal/ubuntu noble/main armhf libpipeline1 armhf 1.5.7-1 [26.2 kB] Get:78 http://ftpmaster.internal/ubuntu noble/main armhf libpsl5 armhf 0.21.2-1build1 [55.5 kB] Get:79 http://ftpmaster.internal/ubuntu noble-proposed/main armhf man-db armhf 2.12.0-1 [1195 kB] Get:80 http://ftpmaster.internal/ubuntu noble/main armhf autoconf all 2.71-3 [339 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main armhf autotools-dev all 20220109.1 [44.9 kB] Get:82 http://ftpmaster.internal/ubuntu noble/main armhf automake all 1:1.16.5-1.3 [558 kB] Get:83 http://ftpmaster.internal/ubuntu noble-proposed/main armhf autopoint all 0.21-13build1 [422 kB] Get:84 http://ftpmaster.internal/ubuntu noble/main armhf libtcl8.6 armhf 8.6.13+dfsg-2 [902 kB] Get:85 http://ftpmaster.internal/ubuntu noble/main armhf libxrender1 armhf 1:0.9.10-1.1 [16.5 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main armhf libxft2 armhf 2.3.6-1 [36.8 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main armhf libxss1 armhf 1:1.2.3-1build2 [7580 B] Get:88 http://ftpmaster.internal/ubuntu noble/main armhf libtk8.6 armhf 8.6.13-2 [680 kB] Get:89 http://ftpmaster.internal/ubuntu noble/main armhf tk8.6-blt2.5 armhf 2.5.3+dfsg-4.1build2 [538 kB] Get:90 http://ftpmaster.internal/ubuntu noble/main armhf blt armhf 2.5.3+dfsg-4.1build2 [4838 B] Get:91 http://ftpmaster.internal/ubuntu noble/universe armhf bwa armhf 0.7.17-7 [194 kB] Get:92 http://ftpmaster.internal/ubuntu noble/universe armhf libargtable2-0 armhf 13-1.1 [11.9 kB] Get:93 http://ftpmaster.internal/ubuntu noble/universe armhf clustalo armhf 1.2.4-7 [225 kB] Get:94 http://ftpmaster.internal/ubuntu noble/universe armhf clustalw armhf 2.1+lgpl-7 [249 kB] Get:95 http://ftpmaster.internal/ubuntu noble/main armhf libdebhelper-perl all 13.11.7ubuntu1 [85.8 kB] Get:96 http://ftpmaster.internal/ubuntu noble/main armhf libtool all 2.4.7-7 [166 kB] Get:97 http://ftpmaster.internal/ubuntu noble/main armhf dh-autoreconf all 20 [16.1 kB] Get:98 http://ftpmaster.internal/ubuntu noble/main armhf libarchive-zip-perl all 1.68-1 [90.2 kB] Get:99 http://ftpmaster.internal/ubuntu noble/main armhf libsub-override-perl all 0.09-4 [8706 B] Get:100 http://ftpmaster.internal/ubuntu noble/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:101 http://ftpmaster.internal/ubuntu noble/main armhf dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:102 http://ftpmaster.internal/ubuntu noble/main armhf libdw1 armhf 0.189-4 [233 kB] Get:103 http://ftpmaster.internal/ubuntu noble/main armhf debugedit armhf 1:5.0-5 [42.8 kB] Get:104 http://ftpmaster.internal/ubuntu noble/main armhf dwz armhf 0.15-1 [109 kB] Get:105 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gettext armhf 0.21-13build1 [799 kB] Get:106 http://ftpmaster.internal/ubuntu noble/main armhf intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:107 http://ftpmaster.internal/ubuntu noble/main armhf po-debconf all 1.0.21+nmu1 [233 kB] Get:108 http://ftpmaster.internal/ubuntu noble/main armhf debhelper all 13.11.7ubuntu1 [940 kB] Get:109 http://ftpmaster.internal/ubuntu noble/main armhf python3-lib2to3 all 3.11.5-1 [79.0 kB] Get:110 http://ftpmaster.internal/ubuntu noble/main armhf python3-distutils all 3.11.5-1 [131 kB] Get:111 http://ftpmaster.internal/ubuntu noble/main armhf python3-setuptools all 68.1.2-2 [396 kB] Get:112 http://ftpmaster.internal/ubuntu noble/universe armhf dh-python all 6.20231025 [110 kB] Get:113 http://ftpmaster.internal/ubuntu noble/universe armhf dialign armhf 2.2.1-11 [137 kB] Get:114 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libboost-regex1.74.0 armhf 1.74.0+ds1-23ubuntu2 [472 kB] Get:115 http://ftpmaster.internal/ubuntu noble/universe armhf libcifpp-data all 5.0.7.1-3 [450 kB] Get:116 http://ftpmaster.internal/ubuntu noble/universe armhf libcifpp5 armhf 5.0.7.1-3 [810 kB] Get:117 http://ftpmaster.internal/ubuntu noble/universe armhf dssp armhf 4.2.2-2 [626 kB] Get:118 http://ftpmaster.internal/ubuntu noble/main armhf libxpm4 armhf 1:3.5.12-1.1ubuntu1 [30.8 kB] Get:119 http://ftpmaster.internal/ubuntu noble/main armhf libgd3 armhf 2.3.3-9ubuntu1 [106 kB] Get:120 http://ftpmaster.internal/ubuntu noble/universe armhf libhpdf-2.3.0 armhf 2.3.0+dfsg-1build1 [330 kB] Get:121 http://ftpmaster.internal/ubuntu noble/main armhf mysql-common all 5.8+1.1.0 [6626 B] Get:122 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmysqlclient21 armhf 8.0.35-1 [1288 kB] Get:123 http://ftpmaster.internal/ubuntu noble/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-3 [18.9 kB] Get:124 http://ftpmaster.internal/ubuntu noble/main armhf libsasl2-2 armhf 2.1.28+dfsg1-3 [49.6 kB] Get:125 http://ftpmaster.internal/ubuntu noble/main armhf libldap2 armhf 2.6.6+dfsg-1~exp1ubuntu1 [170 kB] Get:126 http://ftpmaster.internal/ubuntu noble/main armhf libpq5 armhf 15.4-1ubuntu1 [117 kB] Get:127 http://ftpmaster.internal/ubuntu noble/universe armhf emboss-lib armhf 6.6.0+dfsg-12ubuntu1 [2407 kB] Get:128 http://ftpmaster.internal/ubuntu noble/universe armhf emboss-data all 6.6.0+dfsg-12ubuntu1 [61.0 MB] Get:129 http://ftpmaster.internal/ubuntu noble/universe armhf emboss armhf 6.6.0+dfsg-12ubuntu1 [932 kB] Get:130 http://ftpmaster.internal/ubuntu noble/main armhf fonts-dejavu-extra all 2.37-8 [1947 kB] Get:131 http://ftpmaster.internal/ubuntu noble/universe armhf fonts-lmodern all 2.005-1 [4799 kB] Get:132 http://ftpmaster.internal/ubuntu noble/universe armhf fonts-lyx all 2.3.7-1 [167 kB] Get:133 http://ftpmaster.internal/ubuntu noble/main armhf libgs-common all 10.01.2~dfsg1-0ubuntu2.1 [175 kB] Get:134 http://ftpmaster.internal/ubuntu noble/main armhf libgs10-common all 10.01.2~dfsg1-0ubuntu2.1 [601 kB] Get:135 http://ftpmaster.internal/ubuntu noble/main armhf libavahi-common-data armhf 0.8-10ubuntu1 [27.7 kB] Get:136 http://ftpmaster.internal/ubuntu noble/main armhf libavahi-common3 armhf 0.8-10ubuntu1 [19.9 kB] Get:137 http://ftpmaster.internal/ubuntu noble/main armhf libavahi-client3 armhf 0.8-10ubuntu1 [24.2 kB] Get:138 http://ftpmaster.internal/ubuntu noble/main armhf libcups2 armhf 2.4.6-0ubuntu3 [236 kB] Get:139 http://ftpmaster.internal/ubuntu noble/main armhf libidn12 armhf 1.41-1 [55.0 kB] Get:140 http://ftpmaster.internal/ubuntu noble/main armhf libijs-0.35 armhf 0.35-15.1 [13.6 kB] Get:141 http://ftpmaster.internal/ubuntu noble/main armhf libjbig2dec0 armhf 0.19-3build2 [58.2 kB] Get:142 http://ftpmaster.internal/ubuntu noble/main armhf libpaper1 armhf 1.1.29 [12.5 kB] Get:143 http://ftpmaster.internal/ubuntu noble/main armhf libice6 armhf 2:1.0.10-1build2 [36.4 kB] Get:144 http://ftpmaster.internal/ubuntu noble/main armhf libsm6 armhf 2:1.2.3-1build2 [15.1 kB] Get:145 http://ftpmaster.internal/ubuntu noble/main armhf libxt6 armhf 1:1.2.1-1.1 [142 kB] Get:146 http://ftpmaster.internal/ubuntu noble/main armhf libgs10 armhf 10.01.2~dfsg1-0ubuntu2.1 [4363 kB] Get:147 http://ftpmaster.internal/ubuntu noble/main armhf ghostscript armhf 10.01.2~dfsg1-0ubuntu2.1 [43.3 kB] Get:148 http://ftpmaster.internal/ubuntu noble/universe armhf libnetpbm11 armhf 2:11.03.06-1 [92.7 kB] Get:149 http://ftpmaster.internal/ubuntu noble/universe armhf netpbm armhf 2:11.03.06-1 [1897 kB] Get:150 http://ftpmaster.internal/ubuntu noble/universe armhf tex-common all 6.18 [32.8 kB] Get:151 http://ftpmaster.internal/ubuntu noble/main armhf libpaper-utils armhf 1.1.29 [8170 B] Get:152 http://ftpmaster.internal/ubuntu noble/main armhf libkpathsea6 armhf 2023.20230311.66589-6 [57.1 kB] Get:153 http://ftpmaster.internal/ubuntu noble/main armhf libptexenc1 armhf 2023.20230311.66589-6 [36.8 kB] Get:154 http://ftpmaster.internal/ubuntu noble/main armhf libsynctex2 armhf 2023.20230311.66589-6 [46.9 kB] Get:155 http://ftpmaster.internal/ubuntu noble/main armhf libtexlua53-5 armhf 2023.20230311.66589-6 [97.0 kB] Get:156 http://ftpmaster.internal/ubuntu noble/main armhf t1utils armhf 1.41-4build2 [53.1 kB] Get:157 http://ftpmaster.internal/ubuntu noble/main armhf libpixman-1-0 armhf 0.42.2-1 [184 kB] Get:158 http://ftpmaster.internal/ubuntu noble/main armhf libxcb-render0 armhf 1.15-1 [15.2 kB] Get:159 http://ftpmaster.internal/ubuntu noble/main armhf libxcb-shm0 armhf 1.15-1 [5852 B] Get:160 http://ftpmaster.internal/ubuntu noble/main armhf libcairo2 armhf 1.18.0-1 [481 kB] Get:161 http://ftpmaster.internal/ubuntu noble/main armhf libgraphite2-3 armhf 1.3.14-1build2 [65.2 kB] Get:162 http://ftpmaster.internal/ubuntu noble/main armhf libharfbuzz0b armhf 8.0.1-1 [433 kB] Get:163 http://ftpmaster.internal/ubuntu noble/universe armhf libpotrace0 armhf 1.16-2 [14.6 kB] Get:164 http://ftpmaster.internal/ubuntu noble/universe armhf libteckit0 armhf 2.5.11+ds1-1 [336 kB] Get:165 http://ftpmaster.internal/ubuntu noble/main armhf libxmu6 armhf 2:1.1.3-3 [41.6 kB] Get:166 http://ftpmaster.internal/ubuntu noble/main armhf libxaw7 armhf 2:1.0.14-1 [157 kB] Get:167 http://ftpmaster.internal/ubuntu noble/main armhf libxi6 armhf 2:1.8-1build1 [26.6 kB] Get:168 http://ftpmaster.internal/ubuntu noble/universe armhf libzzip-0-13 armhf 0.13.72+dfsg.1-1.1 [23.0 kB] Get:169 http://ftpmaster.internal/ubuntu noble/universe armhf texlive-binaries armhf 2023.20230311.66589-6 [7159 kB] Get:170 http://ftpmaster.internal/ubuntu noble/main armhf xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] Get:171 http://ftpmaster.internal/ubuntu noble/universe armhf texlive-base all 2023.20231007-1 [21.7 MB] Get:172 http://ftpmaster.internal/ubuntu noble/main armhf hicolor-icon-theme all 0.17-2 [9976 B] Get:173 http://ftpmaster.internal/ubuntu noble/universe armhf imagemagick-6.q16 armhf 8:6.9.11.60+dfsg-1.6ubuntu1 [222 kB] Get:174 http://ftpmaster.internal/ubuntu noble/universe armhf imagemagick armhf 8:6.9.11.60+dfsg-1.6ubuntu1 [14.6 kB] Get:175 http://ftpmaster.internal/ubuntu noble/universe armhf hevea armhf 2.36-2 [1938 kB] Get:176 http://ftpmaster.internal/ubuntu noble/universe armhf libapache-pom-java all 29-2 [5284 B] Get:177 http://ftpmaster.internal/ubuntu noble/main armhf libblas3 armhf 3.11.0-2build1 [123 kB] Get:178 http://ftpmaster.internal/ubuntu noble/universe armhf libcommons-parent-java all 56-1 [10.7 kB] Get:179 http://ftpmaster.internal/ubuntu noble/universe armhf libcommons-logging-java all 1.2-4 [59.8 kB] Get:180 http://ftpmaster.internal/ubuntu noble/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2build4 [52.8 kB] Get:181 http://ftpmaster.internal/ubuntu noble/main armhf libssh-4 armhf 0.10.5-3ubuntu1 [166 kB] Get:182 http://ftpmaster.internal/ubuntu noble/main armhf libcurl3-gnutls armhf 8.2.1-1ubuntu3.1 [275 kB] Get:183 http://ftpmaster.internal/ubuntu noble/main armhf libexpat1-dev armhf 2.5.0-2 [119 kB] Get:184 http://ftpmaster.internal/ubuntu noble/main armhf libgfortran5 armhf 13.2.0-6ubuntu1 [300 kB] Get:185 http://ftpmaster.internal/ubuntu noble/universe armhf libhtscodecs2 armhf 1.5.2-1 [65.4 kB] Get:186 http://ftpmaster.internal/ubuntu noble/universe armhf libhts3 armhf 1.17+ds-1 [381 kB] Get:187 http://ftpmaster.internal/ubuntu noble/main armhf libimagequant0 armhf 2.17.0-1 [28.8 kB] Get:188 http://ftpmaster.internal/ubuntu noble/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] Get:189 http://ftpmaster.internal/ubuntu noble/universe armhf libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] Get:190 http://ftpmaster.internal/ubuntu noble/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] Get:191 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libjs-sphinxdoc all 7.2.6-2 [149 kB] Get:192 http://ftpmaster.internal/ubuntu noble/main armhf liblapack3 armhf 3.11.0-2build1 [1988 kB] Get:193 http://ftpmaster.internal/ubuntu noble/universe armhf liblbfgsb0 armhf 3.0+dfsg.4-1 [27.1 kB] Get:194 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libmbedcrypto7 armhf 2.28.5-1 [175 kB] Get:195 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libmbedx509-1 armhf 2.28.5-1 [42.1 kB] Get:196 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libmbedtls14 armhf 2.28.5-1 [75.7 kB] Get:197 http://ftpmaster.internal/ubuntu noble/main armhf libpython3.11 armhf 3.11.6-3 [1940 kB] Get:198 http://ftpmaster.internal/ubuntu noble/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-1ubuntu5 [880 kB] Get:199 http://ftpmaster.internal/ubuntu noble/main armhf libpython3.11-dev armhf 3.11.6-3 [3914 kB] Get:200 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3-dev armhf 3.11.4-5ubuntu1 [9826 B] Get:201 http://ftpmaster.internal/ubuntu noble/main armhf libpython3.12-stdlib armhf 3.12.0-1 [1887 kB] Get:202 http://ftpmaster.internal/ubuntu noble/main armhf libpython3.12 armhf 3.12.0-1 [2110 kB] Get:203 http://ftpmaster.internal/ubuntu noble/main armhf libpython3.12-dev armhf 3.12.0-1 [4188 kB] Get:204 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3-all-dev armhf 3.11.4-5ubuntu1 [914 B] Get:205 http://ftpmaster.internal/ubuntu noble/universe armhf libqhull-r8.0 armhf 2020.2-6 [173 kB] Get:206 http://ftpmaster.internal/ubuntu noble/main armhf libraqm0 armhf 0.10.1-1 [12.2 kB] Get:207 http://ftpmaster.internal/ubuntu noble/main armhf libxslt1.1 armhf 1.1.35-1 [147 kB] Get:208 http://ftpmaster.internal/ubuntu noble/universe armhf mafft armhf 7.505-1 [928 kB] Get:209 http://ftpmaster.internal/ubuntu noble/universe armhf ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB] Get:210 http://ftpmaster.internal/ubuntu noble/universe armhf ncbi-blast+ armhf 2.12.0+ds-4 [12.1 MB] Get:211 http://ftpmaster.internal/ubuntu noble/universe armhf phylip armhf 1:3.697+dfsg-2 [755 kB] Get:212 http://ftpmaster.internal/ubuntu noble/universe armhf prank armhf 0.0.170427+dfsg-3 [340 kB] Get:213 http://ftpmaster.internal/ubuntu noble/universe armhf preview-latex-style all 12.2-1ubuntu1 [185 kB] Get:214 http://ftpmaster.internal/ubuntu noble/universe armhf probcons armhf 1.12-14 [120 kB] Get:215 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf python-matplotlib-data all 3.6.3-1ubuntu3 [2936 kB] Get:216 http://ftpmaster.internal/ubuntu noble/main armhf python3.12 armhf 3.12.0-1 [629 kB] Get:217 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-all armhf 3.11.4-5ubuntu1 [910 B] Get:218 http://ftpmaster.internal/ubuntu noble/main armhf python3.11-dev armhf 3.11.6-3 [508 kB] Get:219 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-dev armhf 3.11.4-5ubuntu1 [26.8 kB] Get:220 http://ftpmaster.internal/ubuntu noble/main armhf python3.12-dev armhf 3.12.0-1 [571 kB] Get:221 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-all-dev armhf 3.11.4-5ubuntu1 [918 B] Get:222 http://ftpmaster.internal/ubuntu noble/main armhf python3-appdirs all 1.4.4-4 [10.9 kB] Get:223 http://ftpmaster.internal/ubuntu noble/main armhf python3-attr all 23.1.0-2 [50.6 kB] Get:224 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf python3-brotli armhf 1.1.0-1 [327 kB] Get:225 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-cairo armhf 1.24.0-3build1 [111 kB] Get:226 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-numpy armhf 1:1.24.2-1ubuntu1 [4410 kB] Get:227 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf python3-contourpy armhf 1.0.7-1build2 [262 kB] Get:228 http://ftpmaster.internal/ubuntu noble/universe armhf python3-cycler all 0.11.0-1 [8156 B] Get:229 http://ftpmaster.internal/ubuntu noble/main armhf python3-six all 1.16.0-4 [12.4 kB] Get:230 http://ftpmaster.internal/ubuntu noble/main armhf python3-dateutil all 2.8.2-3 [79.2 kB] Get:231 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-decorator all 5.1.1-5 [10.1 kB] Get:232 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf python3-scipy armhf 1.10.1-5ubuntu1 [18.3 MB] Get:233 http://ftpmaster.internal/ubuntu noble/universe armhf python3-ufolib2 all 0.16.0+dfsg1-1 [33.5 kB] Get:234 http://ftpmaster.internal/ubuntu noble/universe armhf python3-mpmath all 1.2.1-2 [419 kB] Get:235 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf python3-sympy all 1.12-6 [3966 kB] Get:236 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-tz all 2023.3.post1-1 [31.3 kB] Get:237 http://ftpmaster.internal/ubuntu noble/universe armhf python3-fs all 2.4.16-2 [91.0 kB] Get:238 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-lxml armhf 4.9.3-1build1 [2015 kB] Get:239 http://ftpmaster.internal/ubuntu noble/universe armhf python3-lz4 armhf 4.0.2+dfsg-1build2 [26.0 kB] Get:240 http://ftpmaster.internal/ubuntu noble/universe armhf unicode-data all 15.1.0-1 [8878 kB] Get:241 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf python3-fonttools armhf 4.38.0-1build2 [1175 kB] Get:242 http://ftpmaster.internal/ubuntu noble/universe armhf python3-freetype all 2.4.0-1 [83.1 kB] Get:243 http://ftpmaster.internal/ubuntu noble/universe armhf python3-isodate all 0.6.1-1 [24.7 kB] Get:244 http://ftpmaster.internal/ubuntu noble/universe armhf python3-kiwisolver armhf 1.4.4-1build2 [75.6 kB] Get:245 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-pil armhf 10.1.0-1 [442 kB] Get:246 http://ftpmaster.internal/ubuntu noble/main armhf python3-tk armhf 3.11.5-1 [108 kB] Get:247 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf python3-pil.imagetk armhf 10.1.0-1 [9038 B] Get:248 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-pyparsing all 3.1.1-1 [86.2 kB] Get:249 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-packaging all 23.2-1 [40.6 kB] Get:250 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf python3-matplotlib armhf 3.6.3-1ubuntu3 [7224 kB] Get:251 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-msgpack armhf 1.0.3-3build1 [93.4 kB] Get:252 http://ftpmaster.internal/ubuntu noble/universe armhf python3-mmtf all 1.1.3-1 [16.2 kB] Get:253 http://ftpmaster.internal/ubuntu noble/main armhf python3-mysqldb armhf 1.4.6-2build2 [49.7 kB] Get:254 http://ftpmaster.internal/ubuntu noble/main armhf python3-networkx all 2.8.8-1ubuntu1 [1468 kB] Get:255 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-psycopg2 armhf 2.9.6-3build1 [162 kB] Get:256 http://ftpmaster.internal/ubuntu noble/universe armhf python3-rdflib all 6.1.1-2 [362 kB] Get:257 http://ftpmaster.internal/ubuntu noble/universe armhf python3-rlpycairo all 0.3.0-3 [9130 B] Get:258 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf python3-reportlab all 4.0.6-1 [682 kB] Get:259 http://ftpmaster.internal/ubuntu noble/main armhf python3-unittest2 all 1.1.0-9 [76.3 kB] Get:260 http://ftpmaster.internal/ubuntu noble/universe armhf samtools armhf 1.17-1 [588 kB] Get:261 http://ftpmaster.internal/ubuntu noble/universe armhf t-coffee armhf 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 [968 kB] Get:262 http://ftpmaster.internal/ubuntu noble/universe armhf texlive-fonts-recommended all 2023.20231007-1 [4972 kB] Get:263 http://ftpmaster.internal/ubuntu noble/universe armhf texlive-latex-base all 2023.20231007-1 [1222 kB] Get:264 http://ftpmaster.internal/ubuntu noble/universe armhf libfontbox-java all 1:1.8.16-4 [208 kB] Get:265 http://ftpmaster.internal/ubuntu noble/universe armhf libpdfbox-java all 1:1.8.16-4 [5521 kB] Get:266 http://ftpmaster.internal/ubuntu noble/universe armhf texlive-latex-recommended all 2023.20231007-1 [8818 kB] Get:267 http://ftpmaster.internal/ubuntu noble/universe armhf texlive-pictures all 2023.20231007-1 [15.9 MB] Get:268 http://ftpmaster.internal/ubuntu noble/universe armhf texlive-latex-extra all 2023.20231007-2 [19.1 MB] Get:269 http://ftpmaster.internal/ubuntu noble/universe armhf wise-data all 2.4.1-23 [76.8 kB] Get:270 http://ftpmaster.internal/ubuntu noble/universe armhf wise armhf 2.4.1-23 [790 kB] Get:271 http://ftpmaster.internal/ubuntu noble/universe armhf fasttree armhf 2.1.11-2 [162 kB] Preconfiguring packages ... Fetched 338 MB in 12s (27.1 MB/s) Selecting previously unselected package libpython3.11-minimal:armhf. (Reading database ... 13368 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.6-3_armhf.deb ... Unpacking libpython3.11-minimal:armhf (3.11.6-3) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.5.0-2_armhf.deb ... Unpacking libexpat1:armhf (2.5.0-2) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.6-3_armhf.deb ... Unpacking python3.11-minimal (3.11.6-3) ... Setting up libpython3.11-minimal:armhf (3.11.6-3) ... Setting up libexpat1:armhf (2.5.0-2) ... Setting up python3.11-minimal (3.11.6-3) ... Selecting previously unselected package python3-minimal. (Reading database ... 13682 files and directories currently installed.) Preparing to unpack .../python3-minimal_3.11.4-5ubuntu1_armhf.deb ... 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Setting up mysql-common (5.8+1.1.0) ... update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode Setting up libmysqlclient21:armhf (8.0.35-1) ... Setting up libxau6:armhf (1:1.0.9-1build5) ... Setting up imagemagick-6-common (8:6.9.11.60+dfsg-1.6ubuntu1) ... Setting up libhpdf-2.3.0:armhf (2.3.0+dfsg-1build1) ... Setting up libpsl5:armhf (0.21.2-1build1) ... Setting up libicu72:armhf (72.1-3ubuntu3) ... Setting up liblerc4:armhf (4.0.0+ds-2ubuntu2) ... Setting up fonts-noto-mono (20201225-2) ... Setting up hicolor-icon-theme (0.17-2) ... Setting up probcons (1.12-14) ... Setting up libmagic-mgc (1:5.45-2) ... Setting up mafft (7.505-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:armhf (2.78.1-2) ... No schema files found: doing nothing. Setting up bwa (0.7.17-7) ... Setting up fonts-lyx (2.3.7-1) ... Setting up libijs-0.35:armhf (0.35-15.1) ... Setting up libpython3.11-stdlib:armhf (3.11.6-3) ... 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Setting up poppler-data (0.4.12-1) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-3) ... Setting up unicode-data (15.1.0-1) ... Setting up libfontenc1:armhf (1:1.1.4-1build3) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:armhf (3.11.0-2build1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up libexpat1-dev:armhf (2.5.0-2) ... Setting up libfreetype6:armhf (2.13.2+dfsg-1) ... Setting up libmbedcrypto7:armhf (2.28.5-1) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libjbig2dec0:armhf (0.19-3build2) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2build4) ... Setting up libteckit0:armhf (2.5.11+ds1-1) ... Setting up libapache-pom-java (29-2) ... Setting up libavahi-common-data:armhf (0.8-10ubuntu1) ... Setting up libncurses6:armhf (6.4+20231016-1) ... Setting up libdbus-1-3:armhf (1.14.10-1ubuntu1) ... 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Setting up autoconf (2.71-3) ... Setting up libwebp7:armhf (1.3.2-0.3) ... Setting up zlib1g-dev:armhf (1:1.2.13.dfsg-1ubuntu5) ... Setting up fonts-dejavu-extra (2.37-8) ... Setting up libdav1d7:armhf (1.3.0-2) ... Setting up liblqr-1-0:armhf (0.4.2-2.1) ... Setting up libuchardet0:armhf (0.0.7-1build2) ... Setting up clustalw (2.1+lgpl-7) ... Setting up fonts-lmodern (2.005-1) ... Setting up libopenjp2-7:armhf (2.5.0-2) ... Setting up libsub-override-perl (0.09-4) ... Setting up libharfbuzz0b:armhf (8.0.1-1) ... Setting up fasttree (2.1.11-2) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libde265-0:armhf (1.0.12-2) ... Setting up python-matplotlib-data (3.6.3-1ubuntu3) ... Setting up libwebpmux3:armhf (1.3.2-0.3) ... Setting up libbsd0:armhf (0.11.7-4) ... Setting up libelf1:armhf (0.189-4) ... Setting up dialign (2.2.1-11) ... Setting up libxml2:armhf (2.9.14+dfsg-1.3build1) ... Setting up fonts-noto-core (20201225-2) ... Setting up xdg-utils (1.1.3-4.1ubuntu3) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libldap2:armhf (2.6.6+dfsg-1~exp1ubuntu1) ... Setting up libsynctex2:armhf (2023.20230311.66589-6) ... Setting up libpython3-stdlib:armhf (3.11.4-5ubuntu1) ... Setting up prank (0.0.170427+dfsg-3) ... Setting up libargtable2-0 (13-1.1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libpotrace0:armhf (1.16-2) ... Setting up libjpeg8:armhf (8c-2ubuntu11) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up python3.12-minimal (3.12.0-1) ... Setting up libpaper1:armhf (1.1.29) ... Creating config file /etc/papersize with new version Setting up python3.11 (3.11.6-3) ... Setting up libice6:armhf (2:1.0.10-1build2) ... Setting up libdw1:armhf (0.189-4) ... Setting up libxdmcp6:armhf (1:1.1.3-0ubuntu5) ... Setting up flex (2.6.4-8.2) ... Setting up liblapack3:armhf (3.11.0-2build1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up libxcb1:armhf (1.15-1) ... Setting up gettext (0.21-13build1) ... Setting up libpdfbox-java (1:1.8.16-4) ... Setting up libpython3.12-stdlib:armhf (3.12.0-1) ... Setting up libpython3.11:armhf (3.11.6-3) ... Setting up libmbedx509-1:armhf (2.28.5-1) ... Setting up libmbedtls14:armhf (2.28.5-1) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:armhf (1.15-1) ... Setting up fontconfig-config (2.14.2-4ubuntu1) ... Setting up wise (2.4.1-23) ... Setting up libwebpdemux2:armhf (1.3.2-0.3) ... Setting up python3.12 (3.12.0-1) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:armhf (0.8-10ubuntu1) ... Setting up libpq5:armhf (15.4-1ubuntu1) ... Setting up libcommons-logging-java (1.2-4) ... Setting up libcurl3-gnutls:armhf (8.2.1-1ubuntu3.1) ... Setting up python3 (3.11.4-5ubuntu1) ... Setting up libxcb-shm0:armhf (1.15-1) ... Setting up libpaper-utils (1.1.29) ... Setting up clustalo (1.2.4-7) ... Setting up python3-freetype (2.4.0-1) ... Setting up xfonts-utils (1:7.7+6build2) ... Setting up python3-tz (2023.3.post1-1) ... /usr/lib/python3/dist-packages/pytz/__init__.py:30: SyntaxWarning: invalid escape sequence '\s' match = re.match("^#\s*version\s*([0-9a-z]*)\s*$", line) Setting up intltool-debian (0.35.0+20060710.6) ... Setting up ncbi-blast+ (2.12.0+ds-4) ... Setting up libcifpp5:armhf (5.0.7.1-3) ... Setting up python3-mysqldb (1.4.6-2build2) ... Setting up python3-six (1.16.0-4) ... Setting up dh-autoreconf (20) ... Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up python3-isodate (0.6.1-1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (23.2-1) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libptexenc1:armhf (2023.20230311.66589-6) ... Setting up python3-pyparsing (3.1.1-1) ... Setting up libpython3.11-dev:armhf (3.11.6-3) ... Setting up python3-brotli (1.1.0-1) ... Setting up libraqm0:armhf (0.10.1-1) ... Setting up python3-cycler (0.11.0-1) ... Setting up python3-kiwisolver (1.4.4-1build2) ... Setting up python3-psycopg2 (2.9.6-3build1) ... Setting up libjs-sphinxdoc (7.2.6-2) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-3) ... Setting up libtiff6:armhf (4.5.1+git230720-1ubuntu1) ... Setting up libxslt1.1:armhf (1.1.35-1) ... Setting up debugedit (1:5.0-5) ... Setting up libx11-6:armhf (2:1.8.7-1) ... Setting up python3-dateutil (2.8.2-3) ... Setting up python3-msgpack (1.0.3-3build1) ... Setting up libfontconfig1:armhf (2.14.2-4ubuntu1) ... Setting up python3-mpmath (1.2.1-2) ... Setting up python3-lib2to3 (3.11.5-1) ... Setting up python3-appdirs (1.4.4-4) ... Setting up libsm6:armhf (2:1.2.3-1build2) ... Setting up libpython3.12:armhf (3.12.0-1) ... Setting up libavahi-client3:armhf (0.8-10ubuntu1) ... Setting up liblbfgsb0:armhf (3.0+dfsg.4-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.11.5-1) ... python3.12: can't get files for byte-compilation Setting up python3-sympy (1.12-6) ... Setting up python3-attr (23.1.0-2) ... Setting up libhts3:armhf (1.17+ds-1) ... Setting up libpython3-dev:armhf (3.11.4-5ubuntu1) ... Setting up python3-setuptools (68.1.2-2) ... Setting up libxpm4:armhf (1:3.5.12-1.1ubuntu1) ... Setting up libxrender1:armhf (1:0.9.10-1.1) ... Setting up python3-lz4 (4.0.2+dfsg-1build2) ... Setting up python3.11-dev (3.11.6-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up preview-latex-style (12.2-1ubuntu1) ... Setting up libxext6:armhf (2:1.3.4-1build1) ... Setting up python3-all (3.11.4-5ubuntu1) ... Setting up libpython3.12-dev:armhf (3.12.0-1) ... Setting up fonts-urw-base35 (20200910-7) ... Setting up dssp (4.2.2-2) ... Setting up python3-networkx (2.8.8-1ubuntu1) ... /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:556: SyntaxWarning: invalid octal escape sequence '\420' "graph [edge [ source u'u\4200' target u'u\4200' ] " /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:557: SyntaxWarning: invalid octal escape sequence '\420' + "node [ id u'u\4200' label b ] ]" Setting up man-db (2.12.0-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up libcairo2:armhf (1.18.0-1) ... Setting up samtools (1.17-1) ... Setting up python3-fs (2.4.16-2) ... Setting up python3-pil:armhf (10.1.0-1) ... Setting up python3-pygments (2.15.1+dfsg-1) ... Setting up libpython3-all-dev:armhf (3.11.4-5ubuntu1) ... Setting up python3-dev (3.11.4-5ubuntu1) ... Setting up libgd3:armhf (2.3.3-9ubuntu1) ... Setting up python3-unittest2 (1.1.0-9) ... update-alternatives: using /usr/bin/python3-unit2 to provide /usr/bin/unit2 (unit2) in auto mode /usr/lib/python3/dist-packages/unittest2/test/test_assertions.py:211: SyntaxWarning: invalid escape sequence '\+' ["\+ \[None\]$", "^oops$", r"\+ \[None\]$", /usr/lib/python3/dist-packages/unittest2/test/test_assertions.py:221: SyntaxWarning: invalid escape sequence '\[' ['^None not found in \[\]$', "^oops$", /usr/lib/python3/dist-packages/unittest2/test/test_assertions.py:222: SyntaxWarning: invalid escape sequence '\[' '^None not found in \[\]$', /usr/lib/python3/dist-packages/unittest2/test/test_assertions.py:223: SyntaxWarning: invalid escape sequence '\[' '^None not found in \[\] : oops$']) /usr/lib/python3/dist-packages/unittest2/test/test_assertions.py:227: SyntaxWarning: invalid escape sequence '\[' ['^None unexpectedly found in \[None\]$', "^oops$", /usr/lib/python3/dist-packages/unittest2/test/test_assertions.py:228: SyntaxWarning: invalid escape sequence '\[' '^None unexpectedly found in \[None\]$', /usr/lib/python3/dist-packages/unittest2/test/test_assertions.py:229: SyntaxWarning: invalid escape sequence '\[' '^None unexpectedly found in \[None\] : oops$']) /usr/lib/python3/dist-packages/unittest2/test/test_assertions.py:234: SyntaxWarning: invalid escape sequence '\+' "\+ \{'key': 'value'\}$", /usr/lib/python3/dist-packages/unittest2/test/test_assertions.py:235: SyntaxWarning: invalid escape sequence '\+' "\+ \{'key': 'value'\} : oops$"]) /usr/lib/python3/dist-packages/unittest2/test/test_loader.py:396: SyntaxWarning: invalid escape sequence '\(' expected_regex = "Failed to import test module: abc \(\) //" /usr/lib/python3/dist-packages/unittest2/test/test_loader.py:519: SyntaxWarning: invalid escape sequence '\(' error, test, 'unittest2', 'abc () //', 'abc \(\) //') /usr/lib/python3/dist-packages/unittest2/test/test_loader.py:822: SyntaxWarning: invalid escape sequence '\(' expected_regex = "Failed to import test module: abc \(\) //" /usr/lib/python3/dist-packages/unittest2/test/test_loader.py:929: SyntaxWarning: invalid escape sequence '\(' error, test, 'unittest2', 'abc () //', 'abc \(\) //') Setting up python3.12-dev (3.12.0-1) ... Setting up netpbm (2:11.03.06-1) ... Setting up libxt6:armhf (1:1.2.1-1.1) ... Setting up python3-numpy (1:1.24.2-1ubuntu1) ... Setting up libcups2:armhf (2.4.6-0ubuntu3) ... Setting up python3-lxml:armhf (4.9.3-1build1) ... Setting up python3-rdflib (6.1.1-2) ... /usr/lib/python3/dist-packages/rdflib/extras/external_graph_libs.py:75: SyntaxWarning: invalid escape sequence '\*' """Converts the given graph into a networkx.MultiDiGraph. /usr/lib/python3/dist-packages/rdflib/extras/external_graph_libs.py:132: SyntaxWarning: invalid escape sequence '\*' """Converts the given graph into a networkx.DiGraph. /usr/lib/python3/dist-packages/rdflib/extras/external_graph_libs.py:195: SyntaxWarning: invalid escape sequence '\*' """Converts the given graph into a networkx.Graph. Setting up python3-contourpy (1.0.7-1build2) ... Setting up emboss-lib (6.6.0+dfsg-12ubuntu1) ... Setting up libxss1:armhf (1:1.2.3-1build2) ... Setting up dh-python (6.20231025) ... Setting up python3-all-dev (3.11.4-5ubuntu1) ... Setting up libgs10-common (10.01.2~dfsg1-0ubuntu2.1) ... Setting up libxft2:armhf (2.3.6-1) ... Setting up libxmu6:armhf (2:1.1.3-3) ... Setting up python3-scipy (1.10.1-5ubuntu1) ... Setting up python3-cairo:armhf (1.24.0-3build1) ... Setting up emboss (6.6.0+dfsg-12ubuntu1) ... Setting up libxi6:armhf (2:1.8-1build1) ... Setting up libtk8.6:armhf (8.6.13-2) ... Setting up debhelper (13.11.7ubuntu1) ... Setting up libxaw7:armhf (2:1.0.14-1) ... Setting up python3-mmtf (1.1.3-1) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-reportlab (4.0.6-1) ... Setting up texlive-binaries (2023.20230311.66589-6) ... 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 (2023.20231007-1) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up libgs10:armhf (10.01.2~dfsg1-0ubuntu2.1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-4.1build2) ... Setting up blt (2.5.3+dfsg-4.1build2) ... Setting up python3-tk:armhf (3.11.5-1) ... Setting up ghostscript (10.01.2~dfsg1-0ubuntu2.1) ... Setting up texlive-latex-base (2023.20231007-1) ... Setting up python3-pil.imagetk:armhf (10.1.0-1) ... Setting up texlive-latex-recommended (2023.20231007-1) ... Setting up texlive-pictures (2023.20231007-1) ... Setting up texlive-fonts-recommended (2023.20231007-1) ... Setting up texlive-latex-extra (2023.20231007-2) ... Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... Setting up libheif-plugin-dav1d:armhf (1.17.1-1ubuntu3) ... Setting up libheif-plugin-libde265:armhf (1.17.1-1ubuntu3) ... Setting up libheif1:armhf (1.17.1-1ubuntu3) ... Setting up python3-fonttools (4.38.0-1build2) ... /usr/lib/python3/dist-packages/fontTools/cffLib/specializer.py:40: SyntaxWarning: invalid escape sequence '\_' """Takes a T2CharString program list and returns list of commands. Setting up libmagickcore-6.q16-6:armhf (8:6.9.11.60+dfsg-1.6ubuntu1) ... Setting up libmagickwand-6.q16-6:armhf (8:6.9.11.60+dfsg-1.6ubuntu1) ... Setting up python3-matplotlib (3.6.3-1ubuntu3) ... Setting up imagemagick-6.q16 (8:6.9.11.60+dfsg-1.6ubuntu1) ... update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare (compare) in auto mode update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare-im6 (compare-im6) in auto mode update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate (animate) in auto mode update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate-im6 (animate-im6) in auto mode update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert (convert) in auto mode update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert-im6 (convert-im6) in auto mode update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite (composite) in auto mode update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite-im6 (composite-im6) in auto mode update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure (conjure) in auto mode update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure-im6 (conjure-im6) in auto mode update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import (import) in auto mode update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import-im6 (import-im6) in auto mode update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify (identify) in auto mode update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify-im6 (identify-im6) in auto mode update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream (stream) in auto mode update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream-im6 (stream-im6) in auto mode update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display (display) in auto mode update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display-im6 (display-im6) in auto mode update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage (montage) in auto mode update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage-im6 (montage-im6) in auto mode update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify (mogrify) in auto mode update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify-im6 (mogrify-im6) in auto mode Setting up hevea (2.36-2) ... Setting up imagemagick (8:6.9.11.60+dfsg-1.6ubuntu1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.38-3ubuntu1) ... Processing triggers for systemd (253.5-1ubuntu7) ... Processing triggers for tex-common (6.18) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armhf included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-164-generic #181-Ubuntu SMP Fri Sep 1 13:42:23 UTC 2023 arm64 (armv7l) Toolchain package versions: binutils_2.41-6ubuntu1 dpkg-dev_1.22.1ubuntu2 g++-13_13.2.0-6ubuntu1 gcc-13_13.2.0-6ubuntu1 libc6-dev_2.38-3ubuntu1 libstdc++-13-dev_13.2.0-6ubuntu1 libstdc++6_13.2.0-6ubuntu1 linux-libc-dev_6.5.0-9.9 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1 apt_2.7.6 apt-utils_2.7.6 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-13build1 autotools-dev_20220109.1 base-files_13ubuntu4 base-passwd_3.6.2 bash_5.2.15-2ubuntu1 bash-completion_1:2.11-8 binutils_2.41-6ubuntu1 binutils-arm-linux-gnueabihf_2.41-6ubuntu1 binutils-common_2.41-6ubuntu1 blt_2.5.3+dfsg-4.1build2 bsdextrautils_2.39.1-4ubuntu2 bsdutils_1:2.39.1-4ubuntu2 build-essential_12.10ubuntu1 bwa_0.7.17-7 bzip2_1.0.8-5build1 ca-certificates_20230311ubuntu1 clustalo_1.2.4-7 clustalw_2.1+lgpl-7 coreutils_9.1-1ubuntu2 cpp_4:13.2.0-1ubuntu1 cpp-13_13.2.0-6ubuntu1 dash_0.5.12-6ubuntu1 debconf_1.5.82 debconf-i18n_1.5.82 debhelper_13.11.7ubuntu1 debianutils_5.14 debugedit_1:5.0-5 dh-autoreconf_20 dh-python_6.20231025 dh-strip-nondeterminism_1.13.1-1 dialign_2.2.1-11 diffutils_1:3.10-1 dpkg_1.22.1ubuntu2 dpkg-dev_1.22.1ubuntu2 dssp_4.2.2-2 dwz_0.15-1 e2fsprogs_1.47.0-2ubuntu1 emboss_6.6.0+dfsg-12ubuntu1 emboss-data_6.6.0+dfsg-12ubuntu1 emboss-lib_6.6.0+dfsg-12ubuntu1 fakeroot_1.32.2-1 fasttree_2.1.11-2 file_1:5.45-2 findutils_4.9.0-5 flex_2.6.4-8.2 fontconfig-config_2.14.2-4ubuntu1 fonts-dejavu-core_2.37-8 fonts-dejavu-extra_2.37-8 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python3-biopython, python-biopython-doc, python3-biopython-sql Architecture: any all Version: 1.81+dfsg-1build1 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Étienne Mollier Homepage: https://biopython.org Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/python-biopython Vcs-Git: https://salsa.debian.org/med-team/python-biopython.git Testsuite: autopkgtest Testsuite-Triggers: @builddeps@, python3-all, python3-setuptools Build-Depends: debhelper-compat (= 13), dh-python, python3-all-dev, python3-numpy, flex, python3-reportlab (>= 4.0.4-1~) , hevea, texlive-latex-base, texlive-latex-extra, texlive-fonts-recommended, bwa , clustalo , clustalw , dialign , dssp , emboss , fasttree , mafft , muscle3 [i386 amd64 x32] , ncbi-blast+ , phylip , phyml [any-amd64 any-i386] , prank , probcons , python3-networkx , python3-mysqldb , python3-matplotlib , python3-mmtf , python3-pil , python3-rdflib , python3-psycopg2 , python3-pygments , python3-scipy , python3-setuptools, python3-unittest2 , raxml [any-amd64 any-i386] , samtools , t-coffee , wise Package-List: python-biopython-doc deb doc optional arch=all python3-biopython deb python optional arch=any python3-biopython-sql deb python optional arch=all Checksums-Sha1: d8b39f189078bd119960a3e5c3136e1cc53e4d64 11483844 python-biopython_1.81+dfsg.orig.tar.xz 74bccc16e92b1adf66805b47561bf7e5ee06a173 20420 python-biopython_1.81+dfsg-1build1.debian.tar.xz Checksums-Sha256: 459868a86c2e47a0cc2f19be1371dd5309474b3106d17093cadebf7abdd03413 11483844 python-biopython_1.81+dfsg.orig.tar.xz fd09f6b595c843e5a6792d616aacb5a6351caa056c56e9b50e641cd2928daf04 20420 python-biopython_1.81+dfsg-1build1.debian.tar.xz Files: 67dfa4cf427956d8dbb5be53c2b62d49 11483844 python-biopython_1.81+dfsg.orig.tar.xz 8520cf5497fb39acde586d736cb53c70 20420 python-biopython_1.81+dfsg-1build1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJEBAEBCAAuFiEE1WVxuIqLuvFAv2PWvX6qYHePpvUFAmVDYxoQHGRva29AdWJ1 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for ./python-biopython_1.81+dfsg-1build1.dsc: no acceptable signature found dpkg-source: info: extracting python-biopython in /<> dpkg-source: info: unpacking python-biopython_1.81+dfsg.orig.tar.xz dpkg-source: info: unpacking python-biopython_1.81+dfsg-1build1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying remove_mathml-qname.patch dpkg-source: info: applying privacy_breach.patch dpkg-source: info: applying privacy_breach_ie9.patch dpkg-source: info: applying fix-use-of-unversioned-python.patch dpkg-source: info: applying reproduciblebuild.patch dpkg-source: info: applying croak-on-muscle5.patch dpkg-source: info: applying muscle3.patch dpkg-source: info: applying port_tutorial_to_muscle3.patch dpkg-source: info: applying remove-distutils-import.patch 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-26951322 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-26951322 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-26951322 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -B -rfakeroot dpkg-buildpackage: info: source package python-biopython dpkg-buildpackage: info: source version 1.81+dfsg-1build1 dpkg-buildpackage: info: source distribution noble dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean pybuild --clean -i python{version} -p "3.12 3.11" I: pybuild base:310: python3.12 setup.py clean running clean removing '/<>/.pybuild/cpython3_3.12/build' (and everything under it) 'build/bdist.linux-armv7l' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it I: pybuild base:310: python3.11 setup.py clean running clean removing '/<>/.pybuild/cpython3_3.11/build' (and everything under it) 'build/bdist.linux-armv7l' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it rm -rf .pybuild/ find . -name \*.pyc -exec rm {} \; cd Doc && make distclean make[2]: Entering directory '/<>/Doc' ( for f in ; do make clean -C $f ; done ) rm -f Tutorial.aux rm -f Tutorial.toc rm -f Tutorial.log rm -f Tutorial.out rm -f Tutorial.haux rm -f Tutorial.htoc rm -f biopdb_faq.aux rm -f biopdb_faq.log rm -f biopdb_faq.out rm -f Tutorial/*.aux rm -rf _minted-Tutorial ( for f in ; do make distclean -C $f ; done ) rm -f version.sh rm -f biopdb_faq.pdf rm -f Tutorial.pdf rm -f Tutorial.html rm -f Tutorial.txt rm -f *_motif.gif #output from hacha make[2]: Leaving directory '/<>/Doc' rm -f Doc/install/Installation.pdf rm -f Doc/install/Installation.txt rm -f Doc/install/Installation.html rm -f Doc/Tutorial.pdf Doc/biopdb_faq.pdf rm -f Doc/Tutorial/*.aux find Doc -name "*.pygtex" -o -name "*.pygstyle" -delete rm -rf biopython.egg-info rm -rf .pybuild if [ -d Tests_avoid ] ; then \ mv Tests_avoid/* Tests ; \ rmdir Tests_avoid ; \ fi rm -rf debian/tmp_tests make[1]: Leaving directory '/<>' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/python3-biopython.substvars debian/python-biopython-doc.substvars debian/python3-biopython-sql.substvars debian/files rm -fr -- debian/python3-biopython/ debian/tmp/ debian/python-biopython-doc/ debian/python3-biopython-sql/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules binary-arch dh binary-arch --with python3 --buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_autoreconf -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild pybuild --configure -i python{version} -p "3.12 3.11" I: pybuild base:310: python3.12 setup.py config running config I: pybuild base:310: python3.11 setup.py config running config debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build pybuild --build -i python{version} -p "3.12 3.11" I: pybuild base:310: /usr/bin/python3.12 setup.py build running build running build_py creating /<>/.pybuild/cpython3_3.12/build/Bio copying Bio/_utils.py -> /<>/.pybuild/cpython3_3.12/build/Bio copying Bio/bgzf.py -> /<>/.pybuild/cpython3_3.12/build/Bio copying Bio/MarkovModel.py -> /<>/.pybuild/cpython3_3.12/build/Bio copying Bio/kNN.py -> /<>/.pybuild/cpython3_3.12/build/Bio copying Bio/File.py -> /<>/.pybuild/cpython3_3.12/build/Bio copying Bio/SeqFeature.py -> /<>/.pybuild/cpython3_3.12/build/Bio copying Bio/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio copying Bio/SeqRecord.py -> /<>/.pybuild/cpython3_3.12/build/Bio copying Bio/LogisticRegression.py -> /<>/.pybuild/cpython3_3.12/build/Bio copying Bio/Seq.py -> /<>/.pybuild/cpython3_3.12/build/Bio copying Bio/NaiveBayes.py -> /<>/.pybuild/cpython3_3.12/build/Bio copying Bio/MaxEntropy.py -> /<>/.pybuild/cpython3_3.12/build/Bio copying Bio/pairwise2.py -> /<>/.pybuild/cpython3_3.12/build/Bio creating /<>/.pybuild/cpython3_3.12/build/Bio/Affy copying Bio/Affy/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Affy copying Bio/Affy/CelFile.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Affy creating /<>/.pybuild/cpython3_3.12/build/Bio/Align copying Bio/Align/bed.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Align copying Bio/Align/interfaces.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Align copying Bio/Align/AlignInfo.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Align copying Bio/Align/stockholm.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Align copying Bio/Align/psl.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Align copying Bio/Align/nexus.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Align copying Bio/Align/hhr.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Align copying Bio/Align/emboss.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Align copying Bio/Align/fasta.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Align copying Bio/Align/bigbed.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Align copying Bio/Align/a2m.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Align copying Bio/Align/mauve.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Align copying Bio/Align/exonerate.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Align copying Bio/Align/phylip.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Align copying Bio/Align/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Align copying Bio/Align/sam.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Align copying Bio/Align/clustal.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Align copying Bio/Align/tabular.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Align copying Bio/Align/bigmaf.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Align copying Bio/Align/msf.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Align copying Bio/Align/bigpsl.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Align copying Bio/Align/maf.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Align creating /<>/.pybuild/cpython3_3.12/build/Bio/Align/Applications copying Bio/Align/Applications/_Clustalw.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/Applications copying Bio/Align/Applications/_Prank.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/Applications copying Bio/Align/Applications/_Dialign.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/Applications copying Bio/Align/Applications/_TCoffee.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/Applications copying Bio/Align/Applications/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/Applications copying Bio/Align/Applications/_ClustalOmega.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/Applications copying Bio/Align/Applications/_MSAProbs.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/Applications copying Bio/Align/Applications/_Mafft.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/Applications copying Bio/Align/Applications/_Probcons.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/Applications copying Bio/Align/Applications/_Muscle.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/Applications creating /<>/.pybuild/cpython3_3.12/build/Bio/Align/substitution_matrices copying Bio/Align/substitution_matrices/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/substitution_matrices creating /<>/.pybuild/cpython3_3.12/build/Bio/AlignIO copying Bio/AlignIO/StockholmIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/AlignIO copying Bio/AlignIO/Interfaces.py -> /<>/.pybuild/cpython3_3.12/build/Bio/AlignIO copying Bio/AlignIO/MafIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/AlignIO copying Bio/AlignIO/MsfIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/AlignIO copying Bio/AlignIO/NexusIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/AlignIO copying Bio/AlignIO/MauveIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/AlignIO copying Bio/AlignIO/FastaIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/AlignIO copying Bio/AlignIO/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/AlignIO copying Bio/AlignIO/ClustalIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/AlignIO copying Bio/AlignIO/PhylipIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/AlignIO copying Bio/AlignIO/EmbossIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/AlignIO creating /<>/.pybuild/cpython3_3.12/build/Bio/Alphabet copying Bio/Alphabet/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Alphabet creating /<>/.pybuild/cpython3_3.12/build/Bio/Application copying Bio/Application/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Application creating /<>/.pybuild/cpython3_3.12/build/Bio/Blast copying Bio/Blast/Record.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Blast copying Bio/Blast/ParseBlastTable.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Blast copying Bio/Blast/Applications.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Blast copying Bio/Blast/NCBIWWW.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Blast copying Bio/Blast/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Blast copying Bio/Blast/NCBIXML.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Blast creating /<>/.pybuild/cpython3_3.12/build/Bio/CAPS copying Bio/CAPS/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/CAPS creating /<>/.pybuild/cpython3_3.12/build/Bio/Cluster copying Bio/Cluster/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Cluster creating /<>/.pybuild/cpython3_3.12/build/Bio/codonalign copying Bio/codonalign/codonseq.py -> /<>/.pybuild/cpython3_3.12/build/Bio/codonalign copying Bio/codonalign/codonalignment.py -> /<>/.pybuild/cpython3_3.12/build/Bio/codonalign copying Bio/codonalign/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/codonalign creating /<>/.pybuild/cpython3_3.12/build/Bio/Compass copying Bio/Compass/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Compass creating /<>/.pybuild/cpython3_3.12/build/Bio/Data copying Bio/Data/PDBData.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Data copying Bio/Data/CodonTable.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Data copying Bio/Data/SCOPData.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Data copying Bio/Data/IUPACData.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Data copying Bio/Data/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Data creating /<>/.pybuild/cpython3_3.12/build/Bio/Emboss copying Bio/Emboss/Primer3.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Emboss copying Bio/Emboss/Applications.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Emboss copying Bio/Emboss/PrimerSearch.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Emboss copying Bio/Emboss/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Emboss creating /<>/.pybuild/cpython3_3.12/build/Bio/Entrez copying Bio/Entrez/Parser.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez copying Bio/Entrez/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez creating /<>/.pybuild/cpython3_3.12/build/Bio/ExPASy copying Bio/ExPASy/Prodoc.py -> /<>/.pybuild/cpython3_3.12/build/Bio/ExPASy copying Bio/ExPASy/cellosaurus.py -> /<>/.pybuild/cpython3_3.12/build/Bio/ExPASy copying Bio/ExPASy/Enzyme.py -> /<>/.pybuild/cpython3_3.12/build/Bio/ExPASy copying Bio/ExPASy/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/ExPASy copying Bio/ExPASy/Prosite.py -> /<>/.pybuild/cpython3_3.12/build/Bio/ExPASy copying Bio/ExPASy/ScanProsite.py -> /<>/.pybuild/cpython3_3.12/build/Bio/ExPASy creating /<>/.pybuild/cpython3_3.12/build/Bio/GenBank copying Bio/GenBank/Record.py -> /<>/.pybuild/cpython3_3.12/build/Bio/GenBank copying Bio/GenBank/Scanner.py -> /<>/.pybuild/cpython3_3.12/build/Bio/GenBank copying Bio/GenBank/utils.py -> /<>/.pybuild/cpython3_3.12/build/Bio/GenBank copying Bio/GenBank/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/GenBank creating /<>/.pybuild/cpython3_3.12/build/Bio/Geo copying Bio/Geo/Record.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Geo copying Bio/Geo/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Geo creating /<>/.pybuild/cpython3_3.12/build/Bio/Graphics copying Bio/Graphics/ColorSpiral.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Graphics copying Bio/Graphics/DisplayRepresentation.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Graphics copying Bio/Graphics/BasicChromosome.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Graphics copying Bio/Graphics/Comparative.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Graphics copying Bio/Graphics/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Graphics copying Bio/Graphics/KGML_vis.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Graphics copying Bio/Graphics/Distribution.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Graphics creating /<>/.pybuild/cpython3_3.12/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Feature.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Graph.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Colors.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_GraphSet.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Track.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CrossLink.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Diagram.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Graphics/GenomeDiagram creating /<>/.pybuild/cpython3_3.12/build/Bio/HMM copying Bio/HMM/DynamicProgramming.py -> /<>/.pybuild/cpython3_3.12/build/Bio/HMM copying Bio/HMM/Utilities.py -> /<>/.pybuild/cpython3_3.12/build/Bio/HMM copying Bio/HMM/MarkovModel.py -> /<>/.pybuild/cpython3_3.12/build/Bio/HMM copying Bio/HMM/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/HMM copying Bio/HMM/Trainer.py -> /<>/.pybuild/cpython3_3.12/build/Bio/HMM creating /<>/.pybuild/cpython3_3.12/build/Bio/KEGG copying Bio/KEGG/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/KEGG copying Bio/KEGG/REST.py -> /<>/.pybuild/cpython3_3.12/build/Bio/KEGG creating /<>/.pybuild/cpython3_3.12/build/Bio/KEGG/Compound copying Bio/KEGG/Compound/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/KEGG/Compound creating /<>/.pybuild/cpython3_3.12/build/Bio/KEGG/Enzyme copying Bio/KEGG/Enzyme/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/KEGG/Enzyme creating /<>/.pybuild/cpython3_3.12/build/Bio/KEGG/Gene copying Bio/KEGG/Gene/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/KEGG/Gene creating /<>/.pybuild/cpython3_3.12/build/Bio/KEGG/Map copying Bio/KEGG/Map/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/KEGG/Map creating /<>/.pybuild/cpython3_3.12/build/Bio/PDB creating /<>/.pybuild/cpython3_3.12/build/Bio/PDB/mmtf copying Bio/PDB/mmtf/DefaultParser.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB/mmtf copying Bio/PDB/mmtf/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB/mmtf copying Bio/PDB/mmtf/mmtfio.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB/mmtf creating /<>/.pybuild/cpython3_3.12/build/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_parser.py -> /<>/.pybuild/cpython3_3.12/build/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_pathway.py -> /<>/.pybuild/cpython3_3.12/build/Bio/KEGG/KGML copying Bio/KEGG/KGML/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/KEGG/KGML creating /<>/.pybuild/cpython3_3.12/build/Bio/Medline copying Bio/Medline/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Medline creating /<>/.pybuild/cpython3_3.12/build/Bio/motifs copying Bio/motifs/thresholds.py -> /<>/.pybuild/cpython3_3.12/build/Bio/motifs copying Bio/motifs/pfm.py -> /<>/.pybuild/cpython3_3.12/build/Bio/motifs copying Bio/motifs/matrix.py -> /<>/.pybuild/cpython3_3.12/build/Bio/motifs copying Bio/motifs/xms.py -> /<>/.pybuild/cpython3_3.12/build/Bio/motifs copying Bio/motifs/minimal.py -> /<>/.pybuild/cpython3_3.12/build/Bio/motifs copying Bio/motifs/clusterbuster.py -> /<>/.pybuild/cpython3_3.12/build/Bio/motifs copying Bio/motifs/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/motifs copying Bio/motifs/mast.py -> /<>/.pybuild/cpython3_3.12/build/Bio/motifs copying Bio/motifs/meme.py -> /<>/.pybuild/cpython3_3.12/build/Bio/motifs copying Bio/motifs/alignace.py -> /<>/.pybuild/cpython3_3.12/build/Bio/motifs copying Bio/motifs/transfac.py -> /<>/.pybuild/cpython3_3.12/build/Bio/motifs creating /<>/.pybuild/cpython3_3.12/build/Bio/motifs/applications copying Bio/motifs/applications/_xxmotif.py -> /<>/.pybuild/cpython3_3.12/build/Bio/motifs/applications copying Bio/motifs/applications/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/motifs/applications creating /<>/.pybuild/cpython3_3.12/build/Bio/motifs/jaspar copying Bio/motifs/jaspar/db.py -> /<>/.pybuild/cpython3_3.12/build/Bio/motifs/jaspar copying Bio/motifs/jaspar/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/motifs/jaspar creating /<>/.pybuild/cpython3_3.12/build/Bio/Nexus copying Bio/Nexus/Nodes.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Nexus copying Bio/Nexus/Nexus.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Nexus copying Bio/Nexus/StandardData.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Nexus copying Bio/Nexus/Trees.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Nexus copying Bio/Nexus/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Nexus creating /<>/.pybuild/cpython3_3.12/build/Bio/NMR copying Bio/NMR/xpktools.py -> /<>/.pybuild/cpython3_3.12/build/Bio/NMR copying Bio/NMR/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/NMR copying Bio/NMR/NOEtools.py -> /<>/.pybuild/cpython3_3.12/build/Bio/NMR creating /<>/.pybuild/cpython3_3.12/build/Bio/Pathway copying Bio/Pathway/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Pathway creating /<>/.pybuild/cpython3_3.12/build/Bio/Pathway/Rep copying Bio/Pathway/Rep/Graph.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Pathway/Rep copying Bio/Pathway/Rep/MultiGraph.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Pathway/Rep copying Bio/Pathway/Rep/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Pathway/Rep copying Bio/PDB/Model.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/FragmentMapper.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/StructureBuilder.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/Residue.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/HSExposure.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/Entity.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/mmcifio.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/internal_coords.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/PDBList.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/Dice.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/Superimposer.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/NACCESS.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/NeighborSearch.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/StructureAlignment.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/qcprot.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/Polypeptide.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/DSSP.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/ic_data.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/ic_rebuild.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/SCADIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/Chain.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/Structure.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/MMCIF2Dict.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/MMCIFParser.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/AbstractPropertyMap.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/parse_pdb_header.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/PDBIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/SASA.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/PDBExceptions.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/PICIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/ResidueDepth.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/PDBParser.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/PSEA.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/Atom.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/cealign.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/vectors.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/Selection.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB creating /<>/.pybuild/cpython3_3.12/build/Bio/phenotype copying Bio/phenotype/pm_fitting.py -> /<>/.pybuild/cpython3_3.12/build/Bio/phenotype copying Bio/phenotype/phen_micro.py -> /<>/.pybuild/cpython3_3.12/build/Bio/phenotype copying Bio/phenotype/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/phenotype creating /<>/.pybuild/cpython3_3.12/build/Bio/PopGen copying Bio/PopGen/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PopGen creating /<>/.pybuild/cpython3_3.12/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/LargeFileParser.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/Controller.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/EasyController.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/FileParser.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PopGen/GenePop creating /<>/.pybuild/cpython3_3.12/build/Bio/Restriction copying Bio/Restriction/Restriction_Dictionary.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Restriction copying Bio/Restriction/PrintFormat.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Restriction copying Bio/Restriction/Restriction.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Restriction copying Bio/Restriction/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Restriction creating /<>/.pybuild/cpython3_3.12/build/Bio/SCOP copying Bio/SCOP/Hie.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SCOP copying Bio/SCOP/Residues.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SCOP copying Bio/SCOP/Des.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SCOP copying Bio/SCOP/Cla.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SCOP copying Bio/SCOP/Dom.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SCOP copying Bio/SCOP/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SCOP copying Bio/SCOP/Raf.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SCOP creating /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO copying Bio/SearchIO/_utils.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO copying Bio/SearchIO/_index.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO copying Bio/SearchIO/FastaIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO copying Bio/SearchIO/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO copying Bio/SearchIO/BlatIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO creating /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO/_legacy copying Bio/SearchIO/_legacy/NCBIStandalone.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO/_legacy copying Bio/SearchIO/_legacy/ParserSupport.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO/_legacy copying Bio/SearchIO/_legacy/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO/_legacy creating /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/hsp.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/_base.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/query.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/hit.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO/_model creating /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_text.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_tab.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_xml.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO/BlastIO creating /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO/HHsuiteIO copying Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO/HHsuiteIO copying Bio/SearchIO/HHsuiteIO/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO/HHsuiteIO creating /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_text.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/_base.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_tab.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO/HmmerIO creating /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/_base.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_text.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO/ExonerateIO creating /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/interproscan_xml.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SearchIO/InterproscanIO creating /<>/.pybuild/cpython3_3.12/build/Bio/SeqIO copying Bio/SeqIO/GckIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SeqIO copying Bio/SeqIO/IgIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SeqIO copying Bio/SeqIO/NibIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SeqIO copying Bio/SeqIO/QualityIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SeqIO copying Bio/SeqIO/PdbIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SeqIO copying Bio/SeqIO/TwoBitIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SeqIO copying Bio/SeqIO/_index.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SeqIO copying Bio/SeqIO/SffIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SeqIO copying Bio/SeqIO/InsdcIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SeqIO copying Bio/SeqIO/Interfaces.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SeqIO copying Bio/SeqIO/TabIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SeqIO copying Bio/SeqIO/SwissIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SeqIO copying Bio/SeqIO/XdnaIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SeqIO copying Bio/SeqIO/AbiIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SeqIO copying Bio/SeqIO/FastaIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SeqIO copying Bio/SeqIO/SnapGeneIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SeqIO copying Bio/SeqIO/UniprotIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SeqIO copying Bio/SeqIO/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SeqIO copying Bio/SeqIO/SeqXmlIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SeqIO copying Bio/SeqIO/AceIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SeqIO copying Bio/SeqIO/PhdIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SeqIO copying Bio/SeqIO/PirIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SeqIO creating /<>/.pybuild/cpython3_3.12/build/Bio/SeqUtils copying Bio/SeqUtils/lcc.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SeqUtils copying Bio/SeqUtils/IsoelectricPoint.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SeqUtils copying Bio/SeqUtils/MeltingTemp.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SeqUtils copying Bio/SeqUtils/ProtParam.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SeqUtils copying Bio/SeqUtils/CodonUsageIndices.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SeqUtils copying Bio/SeqUtils/ProtParamData.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SeqUtils copying Bio/SeqUtils/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SeqUtils copying Bio/SeqUtils/CodonUsage.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SeqUtils copying Bio/SeqUtils/CheckSum.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SeqUtils creating /<>/.pybuild/cpython3_3.12/build/Bio/Sequencing copying Bio/Sequencing/Phd.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Sequencing copying Bio/Sequencing/Ace.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Sequencing copying Bio/Sequencing/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Sequencing creating /<>/.pybuild/cpython3_3.12/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_bwa.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_Novoalign.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_samtools.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Sequencing/Applications creating /<>/.pybuild/cpython3_3.12/build/Bio/SVDSuperimposer copying Bio/SVDSuperimposer/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SVDSuperimposer creating /<>/.pybuild/cpython3_3.12/build/Bio/PDB/QCPSuperimposer copying Bio/PDB/QCPSuperimposer/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB/QCPSuperimposer creating /<>/.pybuild/cpython3_3.12/build/Bio/SwissProt copying Bio/SwissProt/KeyWList.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SwissProt copying Bio/SwissProt/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/SwissProt creating /<>/.pybuild/cpython3_3.12/build/Bio/TogoWS copying Bio/TogoWS/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/TogoWS creating /<>/.pybuild/cpython3_3.12/build/Bio/Phylo copying Bio/Phylo/_utils.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Phylo copying Bio/Phylo/PhyloXMLIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Phylo copying Bio/Phylo/CDAOIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Phylo copying Bio/Phylo/BaseTree.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Phylo copying Bio/Phylo/_cdao_owl.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Phylo copying Bio/Phylo/NeXMLIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Phylo copying Bio/Phylo/NewickIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Phylo copying Bio/Phylo/NexusIO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Phylo copying Bio/Phylo/_io.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Phylo copying Bio/Phylo/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Phylo copying Bio/Phylo/NeXML.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Phylo copying Bio/Phylo/TreeConstruction.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Phylo copying Bio/Phylo/Newick.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Phylo copying Bio/Phylo/PhyloXML.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Phylo copying Bio/Phylo/CDAO.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Phylo copying Bio/Phylo/Consensus.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Phylo creating /<>/.pybuild/cpython3_3.12/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Phyml.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Raxml.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Fasttree.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Phylo/Applications creating /<>/.pybuild/cpython3_3.12/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/chi2.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/yn00.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_baseml.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_codeml.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/baseml.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_paml.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_yn00.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/codeml.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Phylo/PAML creating /<>/.pybuild/cpython3_3.12/build/Bio/UniGene copying Bio/UniGene/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/UniGene creating /<>/.pybuild/cpython3_3.12/build/Bio/UniProt copying Bio/UniProt/GOA.py -> /<>/.pybuild/cpython3_3.12/build/Bio/UniProt copying Bio/UniProt/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/UniProt creating /<>/.pybuild/cpython3_3.12/build/Bio/Wise copying Bio/Wise/psw.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Wise copying Bio/Wise/dnal.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Wise copying Bio/Wise/__init__.py -> /<>/.pybuild/cpython3_3.12/build/Bio/Wise creating /<>/.pybuild/cpython3_3.12/build/BioSQL copying BioSQL/BioSeqDatabase.py -> /<>/.pybuild/cpython3_3.12/build/BioSQL copying BioSQL/BioSeq.py -> /<>/.pybuild/cpython3_3.12/build/BioSQL copying BioSQL/Loader.py -> /<>/.pybuild/cpython3_3.12/build/BioSQL copying BioSQL/__init__.py -> /<>/.pybuild/cpython3_3.12/build/BioSQL copying BioSQL/DBUtils.py -> /<>/.pybuild/cpython3_3.12/build/BioSQL running egg_info creating biopython.egg-info writing biopython.egg-info/PKG-INFO writing dependency_links to biopython.egg-info/dependency_links.txt writing requirements to biopython.egg-info/requires.txt writing top-level names to biopython.egg-info/top_level.txt writing manifest file 'biopython.egg-info/SOURCES.txt' reading manifest file 'biopython.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.py{}' found anywhere in distribution warning: no previously-included files matching '*.py-e' found anywhere in distribution adding license file 'LICENSE' adding license file 'LICENSE.rst' writing manifest file 'biopython.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'Bio.Align.substitution_matrices.data' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'Bio.Align.substitution_matrices.data' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'Bio.Align.substitution_matrices.data' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'Bio.Align.substitution_matrices.data' to be distributed and are already explicitly excluding 'Bio.Align.substitution_matrices.data' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'Bio.Entrez.DTDs' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'Bio.Entrez.DTDs' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'Bio.Entrez.DTDs' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'Bio.Entrez.DTDs' to be distributed and are already explicitly excluding 'Bio.Entrez.DTDs' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'Bio.Entrez.XSDs' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'Bio.Entrez.XSDs' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'Bio.Entrez.XSDs' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'Bio.Entrez.XSDs' to be distributed and are already explicitly excluding 'Bio.Entrez.XSDs' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying Bio/cpairwise2module.c -> /<>/.pybuild/cpython3_3.12/build/Bio copying Bio/Align/_aligners.c -> /<>/.pybuild/cpython3_3.12/build/Bio/Align creating /<>/.pybuild/cpython3_3.12/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER22 -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER6 -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER74 -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLASTN -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLASTP -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM45 -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM50 -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM62 -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM80 -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM90 -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/DAYHOFF -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/FENG -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/GENETIC -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/GONNET1992 -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/HOXD70 -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/JOHNSON -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/JONES -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/LEVIN -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MCLACHLAN -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MDM78 -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MEGABLAST -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/NUC.4.4 -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM250 -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM30 -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM70 -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/RAO -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/RISLER -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/SCHNEIDER -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/STR -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/TRANS -> /<>/.pybuild/cpython3_3.12/build/Bio/Align/substitution_matrices/data copying Bio/Cluster/cluster.c -> /<>/.pybuild/cpython3_3.12/build/Bio/Cluster copying Bio/Cluster/cluster.h -> /<>/.pybuild/cpython3_3.12/build/Bio/Cluster copying Bio/Cluster/clustermodule.c -> /<>/.pybuild/cpython3_3.12/build/Bio/Cluster creating /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/BITS-embedded-index2.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/BITS-question-answer2.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.mod.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.mod.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.mod.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-articlemeta1-3.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-backmatter1-3.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-chars1-3.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-common-atts1-3.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-common1-3.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-default-classes1-3.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-default-mixes1-3.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-display1-3.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-format1-3.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-funding1-3.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-journalmeta1-3.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-link1-3.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-list1-3.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-math1-3.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-modules1-3.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-notat1-3.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-para1-3.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-phrase1-3.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-references1-3.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-related-object1-3.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-section1-3.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-xmlspecchars1-3.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.mod.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying 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Bio/Entrez/DTDs/SP_General.mod.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/XHTMLtablesetup.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivearticle.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-classes.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-mixes.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-models.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-modules.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/articlemeta.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/backmatter.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_100301.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying 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Bio/Entrez/DTDs/nlmcommon_090101.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_011101.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_080101.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_090101.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_080101.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_100101.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/notat.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/para.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/phrase.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pmc-1.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_020114.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_080101.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_090101.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100101.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100301.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_110101.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_120101.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130101.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130501.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_140101.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_150101.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180101.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180601.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_190101.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/references.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/section.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/taxon.dtd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xhtml-table-1.mod -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xmlspecchars.ent -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/DTDs creating /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/XSDs copying Bio/Entrez/XSDs/IPGReportSet.xsd -> /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/XSDs copying Bio/motifs/_pwm.c -> /<>/.pybuild/cpython3_3.12/build/Bio/motifs copying Bio/Nexus/cnexus.c -> /<>/.pybuild/cpython3_3.12/build/Bio/Nexus copying Bio/PDB/ccealignmodule.c -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/PDB/kdtrees.c -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB copying Bio/SeqIO/_twoBitIO.c -> /<>/.pybuild/cpython3_3.12/build/Bio/SeqIO copying Bio/PDB/QCPSuperimposer/qcprotmodule.c -> /<>/.pybuild/cpython3_3.12/build/Bio/PDB/QCPSuperimposer running build_ext building 'Bio.Align._aligners' extension creating build creating build/temp.linux-armv7l-cpython-312 creating build/temp.linux-armv7l-cpython-312/Bio creating build/temp.linux-armv7l-cpython-312/Bio/Align arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c Bio/Align/_aligners.c -o build/temp.linux-armv7l-cpython-312/Bio/Align/_aligners.o Bio/Align/_aligners.c: In function ‘Aligner_watermansmithbeyer_global_align_compare’: Bio/Align/_aligners.c:5735:12: warning: ‘Ix_row’ may be used uninitialized [-Wmaybe-uninitialized] 5735 | if (Ix_row) { \ | ^ Bio/Align/_aligners.c:6319:5: note: in expansion of macro ‘WATERMANSMITHBEYER_EXIT_ALIGN’ 6319 | WATERMANSMITHBEYER_EXIT_ALIGN; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Bio/Align/_aligners.c:5405:14: note: ‘Ix_row’ was declared here 5405 | double** Ix_row; \ | ^~~~~~ Bio/Align/_aligners.c:6308:5: note: in expansion of macro ‘WATERMANSMITHBEYER_ENTER_ALIGN’ 6308 | WATERMANSMITHBEYER_ENTER_ALIGN(Global); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Bio/Align/_aligners.c:5737:16: warning: ‘Iy_row’ may be used uninitialized [-Wmaybe-uninitialized] 5737 | if (Iy_row) { \ | ^ Bio/Align/_aligners.c:6319:5: note: in expansion of macro ‘WATERMANSMITHBEYER_EXIT_ALIGN’ 6319 | WATERMANSMITHBEYER_EXIT_ALIGN; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Bio/Align/_aligners.c:5406:14: note: ‘Iy_row’ was declared here 5406 | double** Iy_row; \ | ^~~~~~ Bio/Align/_aligners.c:6308:5: note: in expansion of macro ‘WATERMANSMITHBEYER_ENTER_ALIGN’ 6308 | WATERMANSMITHBEYER_ENTER_ALIGN(Global); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Bio/Align/_aligners.c: In function ‘Aligner_watermansmithbeyer_local_align_compare’: Bio/Align/_aligners.c:5735:12: warning: ‘Ix_row’ may be used uninitialized [-Wmaybe-uninitialized] 5735 | if (Ix_row) { \ | ^ Bio/Align/_aligners.c:6367:5: note: in expansion of macro ‘WATERMANSMITHBEYER_EXIT_ALIGN’ 6367 | WATERMANSMITHBEYER_EXIT_ALIGN; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Bio/Align/_aligners.c:5405:14: note: ‘Ix_row’ was declared here 5405 | double** Ix_row; \ | ^~~~~~ Bio/Align/_aligners.c:6356:5: note: in expansion of macro ‘WATERMANSMITHBEYER_ENTER_ALIGN’ 6356 | WATERMANSMITHBEYER_ENTER_ALIGN(Local); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Bio/Align/_aligners.c:5737:16: warning: ‘Iy_row’ may be used uninitialized [-Wmaybe-uninitialized] 5737 | if (Iy_row) { \ | ^ Bio/Align/_aligners.c:6367:5: note: in expansion of macro ‘WATERMANSMITHBEYER_EXIT_ALIGN’ 6367 | WATERMANSMITHBEYER_EXIT_ALIGN; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Bio/Align/_aligners.c:5406:14: note: ‘Iy_row’ was declared here 5406 | double** Iy_row; \ | ^~~~~~ Bio/Align/_aligners.c:6356:5: note: in expansion of macro ‘WATERMANSMITHBEYER_ENTER_ALIGN’ 6356 | WATERMANSMITHBEYER_ENTER_ALIGN(Local); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘Aligner_watermansmithbeyer_global_align_matrix’, inlined from ‘Aligner_align’ at Bio/Align/_aligners.c:6872:34: Bio/Align/_aligners.c:5735:12: warning: ‘Ix_row’ may be used uninitialized [-Wmaybe-uninitialized] 5735 | if (Ix_row) { \ | ^ Bio/Align/_aligners.c:6341:5: note: in expansion of macro ‘WATERMANSMITHBEYER_EXIT_ALIGN’ 6341 | WATERMANSMITHBEYER_EXIT_ALIGN; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Bio/Align/_aligners.c: In function ‘Aligner_align’: Bio/Align/_aligners.c:5405:14: note: ‘Ix_row’ was declared here 5405 | double** Ix_row; \ | ^~~~~~ Bio/Align/_aligners.c:6330:5: note: in expansion of macro ‘WATERMANSMITHBEYER_ENTER_ALIGN’ 6330 | WATERMANSMITHBEYER_ENTER_ALIGN(Global); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘Aligner_watermansmithbeyer_global_align_matrix’, inlined from ‘Aligner_align’ at Bio/Align/_aligners.c:6872:34: Bio/Align/_aligners.c:5737:16: warning: ‘Iy_row’ may be used uninitialized [-Wmaybe-uninitialized] 5737 | if (Iy_row) { \ | ^ Bio/Align/_aligners.c:6341:5: note: in expansion of macro ‘WATERMANSMITHBEYER_EXIT_ALIGN’ 6341 | WATERMANSMITHBEYER_EXIT_ALIGN; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Bio/Align/_aligners.c: In function ‘Aligner_align’: Bio/Align/_aligners.c:5406:14: note: ‘Iy_row’ was declared here 5406 | double** Iy_row; \ | ^~~~~~ Bio/Align/_aligners.c:6330:5: note: in expansion of macro ‘WATERMANSMITHBEYER_ENTER_ALIGN’ 6330 | WATERMANSMITHBEYER_ENTER_ALIGN(Global); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘Aligner_watermansmithbeyer_local_align_matrix’, inlined from ‘Aligner_align’ at Bio/Align/_aligners.c:6878:34: Bio/Align/_aligners.c:5735:12: warning: ‘Ix_row’ may be used uninitialized [-Wmaybe-uninitialized] 5735 | if (Ix_row) { \ | ^ Bio/Align/_aligners.c:6392:5: note: in expansion of macro ‘WATERMANSMITHBEYER_EXIT_ALIGN’ 6392 | WATERMANSMITHBEYER_EXIT_ALIGN; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Bio/Align/_aligners.c: In function ‘Aligner_align’: Bio/Align/_aligners.c:5405:14: note: ‘Ix_row’ was declared here 5405 | double** Ix_row; \ | ^~~~~~ Bio/Align/_aligners.c:6381:5: note: in expansion of macro ‘WATERMANSMITHBEYER_ENTER_ALIGN’ 6381 | WATERMANSMITHBEYER_ENTER_ALIGN(Local); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘Aligner_watermansmithbeyer_local_align_matrix’, inlined from ‘Aligner_align’ at Bio/Align/_aligners.c:6878:34: Bio/Align/_aligners.c:5737:16: warning: ‘Iy_row’ may be used uninitialized [-Wmaybe-uninitialized] 5737 | if (Iy_row) { \ | ^ Bio/Align/_aligners.c:6392:5: note: in expansion of macro ‘WATERMANSMITHBEYER_EXIT_ALIGN’ 6392 | WATERMANSMITHBEYER_EXIT_ALIGN; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Bio/Align/_aligners.c: In function ‘Aligner_align’: Bio/Align/_aligners.c:5406:14: note: ‘Iy_row’ was declared here 5406 | double** Iy_row; \ | ^~~~~~ Bio/Align/_aligners.c:6381:5: note: in expansion of macro ‘WATERMANSMITHBEYER_ENTER_ALIGN’ 6381 | WATERMANSMITHBEYER_ENTER_ALIGN(Local); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/Bio/Align/_aligners.o -L/usr/lib/arm-linux-gnueabihf -o /<>/.pybuild/cpython3_3.12/build/Bio/Align/_aligners.cpython-312-arm-linux-gnueabihf.so building 'Bio.cpairwise2' extension arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c Bio/cpairwise2module.c -o build/temp.linux-armv7l-cpython-312/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/python3.12/Python.h:95, from Bio/cpairwise2module.c:16: /usr/include/python3.12/ceval.h:27:43: note: declared here 27 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/Bio/cpairwise2module.o -L/usr/lib/arm-linux-gnueabihf -o /<>/.pybuild/cpython3_3.12/build/Bio/cpairwise2.cpython-312-arm-linux-gnueabihf.so building 'Bio.Nexus.cnexus' extension creating build/temp.linux-armv7l-cpython-312/Bio/Nexus arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c Bio/Nexus/cnexus.c -o build/temp.linux-armv7l-cpython-312/Bio/Nexus/cnexus.o arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/Bio/Nexus/cnexus.o -L/usr/lib/arm-linux-gnueabihf -o /<>/.pybuild/cpython3_3.12/build/Bio/Nexus/cnexus.cpython-312-arm-linux-gnueabihf.so building 'Bio.PDB.QCPSuperimposer.qcprotmodule' extension creating build/temp.linux-armv7l-cpython-312/Bio/PDB creating build/temp.linux-armv7l-cpython-312/Bio/PDB/QCPSuperimposer arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c Bio/PDB/QCPSuperimposer/qcprotmodule.c -o build/temp.linux-armv7l-cpython-312/Bio/PDB/QCPSuperimposer/qcprotmodule.o arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/Bio/PDB/QCPSuperimposer/qcprotmodule.o -L/usr/lib/arm-linux-gnueabihf -o /<>/.pybuild/cpython3_3.12/build/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-312-arm-linux-gnueabihf.so building 'Bio.motifs._pwm' extension creating build/temp.linux-armv7l-cpython-312/Bio/motifs arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c Bio/motifs/_pwm.c -o build/temp.linux-armv7l-cpython-312/Bio/motifs/_pwm.o arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/Bio/motifs/_pwm.o -L/usr/lib/arm-linux-gnueabihf -o /<>/.pybuild/cpython3_3.12/build/Bio/motifs/_pwm.cpython-312-arm-linux-gnueabihf.so building 'Bio.Cluster._cluster' extension creating build/temp.linux-armv7l-cpython-312/Bio/Cluster arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c Bio/Cluster/cluster.c -o build/temp.linux-armv7l-cpython-312/Bio/Cluster/cluster.o arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c Bio/Cluster/clustermodule.c -o build/temp.linux-armv7l-cpython-312/Bio/Cluster/clustermodule.o arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/Bio/Cluster/cluster.o build/temp.linux-armv7l-cpython-312/Bio/Cluster/clustermodule.o -L/usr/lib/arm-linux-gnueabihf -o /<>/.pybuild/cpython3_3.12/build/Bio/Cluster/_cluster.cpython-312-arm-linux-gnueabihf.so building 'Bio.PDB.kdtrees' extension arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c Bio/PDB/kdtrees.c -o build/temp.linux-armv7l-cpython-312/Bio/PDB/kdtrees.o arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/Bio/PDB/kdtrees.o -L/usr/lib/arm-linux-gnueabihf -o /<>/.pybuild/cpython3_3.12/build/Bio/PDB/kdtrees.cpython-312-arm-linux-gnueabihf.so building 'Bio.PDB.ccealign' extension arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c Bio/PDB/ccealignmodule.c -o build/temp.linux-armv7l-cpython-312/Bio/PDB/ccealignmodule.o arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/Bio/PDB/ccealignmodule.o -L/usr/lib/arm-linux-gnueabihf -o /<>/.pybuild/cpython3_3.12/build/Bio/PDB/ccealign.cpython-312-arm-linux-gnueabihf.so building 'Bio.SeqIO._twoBitIO' extension creating build/temp.linux-armv7l-cpython-312/Bio/SeqIO arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c Bio/SeqIO/_twoBitIO.c -o build/temp.linux-armv7l-cpython-312/Bio/SeqIO/_twoBitIO.o arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/Bio/SeqIO/_twoBitIO.o -L/usr/lib/arm-linux-gnueabihf -o /<>/.pybuild/cpython3_3.12/build/Bio/SeqIO/_twoBitIO.cpython-312-arm-linux-gnueabihf.so I: pybuild base:310: /usr/bin/python3 setup.py build running build running build_py creating /<>/.pybuild/cpython3_3.11/build/Bio copying Bio/_utils.py -> /<>/.pybuild/cpython3_3.11/build/Bio copying Bio/bgzf.py -> /<>/.pybuild/cpython3_3.11/build/Bio copying Bio/MarkovModel.py -> /<>/.pybuild/cpython3_3.11/build/Bio copying Bio/kNN.py -> /<>/.pybuild/cpython3_3.11/build/Bio copying Bio/File.py -> /<>/.pybuild/cpython3_3.11/build/Bio copying Bio/SeqFeature.py -> /<>/.pybuild/cpython3_3.11/build/Bio copying Bio/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio copying Bio/SeqRecord.py -> /<>/.pybuild/cpython3_3.11/build/Bio copying Bio/LogisticRegression.py -> /<>/.pybuild/cpython3_3.11/build/Bio copying Bio/Seq.py -> /<>/.pybuild/cpython3_3.11/build/Bio copying Bio/NaiveBayes.py -> /<>/.pybuild/cpython3_3.11/build/Bio copying Bio/MaxEntropy.py -> /<>/.pybuild/cpython3_3.11/build/Bio copying Bio/pairwise2.py -> /<>/.pybuild/cpython3_3.11/build/Bio creating /<>/.pybuild/cpython3_3.11/build/Bio/Affy copying Bio/Affy/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Affy copying Bio/Affy/CelFile.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Affy creating /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/bed.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/interfaces.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/AlignInfo.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/stockholm.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/psl.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/nexus.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/hhr.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/emboss.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/fasta.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/bigbed.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/a2m.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/mauve.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/exonerate.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/phylip.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/sam.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/clustal.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/tabular.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/bigmaf.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/msf.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/bigpsl.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align copying Bio/Align/maf.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align creating /<>/.pybuild/cpython3_3.11/build/Bio/Align/Applications copying Bio/Align/Applications/_Clustalw.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/Applications copying Bio/Align/Applications/_Prank.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/Applications copying Bio/Align/Applications/_Dialign.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/Applications copying Bio/Align/Applications/_TCoffee.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/Applications copying Bio/Align/Applications/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/Applications copying Bio/Align/Applications/_ClustalOmega.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/Applications copying Bio/Align/Applications/_MSAProbs.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/Applications copying Bio/Align/Applications/_Mafft.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/Applications copying Bio/Align/Applications/_Probcons.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/Applications copying Bio/Align/Applications/_Muscle.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/Applications creating /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices copying Bio/Align/substitution_matrices/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices creating /<>/.pybuild/cpython3_3.11/build/Bio/AlignIO copying Bio/AlignIO/StockholmIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/AlignIO copying Bio/AlignIO/Interfaces.py -> /<>/.pybuild/cpython3_3.11/build/Bio/AlignIO copying Bio/AlignIO/MafIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/AlignIO copying Bio/AlignIO/MsfIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/AlignIO copying Bio/AlignIO/NexusIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/AlignIO copying Bio/AlignIO/MauveIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/AlignIO copying Bio/AlignIO/FastaIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/AlignIO copying Bio/AlignIO/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/AlignIO copying Bio/AlignIO/ClustalIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/AlignIO copying Bio/AlignIO/PhylipIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/AlignIO copying Bio/AlignIO/EmbossIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/AlignIO creating /<>/.pybuild/cpython3_3.11/build/Bio/Alphabet copying Bio/Alphabet/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Alphabet creating /<>/.pybuild/cpython3_3.11/build/Bio/Application copying Bio/Application/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Application creating /<>/.pybuild/cpython3_3.11/build/Bio/Blast copying Bio/Blast/Record.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Blast copying Bio/Blast/ParseBlastTable.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Blast copying Bio/Blast/Applications.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Blast copying Bio/Blast/NCBIWWW.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Blast copying Bio/Blast/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Blast copying Bio/Blast/NCBIXML.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Blast creating /<>/.pybuild/cpython3_3.11/build/Bio/CAPS copying Bio/CAPS/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/CAPS creating /<>/.pybuild/cpython3_3.11/build/Bio/Cluster copying Bio/Cluster/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Cluster creating /<>/.pybuild/cpython3_3.11/build/Bio/codonalign copying Bio/codonalign/codonseq.py -> /<>/.pybuild/cpython3_3.11/build/Bio/codonalign copying Bio/codonalign/codonalignment.py -> /<>/.pybuild/cpython3_3.11/build/Bio/codonalign copying Bio/codonalign/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/codonalign creating /<>/.pybuild/cpython3_3.11/build/Bio/Compass copying Bio/Compass/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Compass creating /<>/.pybuild/cpython3_3.11/build/Bio/Data copying Bio/Data/PDBData.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Data copying Bio/Data/CodonTable.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Data copying Bio/Data/SCOPData.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Data copying Bio/Data/IUPACData.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Data copying Bio/Data/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Data creating /<>/.pybuild/cpython3_3.11/build/Bio/Emboss copying Bio/Emboss/Primer3.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Emboss copying Bio/Emboss/Applications.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Emboss copying Bio/Emboss/PrimerSearch.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Emboss copying Bio/Emboss/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Emboss creating /<>/.pybuild/cpython3_3.11/build/Bio/Entrez copying Bio/Entrez/Parser.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez copying Bio/Entrez/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez creating /<>/.pybuild/cpython3_3.11/build/Bio/ExPASy copying Bio/ExPASy/Prodoc.py -> /<>/.pybuild/cpython3_3.11/build/Bio/ExPASy copying Bio/ExPASy/cellosaurus.py -> /<>/.pybuild/cpython3_3.11/build/Bio/ExPASy copying Bio/ExPASy/Enzyme.py -> /<>/.pybuild/cpython3_3.11/build/Bio/ExPASy copying Bio/ExPASy/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/ExPASy copying Bio/ExPASy/Prosite.py -> /<>/.pybuild/cpython3_3.11/build/Bio/ExPASy copying Bio/ExPASy/ScanProsite.py -> /<>/.pybuild/cpython3_3.11/build/Bio/ExPASy creating /<>/.pybuild/cpython3_3.11/build/Bio/GenBank copying Bio/GenBank/Record.py -> /<>/.pybuild/cpython3_3.11/build/Bio/GenBank copying Bio/GenBank/Scanner.py -> /<>/.pybuild/cpython3_3.11/build/Bio/GenBank copying Bio/GenBank/utils.py -> /<>/.pybuild/cpython3_3.11/build/Bio/GenBank copying Bio/GenBank/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/GenBank creating /<>/.pybuild/cpython3_3.11/build/Bio/Geo copying Bio/Geo/Record.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Geo copying Bio/Geo/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Geo creating /<>/.pybuild/cpython3_3.11/build/Bio/Graphics copying Bio/Graphics/ColorSpiral.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics copying Bio/Graphics/DisplayRepresentation.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics copying Bio/Graphics/BasicChromosome.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics copying Bio/Graphics/Comparative.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics copying Bio/Graphics/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics copying Bio/Graphics/KGML_vis.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics copying Bio/Graphics/Distribution.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics creating /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Feature.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Graph.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Colors.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_GraphSet.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Track.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CrossLink.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Diagram.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram creating /<>/.pybuild/cpython3_3.11/build/Bio/HMM copying Bio/HMM/DynamicProgramming.py -> /<>/.pybuild/cpython3_3.11/build/Bio/HMM copying Bio/HMM/Utilities.py -> /<>/.pybuild/cpython3_3.11/build/Bio/HMM copying Bio/HMM/MarkovModel.py -> /<>/.pybuild/cpython3_3.11/build/Bio/HMM copying Bio/HMM/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/HMM copying Bio/HMM/Trainer.py -> /<>/.pybuild/cpython3_3.11/build/Bio/HMM creating /<>/.pybuild/cpython3_3.11/build/Bio/KEGG copying Bio/KEGG/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/KEGG copying Bio/KEGG/REST.py -> /<>/.pybuild/cpython3_3.11/build/Bio/KEGG creating /<>/.pybuild/cpython3_3.11/build/Bio/KEGG/Compound copying Bio/KEGG/Compound/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/KEGG/Compound creating /<>/.pybuild/cpython3_3.11/build/Bio/KEGG/Enzyme copying Bio/KEGG/Enzyme/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/KEGG/Enzyme creating /<>/.pybuild/cpython3_3.11/build/Bio/KEGG/Gene copying Bio/KEGG/Gene/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/KEGG/Gene creating /<>/.pybuild/cpython3_3.11/build/Bio/KEGG/Map copying Bio/KEGG/Map/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/KEGG/Map creating /<>/.pybuild/cpython3_3.11/build/Bio/PDB creating /<>/.pybuild/cpython3_3.11/build/Bio/PDB/mmtf copying Bio/PDB/mmtf/DefaultParser.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB/mmtf copying Bio/PDB/mmtf/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB/mmtf copying Bio/PDB/mmtf/mmtfio.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB/mmtf creating /<>/.pybuild/cpython3_3.11/build/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_parser.py -> /<>/.pybuild/cpython3_3.11/build/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_pathway.py -> /<>/.pybuild/cpython3_3.11/build/Bio/KEGG/KGML copying Bio/KEGG/KGML/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/KEGG/KGML creating /<>/.pybuild/cpython3_3.11/build/Bio/Medline copying Bio/Medline/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Medline creating /<>/.pybuild/cpython3_3.11/build/Bio/motifs copying Bio/motifs/thresholds.py -> /<>/.pybuild/cpython3_3.11/build/Bio/motifs copying Bio/motifs/pfm.py -> /<>/.pybuild/cpython3_3.11/build/Bio/motifs copying Bio/motifs/matrix.py -> /<>/.pybuild/cpython3_3.11/build/Bio/motifs copying Bio/motifs/xms.py -> /<>/.pybuild/cpython3_3.11/build/Bio/motifs copying Bio/motifs/minimal.py -> /<>/.pybuild/cpython3_3.11/build/Bio/motifs copying Bio/motifs/clusterbuster.py -> /<>/.pybuild/cpython3_3.11/build/Bio/motifs copying Bio/motifs/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/motifs copying Bio/motifs/mast.py -> /<>/.pybuild/cpython3_3.11/build/Bio/motifs copying Bio/motifs/meme.py -> /<>/.pybuild/cpython3_3.11/build/Bio/motifs copying Bio/motifs/alignace.py -> /<>/.pybuild/cpython3_3.11/build/Bio/motifs copying Bio/motifs/transfac.py -> /<>/.pybuild/cpython3_3.11/build/Bio/motifs creating /<>/.pybuild/cpython3_3.11/build/Bio/motifs/applications copying Bio/motifs/applications/_xxmotif.py -> /<>/.pybuild/cpython3_3.11/build/Bio/motifs/applications copying Bio/motifs/applications/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/motifs/applications creating /<>/.pybuild/cpython3_3.11/build/Bio/motifs/jaspar copying Bio/motifs/jaspar/db.py -> /<>/.pybuild/cpython3_3.11/build/Bio/motifs/jaspar copying Bio/motifs/jaspar/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/motifs/jaspar creating /<>/.pybuild/cpython3_3.11/build/Bio/Nexus copying Bio/Nexus/Nodes.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Nexus copying Bio/Nexus/Nexus.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Nexus copying Bio/Nexus/StandardData.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Nexus copying Bio/Nexus/Trees.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Nexus copying Bio/Nexus/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Nexus creating /<>/.pybuild/cpython3_3.11/build/Bio/NMR copying Bio/NMR/xpktools.py -> /<>/.pybuild/cpython3_3.11/build/Bio/NMR copying Bio/NMR/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/NMR copying Bio/NMR/NOEtools.py -> /<>/.pybuild/cpython3_3.11/build/Bio/NMR creating /<>/.pybuild/cpython3_3.11/build/Bio/Pathway copying Bio/Pathway/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Pathway creating /<>/.pybuild/cpython3_3.11/build/Bio/Pathway/Rep copying Bio/Pathway/Rep/Graph.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Pathway/Rep copying Bio/Pathway/Rep/MultiGraph.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Pathway/Rep copying Bio/Pathway/Rep/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Pathway/Rep copying Bio/PDB/Model.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/FragmentMapper.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/StructureBuilder.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/Residue.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/HSExposure.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/Entity.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/mmcifio.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/internal_coords.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/PDBList.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/Dice.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/Superimposer.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/NACCESS.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/NeighborSearch.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/StructureAlignment.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/qcprot.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/Polypeptide.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/DSSP.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/ic_data.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/ic_rebuild.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/SCADIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/Chain.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/Structure.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/MMCIF2Dict.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/MMCIFParser.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/AbstractPropertyMap.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/parse_pdb_header.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/PDBIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/SASA.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/PDBExceptions.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/PICIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/ResidueDepth.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/PDBParser.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/PSEA.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/Atom.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/cealign.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/vectors.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/Selection.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB creating /<>/.pybuild/cpython3_3.11/build/Bio/phenotype copying Bio/phenotype/pm_fitting.py -> /<>/.pybuild/cpython3_3.11/build/Bio/phenotype copying Bio/phenotype/phen_micro.py -> /<>/.pybuild/cpython3_3.11/build/Bio/phenotype copying Bio/phenotype/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/phenotype creating /<>/.pybuild/cpython3_3.11/build/Bio/PopGen copying Bio/PopGen/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PopGen creating /<>/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/LargeFileParser.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/Controller.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/EasyController.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/FileParser.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop creating /<>/.pybuild/cpython3_3.11/build/Bio/Restriction copying Bio/Restriction/Restriction_Dictionary.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Restriction copying Bio/Restriction/PrintFormat.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Restriction copying Bio/Restriction/Restriction.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Restriction copying Bio/Restriction/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Restriction creating /<>/.pybuild/cpython3_3.11/build/Bio/SCOP copying Bio/SCOP/Hie.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SCOP copying Bio/SCOP/Residues.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SCOP copying Bio/SCOP/Des.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SCOP copying Bio/SCOP/Cla.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SCOP copying Bio/SCOP/Dom.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SCOP copying Bio/SCOP/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SCOP copying Bio/SCOP/Raf.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SCOP creating /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO copying Bio/SearchIO/_utils.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO copying Bio/SearchIO/_index.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO copying Bio/SearchIO/FastaIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO copying Bio/SearchIO/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO copying Bio/SearchIO/BlatIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO creating /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_legacy copying Bio/SearchIO/_legacy/NCBIStandalone.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_legacy copying Bio/SearchIO/_legacy/ParserSupport.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_legacy copying Bio/SearchIO/_legacy/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_legacy creating /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/hsp.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/_base.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/query.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/hit.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model creating /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_text.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_tab.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_xml.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/BlastIO creating /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HHsuiteIO copying Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HHsuiteIO copying Bio/SearchIO/HHsuiteIO/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HHsuiteIO creating /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_text.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/_base.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_tab.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO creating /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/_base.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_text.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO creating /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/interproscan_xml.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SearchIO/InterproscanIO creating /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/GckIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/IgIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/NibIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/QualityIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/PdbIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/TwoBitIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/_index.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/SffIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/InsdcIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/Interfaces.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/TabIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/SwissIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/XdnaIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/AbiIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/FastaIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/SnapGeneIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/UniprotIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/SeqXmlIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/AceIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/PhdIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/SeqIO/PirIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO creating /<>/.pybuild/cpython3_3.11/build/Bio/SeqUtils copying Bio/SeqUtils/lcc.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqUtils copying Bio/SeqUtils/IsoelectricPoint.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqUtils copying Bio/SeqUtils/MeltingTemp.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqUtils copying Bio/SeqUtils/ProtParam.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqUtils copying Bio/SeqUtils/CodonUsageIndices.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqUtils copying Bio/SeqUtils/ProtParamData.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqUtils copying Bio/SeqUtils/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqUtils copying Bio/SeqUtils/CodonUsage.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqUtils copying Bio/SeqUtils/CheckSum.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqUtils creating /<>/.pybuild/cpython3_3.11/build/Bio/Sequencing copying Bio/Sequencing/Phd.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Sequencing copying Bio/Sequencing/Ace.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Sequencing copying Bio/Sequencing/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Sequencing creating /<>/.pybuild/cpython3_3.11/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_bwa.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_Novoalign.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_samtools.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Sequencing/Applications creating /<>/.pybuild/cpython3_3.11/build/Bio/SVDSuperimposer copying Bio/SVDSuperimposer/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SVDSuperimposer creating /<>/.pybuild/cpython3_3.11/build/Bio/PDB/QCPSuperimposer copying Bio/PDB/QCPSuperimposer/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB/QCPSuperimposer creating /<>/.pybuild/cpython3_3.11/build/Bio/SwissProt copying Bio/SwissProt/KeyWList.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SwissProt copying Bio/SwissProt/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/SwissProt creating /<>/.pybuild/cpython3_3.11/build/Bio/TogoWS copying Bio/TogoWS/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/TogoWS creating /<>/.pybuild/cpython3_3.11/build/Bio/Phylo copying Bio/Phylo/_utils.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo copying Bio/Phylo/PhyloXMLIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo copying Bio/Phylo/CDAOIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo copying Bio/Phylo/BaseTree.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo copying Bio/Phylo/_cdao_owl.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo copying Bio/Phylo/NeXMLIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo copying Bio/Phylo/NewickIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo copying Bio/Phylo/NexusIO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo copying Bio/Phylo/_io.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo copying Bio/Phylo/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo copying Bio/Phylo/NeXML.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo copying Bio/Phylo/TreeConstruction.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo copying Bio/Phylo/Newick.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo copying Bio/Phylo/PhyloXML.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo copying Bio/Phylo/CDAO.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo copying Bio/Phylo/Consensus.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo creating /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Phyml.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Raxml.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Fasttree.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/Applications creating /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/chi2.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/yn00.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_baseml.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_codeml.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/baseml.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_paml.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_yn00.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/codeml.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML creating /<>/.pybuild/cpython3_3.11/build/Bio/UniGene copying Bio/UniGene/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/UniGene creating /<>/.pybuild/cpython3_3.11/build/Bio/UniProt copying Bio/UniProt/GOA.py -> /<>/.pybuild/cpython3_3.11/build/Bio/UniProt copying Bio/UniProt/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/UniProt creating /<>/.pybuild/cpython3_3.11/build/Bio/Wise copying Bio/Wise/psw.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Wise copying Bio/Wise/dnal.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Wise copying Bio/Wise/__init__.py -> /<>/.pybuild/cpython3_3.11/build/Bio/Wise creating /<>/.pybuild/cpython3_3.11/build/BioSQL copying BioSQL/BioSeqDatabase.py -> /<>/.pybuild/cpython3_3.11/build/BioSQL copying BioSQL/BioSeq.py -> /<>/.pybuild/cpython3_3.11/build/BioSQL copying BioSQL/Loader.py -> /<>/.pybuild/cpython3_3.11/build/BioSQL copying BioSQL/__init__.py -> /<>/.pybuild/cpython3_3.11/build/BioSQL copying BioSQL/DBUtils.py -> /<>/.pybuild/cpython3_3.11/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' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'Bio.Align.substitution_matrices.data' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'Bio.Align.substitution_matrices.data' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'Bio.Align.substitution_matrices.data' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'Bio.Align.substitution_matrices.data' to be distributed and are already explicitly excluding 'Bio.Align.substitution_matrices.data' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'Bio.Entrez.DTDs' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'Bio.Entrez.DTDs' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'Bio.Entrez.DTDs' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'Bio.Entrez.DTDs' to be distributed and are already explicitly excluding 'Bio.Entrez.DTDs' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'Bio.Entrez.XSDs' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'Bio.Entrez.XSDs' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'Bio.Entrez.XSDs' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'Bio.Entrez.XSDs' to be distributed and are already explicitly excluding 'Bio.Entrez.XSDs' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying Bio/cpairwise2module.c -> /<>/.pybuild/cpython3_3.11/build/Bio copying Bio/Align/_aligners.c -> /<>/.pybuild/cpython3_3.11/build/Bio/Align creating /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER22 -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER6 -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER74 -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLASTN -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLASTP -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM45 -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM50 -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM62 -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM80 -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM90 -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/DAYHOFF -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/FENG -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/GENETIC -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/GONNET1992 -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/HOXD70 -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/JOHNSON -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/JONES -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/LEVIN -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MCLACHLAN -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MDM78 -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MEGABLAST -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/NUC.4.4 -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM250 -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM30 -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM70 -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/RAO -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/RISLER -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/SCHNEIDER -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/STR -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/TRANS -> /<>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data copying Bio/Cluster/cluster.c -> /<>/.pybuild/cpython3_3.11/build/Bio/Cluster copying Bio/Cluster/cluster.h -> /<>/.pybuild/cpython3_3.11/build/Bio/Cluster copying Bio/Cluster/clustermodule.c -> /<>/.pybuild/cpython3_3.11/build/Bio/Cluster creating /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/BITS-embedded-index2.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/BITS-question-answer2.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-articlemeta1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-backmatter1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-chars1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-common-atts1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-common1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-default-classes1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-default-mixes1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-display1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-format1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-funding1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-journalmeta1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-link1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-list1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-math1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-modules1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-notat1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-para1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-phrase1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-references1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-related-object1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-section1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-xmlspecchars1-3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Gene.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_General.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_General.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medlars.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medline.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mim.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mime.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Organism.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Project.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Protein.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Pub.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PubMed.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_RNA.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Remap.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Rsite.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqres.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqset.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Sequence.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Submit.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Systems.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TSeq.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TxInit.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Variation.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_all.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NSE.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NSE.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/OMSSA.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/OMSSA.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PDB_General.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PDB_General.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PIR_General.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PIR_General.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PRF_General.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PRF_General.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/SP_General.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/SP_General.mod.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/XHTMLtablesetup.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivearticle.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-classes.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-mixes.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-models.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-modules.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/articlemeta.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/backmatter.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_100301.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_110101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_120101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_130101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_140101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_150101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/chars.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/common.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/default-classes.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/default-mixes.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/display.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eInfo_020511.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eLink_090910.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eLink_101123.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/ePost_020511.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSearch_020511.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSpell.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSummary_041029.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/egquery.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/einfo.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/elink.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/elink_020122.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/epost.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esearch.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esummary-v1.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esummary_gene.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/format.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/htmltable.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsa.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsb.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsc.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsn.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamso.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsr.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isobox.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isocyr1.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isocyr2.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isodia.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk1.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk2.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk3.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk4.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isolat1.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isolat2.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomfrk.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomopf.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomscr.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isonum.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isopub.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isotech.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/journalmeta.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/link.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/list.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/math.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml-in-pubmed.mod -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml2.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml3-qname1.mod -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml3.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathmlsetup.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mmlalias.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mmlextra.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/modules.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_011101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_080101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_090101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_011101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_080101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_090101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_080101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_100101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/notat.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/para.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/phrase.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pmc-1.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_020114.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_080101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_090101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100301.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_110101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_120101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130501.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_140101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_150101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180601.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_190101.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/references.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/section.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/taxon.dtd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xhtml-table-1.mod -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xmlspecchars.ent -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs creating /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/XSDs copying Bio/Entrez/XSDs/IPGReportSet.xsd -> /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/XSDs copying Bio/motifs/_pwm.c -> /<>/.pybuild/cpython3_3.11/build/Bio/motifs copying Bio/Nexus/cnexus.c -> /<>/.pybuild/cpython3_3.11/build/Bio/Nexus copying Bio/PDB/ccealignmodule.c -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/PDB/kdtrees.c -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB copying Bio/SeqIO/_twoBitIO.c -> /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO copying Bio/PDB/QCPSuperimposer/qcprotmodule.c -> /<>/.pybuild/cpython3_3.11/build/Bio/PDB/QCPSuperimposer running build_ext building 'Bio.Align._aligners' extension creating build/temp.linux-armv7l-cpython-311 creating build/temp.linux-armv7l-cpython-311/Bio creating build/temp.linux-armv7l-cpython-311/Bio/Align arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/Align/_aligners.c -o build/temp.linux-armv7l-cpython-311/Bio/Align/_aligners.o arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/Bio/Align/_aligners.o -L/usr/lib/arm-linux-gnueabihf -o /<>/.pybuild/cpython3_3.11/build/Bio/Align/_aligners.cpython-311-arm-linux-gnueabihf.so building 'Bio.cpairwise2' extension arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/cpairwise2module.c -o build/temp.linux-armv7l-cpython-311/Bio/cpairwise2module.o Bio/cpairwise2module.c: In function ‘_get_match_score’: Bio/cpairwise2module.c:60:5: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations] 60 | if(!(py_result = PyEval_CallObject(py_match_fn, py_arglist))) | ^~ In file included from /usr/include/python3.11/Python.h:95, from Bio/cpairwise2module.c:16: /usr/include/python3.11/ceval.h:27:43: note: declared here 27 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/Bio/cpairwise2module.o -L/usr/lib/arm-linux-gnueabihf -o /<>/.pybuild/cpython3_3.11/build/Bio/cpairwise2.cpython-311-arm-linux-gnueabihf.so building 'Bio.Nexus.cnexus' extension creating build/temp.linux-armv7l-cpython-311/Bio/Nexus arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/Nexus/cnexus.c -o build/temp.linux-armv7l-cpython-311/Bio/Nexus/cnexus.o arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/Bio/Nexus/cnexus.o -L/usr/lib/arm-linux-gnueabihf -o /<>/.pybuild/cpython3_3.11/build/Bio/Nexus/cnexus.cpython-311-arm-linux-gnueabihf.so building 'Bio.PDB.QCPSuperimposer.qcprotmodule' extension creating build/temp.linux-armv7l-cpython-311/Bio/PDB creating build/temp.linux-armv7l-cpython-311/Bio/PDB/QCPSuperimposer arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/PDB/QCPSuperimposer/qcprotmodule.c -o build/temp.linux-armv7l-cpython-311/Bio/PDB/QCPSuperimposer/qcprotmodule.o arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/Bio/PDB/QCPSuperimposer/qcprotmodule.o -L/usr/lib/arm-linux-gnueabihf -o /<>/.pybuild/cpython3_3.11/build/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-arm-linux-gnueabihf.so building 'Bio.motifs._pwm' extension creating build/temp.linux-armv7l-cpython-311/Bio/motifs arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/motifs/_pwm.c -o build/temp.linux-armv7l-cpython-311/Bio/motifs/_pwm.o arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/Bio/motifs/_pwm.o -L/usr/lib/arm-linux-gnueabihf -o /<>/.pybuild/cpython3_3.11/build/Bio/motifs/_pwm.cpython-311-arm-linux-gnueabihf.so building 'Bio.Cluster._cluster' extension creating build/temp.linux-armv7l-cpython-311/Bio/Cluster arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/Cluster/cluster.c -o build/temp.linux-armv7l-cpython-311/Bio/Cluster/cluster.o arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/Cluster/clustermodule.c -o build/temp.linux-armv7l-cpython-311/Bio/Cluster/clustermodule.o arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/Bio/Cluster/cluster.o build/temp.linux-armv7l-cpython-311/Bio/Cluster/clustermodule.o -L/usr/lib/arm-linux-gnueabihf -o /<>/.pybuild/cpython3_3.11/build/Bio/Cluster/_cluster.cpython-311-arm-linux-gnueabihf.so building 'Bio.PDB.kdtrees' extension arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/PDB/kdtrees.c -o build/temp.linux-armv7l-cpython-311/Bio/PDB/kdtrees.o arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/Bio/PDB/kdtrees.o -L/usr/lib/arm-linux-gnueabihf -o /<>/.pybuild/cpython3_3.11/build/Bio/PDB/kdtrees.cpython-311-arm-linux-gnueabihf.so building 'Bio.PDB.ccealign' extension arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/PDB/ccealignmodule.c -o build/temp.linux-armv7l-cpython-311/Bio/PDB/ccealignmodule.o arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/Bio/PDB/ccealignmodule.o -L/usr/lib/arm-linux-gnueabihf -o /<>/.pybuild/cpython3_3.11/build/Bio/PDB/ccealign.cpython-311-arm-linux-gnueabihf.so building 'Bio.SeqIO._twoBitIO' extension creating build/temp.linux-armv7l-cpython-311/Bio/SeqIO arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/SeqIO/_twoBitIO.c -o build/temp.linux-armv7l-cpython-311/Bio/SeqIO/_twoBitIO.o arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-biopython-1.81+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/Bio/SeqIO/_twoBitIO.o -L/usr/lib/arm-linux-gnueabihf -o /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/_twoBitIO.cpython-311-arm-linux-gnueabihf.so cd Doc && make make[2]: Entering directory '/<>/Doc' sed "s/\@VERSION\@/1.81/g" version.in > version.sh chmod +x version.sh hevea -exec ./version.sh -exec xxdate.exe -fix Tutorial.tex Exclude comment 'comment' ./Tutorial/chapter_introduction.tex:91: Warning: Undefined citation: 'cock2009' ./Tutorial/chapter_introduction.tex:95: Warning: Undefined citation: 'chapman2000' ./Tutorial/chapter_introduction.tex:96: Warning: Undefined citation: 'hamelryck2003a' ./Tutorial/chapter_introduction.tex:97: Warning: Undefined citation: 'dehoon2004' ./Tutorial/chapter_introduction.tex:98: Warning: Undefined citation: 'pritchard2006' ./Tutorial/chapter_introduction.tex:99: Warning: Undefined citation: 'talevich2012' ./Tutorial/chapter_introduction.tex:100: Warning: Undefined citation: 'cock2010' ./Tutorial/chapter_introduction.tex:185: Warning: Undefined label: 'sec:seq-comparison' ./Tutorial/chapter_introduction.tex:191: Warning: Undefined label: 'sec:appendix-handles' ./Tutorial/chapter_quick_start.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:14: Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_quick_start.tex:14: Warning: Undefined label: 'chapter:advanced' ./Tutorial/chapter_quick_start.tex:19: Warning: Undefined label: 'chapter:seq_objects' ./Tutorial/chapter_quick_start.tex:45: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_quick_start.tex:65: Warning: Undefined label: 'sec:sequence-parsing' ./Tutorial/chapter_quick_start.tex:65: Warning: Undefined label: 'chapter:entrez' ./Tutorial/chapter_quick_start.tex:65: Warning: Undefined label: 'chapter:uniprot' ./Tutorial/chapter_quick_start.tex:65: Warning: Undefined label: 'sec:align_clustal' ./Tutorial/chapter_quick_start.tex:72: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_quick_start.tex:79: Warning: Undefined label: 'sec:connecting-with-biological-databases' ./Tutorial/chapter_quick_start.tex:145: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_quick_start.tex:145: Warning: Undefined label: 'chapter:align' ./Tutorial/chapter_quick_start.tex:150: Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_quick_start.tex:158: Warning: Undefined label: 'chapter:entrez' ./Tutorial/chapter_quick_start.tex:159: Warning: Undefined label: 'chapter:uniprot' ./Tutorial/chapter_quick_start.tex:169: Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_seq_objects.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined label: 'chapter:seq_annot' ./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_objects.tex:86: Warning: Undefined label: 'sec:mutable-seq' ./Tutorial/chapter_seq_objects.tex:155: Warning: Undefined label: 'sec:SeqRecord-format' ./Tutorial/chapter_seq_objects.tex:157: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_objects.tex:278: Warning: Undefined label: 'sec:SeqIO-reverse-complement' ./Tutorial/chapter_seq_objects.tex:353: Warning: Undefined label: 'sec:seq-module-functions' ./Tutorial/chapter_seq_objects.tex:469: Warning: Undefined label: 'sec:SeqIO-translate' ./Tutorial/chapter_seq_objects.tex:475: Warning: Undefined label: 'sec:seq-module-functions' ./Tutorial/chapter_seq_objects.tex:598: Warning: Undefined label: 'sec:seq-to-string' ./Tutorial/chapter_seq_objects.tex:741: Warning: Undefined label: 'sec:seq-to-string' ./Tutorial/chapter_seq_annot.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined label: 'chapter:seq_objects' ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined label: 'chapter:seq_objects' ./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_annot.tex:33: Warning: Undefined label: 'sec:FASTQ-filtering-example' ./Tutorial/chapter_seq_annot.tex:37: Warning: Undefined label: 'sec:seq_features' ./Tutorial/chapter_seq_annot.tex:47: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_annot.tex:130: Warning: Undefined label: 'chapter:quick_start' ./Tutorial/chapter_seq_annot.tex:132: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_annot.tex:211: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_annot.tex:275: Warning: Undefined label: 'sec:seq_features' ./Tutorial/chapter_seq_annot.tex:278: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_annot.tex:284: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:292: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:502: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:600: Warning: Undefined label: 'sec:seq-comparison' ./Tutorial/chapter_seq_annot.tex:608: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:648: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_annot.tex:651: Warning: Undefined label: 'sec:Bio.SeqIO-and-StringIO' ./Tutorial/chapter_seq_annot.tex:793: Warning: Undefined label: 'sec:SeqRecord-format' ./Tutorial/chapter_seq_annot.tex:805: Warning: Undefined label: 'sec:FASTQ-slicing-off-primer' ./Tutorial/chapter_seq_annot.tex:806: Warning: Undefined label: 'sec:FASTQ-slicing-off-adaptor' ./Tutorial/chapter_seq_annot.tex:819: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seqio.tex:4: Warning: Undefined label: 'chapter:quick_start' ./Tutorial/chapter_seqio.tex:4: Warning: Undefined label: 'chapter:seq_annot' ./Tutorial/chapter_seqio.tex:12: Warning: Undefined label: 'chapter:seq_annot' ./Tutorial/chapter_seqio.tex:12: Warning: Undefined label: 'chapter:seq_objects' ./Tutorial/chapter_seqio.tex:14: Warning: Undefined label: 'sec:low-level-fasta-fastq' ./Tutorial/chapter_seqio.tex:22: Warning: Undefined label: 'sec:SeqIO_Online' ./Tutorial/chapter_seqio.tex:22: Warning: Undefined label: 'sec:appendix-handles' ./Tutorial/chapter_seqio.tex:43: Warning: Undefined label: 'sec:sequence-parsing' ./Tutorial/chapter_seqio.tex:68: Warning: Undefined label: 'sec:sequence-parsing-plus-pylab' ./Tutorial/chapter_seqio.tex:150: Warning: Undefined label: 'chapter:seq_annot' ./Tutorial/chapter_seqio.tex:306: Warning: Undefined label: 'sec:writing-sequence-files' ./Tutorial/chapter_seqio.tex:326: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:329: Warning: Undefined label: 'sec:appendix-handles' ./Tutorial/chapter_seqio.tex:398: Warning: Undefined label: 'sec:SeqIO-index-bgzf' ./Tutorial/chapter_seqio.tex:401: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:413: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:413: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:414: Warning: Undefined label: 'sec:efetch' ./Tutorial/chapter_seqio.tex:504: Warning: Undefined label: 'chapter:entrez' ./Tutorial/chapter_seqio.tex:504: Warning: Undefined label: 'sec:entrez-guidelines' ./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:509: Warning: Undefined label: 'chapter:uniprot' ./Tutorial/chapter_seqio.tex:565: Warning: Undefined label: 'sec:seqio_todict' ./Tutorial/chapter_seqio.tex:571: Warning: Undefined label: 'sec:SeqIO-index' ./Tutorial/chapter_seqio.tex:575: Warning: Undefined label: 'sec:SeqIO-index-db' ./Tutorial/chapter_seqio.tex:578: Warning: Undefined label: 'sec:SeqIO-indexing-discussion' ./Tutorial/chapter_seqio.tex:581: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:588: Warning: Undefined label: 'sec:SeqIO-index' ./Tutorial/chapter_seqio.tex:661: Warning: Undefined label: 'sec:fasta-parsing' ./Tutorial/chapter_seqio.tex:783: Warning: Undefined label: 'sec:fastq-indexing' ./Tutorial/chapter_seqio.tex:804: Warning: Undefined label: 'sec:seqio-todict-functionkey' ./Tutorial/chapter_seqio.tex:866: Warning: Undefined label: 'sec:SeqIO-sort' ./Tutorial/chapter_seqio.tex:948: Warning: Undefined label: 'sec:seqio-index-getraw' ./Tutorial/chapter_seqio.tex:1189: Warning: Undefined label: 'sec:seqio-index-getraw' ./Tutorial/chapter_seqio.tex:1232: Warning: Undefined label: 'sec:SeqIO-fastq-conversion' ./Tutorial/chapter_seqio.tex:1232: Warning: Undefined label: 'sec:SeqIO-fasta-qual-conversion' ./Tutorial/chapter_seqio.tex:1247: Warning: Undefined label: 'sec:seq-reverse-complement' ./Tutorial/chapter_seqio.tex:1258: Warning: Undefined label: 'sec:SeqRecord-reverse-complement' ./Tutorial/chapter_seqio.tex:1311: Warning: Undefined label: 'sec:SeqIO-translate' ./Tutorial/chapter_seqio.tex:1331: Warning: Undefined label: 'sec:SeqRecord-format' ./Tutorial/chapter_seqio.tex:1412: Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_align.tex:31: Warning: Undefined label: 'sec:appendix-handles' ./Tutorial/chapter_align.tex:35: Warning: Undefined label: 'sec:AlignIO-count-argument' ./Tutorial/chapter_align.tex:113: Warning: Undefined label: 'sec:alignment-format' ./Tutorial/chapter_align.tex:444: Warning: Undefined label: 'sec:SeqIO-conversion' ./Tutorial/chapter_align.tex:633: Warning: Undefined label: 'sec:SeqRecord-format' ./Tutorial/chapter_align.tex:813: Warning: Undefined label: 'sec:SeqRecord-addition' ./Tutorial/chapter_align.tex:892: Warning: Undefined label: 'sec:subs_mat_ex' ./Tutorial/chapter_align.tex:913: Warning: Undefined label: 'sec:pairwise' ./Tutorial/chapter_align.tex:917: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_align.tex:947: Warning: Undefined label: 'sec:emboss-needle-water' ./Tutorial/chapter_align.tex:955: Warning: '_' occurring outside math mode ./Tutorial/chapter_align.tex:1093: Warning: Undefined label: 'chapter:phylo' ./Tutorial/chapter_align.tex:1317: Warning: Undefined label: 'sec:appendix-handles' ./Tutorial/chapter_align.tex:1492: Warning: Undefined citation: 'durbin1998' ./Tutorial/chapter_align.tex:1505: Warning: Undefined label: 'sec:pairwise-aligner' ./Tutorial/chapter_align.tex:1578: Warning: Undefined citation: 'waterman1987' ./Tutorial/chapter_align.tex:1608: Warning: Undefined label: 'sec:pairwise-substitution-scores' ./Tutorial/chapter_align.tex:1608: Warning: Undefined label: 'sec:pairwise-affine-gapscores' 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label: 'sec:parsing-blast' ./Tutorial/chapter_blast.tex:160: Warning: Undefined label: 'sec:parsing-blast' ./Tutorial/chapter_blast.tex:169: Warning: Undefined label: 'sec:parsing-blast' ./Tutorial/chapter_blast.tex:178: Warning: Undefined label: 'sec:running-www-blast' ./Tutorial/chapter_blast.tex:206: Warning: Undefined label: 'sec:alignment-tools' ./Tutorial/chapter_blast.tex:241: Warning: Undefined label: 'sec:parsing-blast' ./Tutorial/chapter_blast.tex:287: Warning: Undefined label: 'sec:running-www-blast' ./Tutorial/chapter_blast.tex:289: Warning: Undefined label: 'sec:running-local-blast' ./Tutorial/chapter_blast.tex:304: Warning: Undefined label: 'sec:appendix-handles' ./Tutorial/chapter_blast.tex:340: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_blast.tex:340: Warning: Undefined label: 'chapter:align' ./Tutorial/chapter_blast.tex:452: Warning: Undefined label: 'fig:blastrecord' ./Tutorial/chapter_blast.tex:468: Warning: Undefined label: 'fig:psiblastrecord' 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occurring outside math mode ./Tutorial/chapter_entrez.tex:1199: Warning: Undefined label: 'sec:orchids' ./Tutorial/chapter_entrez.tex:1254: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1289: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1296: Warning: Undefined label: 'sec:SeqIO_GenBank_Online' ./Tutorial/chapter_entrez.tex:1297: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1349: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_entrez.tex:1373: Warning: Undefined label: 'sec:entrez-guidelines' ./Tutorial/chapter_entrez.tex:1374: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1434: Warning: Undefined label: 'sec:entrez-search-fetch-genbank' ./Tutorial/chapter_entrez.tex:1456: Warning: Undefined label: 'sec:entrez_example_genbank' ./Tutorial/chapter_entrez.tex:1545: Warning: Undefined label: 'sec:entrez-and-medline' ./Tutorial/chapter_entrez.tex:1550: 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'sec:disordered_atoms' ./Tutorial/chapter_pdb.tex:592: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:606: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:610: Warning: Undefined label: 'fig:smcra' ./Tutorial/chapter_pdb.tex:646: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:657: Warning: Undefined label: 'fig:smcra' ./Tutorial/chapter_pdb.tex:683: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:924: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:1261: Warning: Undefined label: 'fig:distanceplot' ./Tutorial/chapter_pdb.tex:1383: Warning: Undefined label: 'fig:phepairs' ./Tutorial/chapter_pdb.tex:1455: Warning: Undefined label: 'table:ic-attribs' ./Tutorial/chapter_pdb.tex:1496: Warning: Undefined citation: 'golub1989' ./Tutorial/chapter_pdb.tex:1524: Warning: Undefined citation: 'hamelryck2005' ./Tutorial/chapter_pdb.tex:1559: Warning: Undefined label: 'table:DSSP-codes' ./Tutorial/chapter_pdb.tex:1599: Warning: Undefined label: 'sec:residue_depth' ./Tutorial/chapter_pdb.tex:1602: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:1650: Warning: Undefined citation: 'hamelryck2003a' ./Tutorial/chapter_pdb.tex:1664: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:1861: Warning: Undefined citation: 'hamelryck2003b' ./Tutorial/chapter_pdb.tex:1862: Warning: Undefined citation: 'majumdar2005' ./Tutorial/chapter_phylo.tex:9: Warning: Undefined citation: 'talevich2012' ./Tutorial/chapter_phylo.tex:96: Warning: Undefined label: 'fig:phylo-simple-draw' ./Tutorial/chapter_phylo.tex:201: Warning: Undefined label: 'fig:phylo-color-draw' ./Tutorial/chapter_phylo.tex:823: Warning: Undefined label: 'sec:PhyloXML' ./Tutorial/chapter_motifs.tex:8: Warning: Undefined label: 'sec:links' ./Tutorial/chapter_motifs.tex:165: Warning: Undefined citation: 'cornish1985' ./Tutorial/chapter_motifs.tex:166: Warning: Undefined citation: 'cavener1987' ./Tutorial/chapter_motifs.tex:542: Warning: Undefined citation: 'bailey1994' ./Tutorial/chapter_motifs.tex:688: Warning: Undefined citation: 'matys2003' ./Tutorial/chapter_motifs.tex:772: Warning: Undefined label: 'table:transfaccodes' ./Tutorial/chapter_cluster.tex:6: Warning: Undefined citation: 'dehoon2004' ./Tutorial/chapter_cluster.tex:30: Warning: Undefined citation: 'lecuyer1988' ./Tutorial/chapter_cluster.tex:30: Warning: Undefined citation: 'kachitvichyanukul1988' ./Tutorial/chapter_cluster.tex:154: Warning: Undefined citation: 'snedecor1989' ./Tutorial/chapter_cluster.tex:183: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:278: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:346: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:556: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:600: Warning: Undefined citation: 'kohonen1997' ./Tutorial/chapter_cluster.tex:600: Warning: Undefined citation: 'tamayo1999' ./Tutorial/chapter_cluster.tex:647: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:660: Warning: Undefined citation: 'yeung2001' ./Tutorial/chapter_cluster.tex:668: Warning: Undefined citation: 'golub1971' ./Tutorial/chapter_cluster.tex:802: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:805: Warning: Undefined label: 'sec:distancematrix' ./Tutorial/chapter_cluster.tex:823: Warning: Undefined label: 'sec:clustercentroids' ./Tutorial/chapter_cluster.tex:846: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:871: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:900: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:922: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:954: Warning: Undefined citation: 'hihara2001' ./Tutorial/chapter_learning.tex:40: Warning: Undefined label: 'eq:OP' ./Tutorial/chapter_learning.tex:40: Warning: Undefined label: 'eq:NOP' ./Tutorial/chapter_learning.tex:75: Warning: Undefined label: 'table:training' ./Tutorial/chapter_learning.tex:197: Warning: Undefined label: 'eq:OP' ./Tutorial/chapter_learning.tex:197: Warning: Undefined label: 'eq:NOP' ./Tutorial/chapter_learning.tex:261: Warning: Undefined label: 'eq:OP' ./Tutorial/chapter_learning.tex:261: Warning: Undefined label: 'eq:NOP' ./Tutorial/chapter_learning.tex:263: Warning: Undefined label: 'eq:OP' ./Tutorial/chapter_learning.tex:263: Warning: Undefined label: 'eq:NOP' ./Tutorial/chapter_learning.tex:273: Warning: Undefined label: 'sec:LogisticRegression' ./Tutorial/chapter_learning.tex:277: Warning: Undefined label: 'table:training' ./Tutorial/chapter_learning.tex:285: Warning: Undefined label: 'sec:LogisticRegressionTraining' ./Tutorial/chapter_graphics.tex:18: Warning: Undefined citation: 'pritchard2006' ./Tutorial/chapter_graphics.tex:28: Warning: Undefined citation: 'toth2006' ./Tutorial/chapter_graphics.tex:31: Warning: Undefined citation: 'vanderauwera2009' ./Tutorial/chapter_graphics.tex:36: Warning: Undefined label: 'chapter:seq_annot' ./Tutorial/chapter_graphics.tex:36: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:64: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:220: Warning: Undefined label: 'sec:seq_features' ./Tutorial/chapter_graphics.tex:268: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:268: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:326: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:326: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:345: Warning: Undefined label: 'sec:gd_nice_example' ./Tutorial/chapter_graphics.tex:352: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:409: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:409: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:485: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:485: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:488: Warning: Undefined label: 'sec:gd_top_down' ./Tutorial/chapter_graphics.tex:591: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:591: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:596: Warning: Undefined citation: 'proux2002' ./Tutorial/chapter_graphics.tex:605: Warning: Undefined label: 'sec:efetch' ./Tutorial/chapter_graphics.tex:608: Warning: Undefined label: 'sec:SeqRecord-slicing' ./Tutorial/chapter_graphics.tex:610: Warning: Undefined label: 'sec:SeqRecord-reverse-complement' ./Tutorial/chapter_graphics.tex:752: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:752: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:759: Warning: Undefined citation: 'proux2002' ./Tutorial/chapter_graphics.tex:1012: Warning: Undefined citation: 'jupe2012' ./Tutorial/chapter_phenotype.tex:231: Warning: Optional argument to \item in itemize environment ./Tutorial/chapter_phenotype.tex:233: Warning: Optional argument to \item in itemize environment ./Tutorial/chapter_phenotype.tex:235: Warning: Optional argument to \item in itemize environment ./Tutorial/chapter_cookbook.tex:22: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_cookbook.tex:58: Warning: Undefined label: 'sec:low-level-fasta-fastq' ./Tutorial/chapter_cookbook.tex:146: Warning: Undefined label: 'sec:Bio.SeqIO-and-StringIO' ./Tutorial/chapter_cookbook.tex:201: Warning: Undefined label: 'sec:translation' ./Tutorial/chapter_cookbook.tex:206: Warning: Undefined label: 'sec:SeqIO-reverse-complement' ./Tutorial/chapter_cookbook.tex:338: Warning: Undefined label: 'sec:seqio-index-getraw' ./Tutorial/chapter_cookbook.tex:443: Warning: Undefined label: 'sec:low-level-fasta-fastq' ./Tutorial/chapter_cookbook.tex:457: Warning: Undefined label: 'sec:low-level-fasta-fastq' ./Tutorial/chapter_cookbook.tex:480: Warning: Undefined label: 'sec:SeqRecord-slicing' ./Tutorial/chapter_cookbook.tex:643: Warning: Undefined label: 'sec:SeqIO-conversion' ./Tutorial/chapter_cookbook.tex:646: Warning: Undefined citation: 'cock2010' ./Tutorial/chapter_cookbook.tex:801: Warning: Undefined label: 'sec:SeqIO-index' ./Tutorial/chapter_cookbook.tex:823: Warning: Undefined label: 'sec:SeqIO-index' ./Tutorial/chapter_cookbook.tex:825: Warning: Undefined label: 'sec:SeqIO-sort' ./Tutorial/chapter_cookbook.tex:839: Warning: Undefined label: 'sec:SeqIO-conversion' ./Tutorial/chapter_cookbook.tex:905: Warning: Undefined label: 'sec:translation' ./Tutorial/chapter_cookbook.tex:1024: Warning: Undefined label: 'sec:gd_nice_example' ./Tutorial/chapter_cookbook.tex:1041: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_cookbook.tex:1418: Warning: Undefined label: 'chapter:align' ./Tutorial/chapter_cookbook.tex:1421: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1425: Warning: Undefined label: 'chapter:align' ./Tutorial/chapter_cookbook.tex:1436: Warning: Undefined label: 'sec:consensus' ./Tutorial/chapter_cookbook.tex:1437: Warning: Undefined label: 'sec:pssm' ./Tutorial/chapter_cookbook.tex:1438: Warning: Undefined label: 'sec:getting_info_content' ./Tutorial/chapter_cookbook.tex:1439: Warning: Undefined label: 'sec:sub_matrix' ./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined label: 'sec:summary_info' ./Tutorial/chapter_cookbook.tex:1538: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1538: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1565: Warning: Undefined label: 'sec:summary_info' ./Tutorial/chapter_cookbook.tex:1617: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1626: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1626: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1640: Warning: Undefined label: 'sec:align_clustal' ./Tutorial/chapter_cookbook.tex:1748: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_testing.tex:55: Warning: Undefined label: 'sec:doctest' ./Tutorial/chapter_testing.tex:282: Warning: Undefined label: 'sec:doctest' ./Tutorial/chapter_contributing.tex:32: Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_contributing.tex:38: Warning: '_' occurring outside math mode ./Tutorial/chapter_contributing.tex:75: Warning: Undefined label: 'chapter:testing' ./Tutorial/chapter_contributing.tex:91: 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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occurring outside math mode ./Tutorial/chapter_seqio.tex:180: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:180: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:198: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:248: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:257: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:257: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:290: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:290: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:291: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:291: Warning: Undefined block in text mode: 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./Tutorial/chapter_seqio.tex:413: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:413: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:421: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:421: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:448: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:448: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:471: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:471: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:504: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:504: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:507: 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[] ./Tutorial/chapter_seqio.tex:1038: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1039: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1039: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1039: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1039: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1041: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1041: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1045: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1045: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1045: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1045: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1050: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1050: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1050: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1050: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1062: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1062: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1062: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1062: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1067: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1067: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1073: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1073: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in 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'CODE' [] ./Tutorial/chapter_align.tex:1069: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1069: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1098: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1098: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1127: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1127: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1150: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1150: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1161: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1161: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1181: Warning: Undefined block in 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text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1811: Warning: Undefined 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./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1910: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1910: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1912: Warning: Undefined 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./Tutorial/chapter_align.tex:2067: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2091: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2091: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2102: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2102: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2164: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2164: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2192: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2192: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2203: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2203: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2295: Warning: line too long ./Tutorial/chapter_align.tex:2311: Warning: line too long ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] 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'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2392: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2392: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2392: Warning: Undefined 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text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2435: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2435: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2479: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2479: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2479: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2479: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2485: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2485: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2493: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2493: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2496: Warning: Multiple definitions for label: sec:pairwise-general-gapscores ./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2519: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2519: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2519: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2519: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2612: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2612: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2612: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2612: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2698: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2698: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2698: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2698: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2758: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2758: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2758: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2758: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2864: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2864: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2932: Warning: '_' occurring outside math mode ./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2934: Warning: Undefined 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'CODE' [] ./Tutorial/chapter_align.tex:3217: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3217: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3263: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3263: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3282: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3282: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3302: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3302: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3315: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3315: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3315: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3315: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3350: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3350: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3369: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3369: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3391: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3391: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3393: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3393: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3396: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3396: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3400: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3400: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3416: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3416: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3425: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3425: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3429: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3429: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3442: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3442: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3443: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3443: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3448: Warning: line too long ./Tutorial/chapter_align.tex:3450: Warning: line too long ./Tutorial/chapter_align.tex:3468: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3468: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3491: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3491: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3508: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3508: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3511: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3511: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3528: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3528: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3529: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3529: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3552: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3552: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3565: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3565: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3572: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3572: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:1: Warning: line too long ./Tutorial/chapter_blast.tex:1: Warning: line too long ./Tutorial/chapter_blast.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:19: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:20: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:20: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:29: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:29: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:29: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:29: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:35: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:35: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:45: Warning: line too long ./Tutorial/chapter_blast.tex:53: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:53: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:60: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:60: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:65: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:65: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:68: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:68: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:69: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:69: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:70: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:70: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:72: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:72: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:74: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:74: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:109: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:121: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:121: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:132: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:132: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:135: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:135: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:146: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:146: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:147: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:147: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:157: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:157: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:159: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:159: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:202: Warning: '_' occurring outside math mode ./Tutorial/chapter_blast.tex:202: Warning: '_' occurring outside math mode ./Tutorial/chapter_blast.tex:225: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:225: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:236: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:236: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:238: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:238: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:240: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:240: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:248: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:248: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:259: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:259: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:259: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:259: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:273: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:273: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:303: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:303: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:303: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:303: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:307: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:307: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:339: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:339: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:339: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:339: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:341: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:341: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:341: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:341: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:342: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:342: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:342: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:342: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:344: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:344: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:344: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:344: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:348: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:348: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:369: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:369: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:388: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:388: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:440: Warning: line too long ./Tutorial/chapter_blast.tex:442: Warning: line too long ./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:452: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:452: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:452: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:452: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:456: Warning: Image in text ./Tutorial/chapter_blast.tex:472: Warning: Image in text ./Tutorial/chapter_blast.tex:488: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:488: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:488: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:488: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:489: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:489: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:494: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:494: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:501: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:501: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:502: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:502: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:507: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:507: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:1: Warning: line too long ./Tutorial/chapter_searchio.tex:17: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:17: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:18: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:18: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:21: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:21: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:27: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:27: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:29: Warning: '_' occurring outside math mode ./Tutorial/chapter_searchio.tex:31: Warning: '_' occurring outside math mode ./Tutorial/chapter_searchio.tex:32: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:32: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:40: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:40: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:41: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:41: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:42: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:42: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:44: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:44: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:46: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:46: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:47: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:47: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:72: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:72: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:77: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:77: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:78: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:78: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:78: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:78: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:79: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:79: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:79: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_searchio.tex:79: 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mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:716: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:749: Warning: overfull line in array : array too wide ./Tutorial/chapter_cluster.tex:749: Warning: line too long ./Tutorial/chapter_cluster.tex:749: Warning: line too long ./Tutorial/chapter_cluster.tex:755: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:755: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:758: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:758: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:761: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:761: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' [] 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Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_appendix.tex:98: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial.tex:126: Warning: line too long ./Tutorial.tex:137: Warning: Application of '\'' on 'e' failed ./Tutorial.tex:137: Warning: Application of '\'' on 'o' failed ./Tutorial.tex:141: Warning: Application of '\"' on 'u' failed ./Tutorial.tex:215: Warning: Application of '\"' on 'o' failed ./Tutorial.tex:215: Warning: Application of '\"' on 'u' failed HeVeA Warning: Label(s) may have changed. Rerun me to get cross-references right. Run, run, again... Exclude comment 'comment' ./Tutorial.tex:73: Warning: tt_mode is an empty style ./Tutorial.haux:567: 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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Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_quick_start.tex:169: Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_seq_objects.tex:1: Warning: line too long ./Tutorial/chapter_seq_objects.tex:1: Warning: line too long ./Tutorial/chapter_seq_objects.tex:1: Warning: line too long ./Tutorial/chapter_seq_objects.tex:1: Warning: line too long ./Tutorial/chapter_seq_objects.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_objects.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined label: 'chapter:seq_annot' ./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_objects.tex:7: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:7: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:9: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:9: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:44: Warning: Undefined block in text mode: 'CODE' [] 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./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:155: Warning: Undefined label: 'sec:SeqRecord-format' ./Tutorial/chapter_seq_objects.tex:156: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:156: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:157: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_objects.tex:161: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:161: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:197: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:197: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:197: Warning: Undefined block in text mode: 'CODE' [] 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./Tutorial/chapter_seq_objects.tex:278: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:279: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:279: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:296: Warning: Command not found: \downarrow ./Tutorial/chapter_seq_objects.tex:305: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:305: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:319: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:319: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:319: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:319: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:339: Warning: Undefined block in text mode: 'CODE' [] 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./Tutorial/chapter_seq_objects.tex:741: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:741: Warning: Undefined label: 'sec:seq-to-string' ./Tutorial/chapter_seq_objects.tex:747: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:747: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:748: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:748: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:748: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:748: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:764: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_objects.tex:764: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined label: 'chapter:seq_objects' ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined label: 'chapter:seq_objects' ./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_annot.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:25: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:25: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:33: Warning: Undefined label: 'sec:FASTQ-filtering-example' ./Tutorial/chapter_seq_annot.tex:37: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:37: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:37: Warning: Undefined label: 'sec:seq_features' ./Tutorial/chapter_seq_annot.tex:44: Warning: Undefined block in text mode: 'CODE' [] 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./Tutorial/chapter_seq_annot.tex:197: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_annot.tex:211: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:211: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:211: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_annot.tex:218: Warning: line too long ./Tutorial/chapter_seq_annot.tex:227: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:227: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:227: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:227: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:248: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:248: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seq_annot.tex:258: Warning: Undefined block in text mode: 'CODE' 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./Tutorial/chapter_seqio.tex:398: Warning: Undefined label: 'sec:SeqIO-index-bgzf' ./Tutorial/chapter_seqio.tex:401: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:404: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:404: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:413: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:413: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:414: Warning: Undefined label: 'sec:efetch' ./Tutorial/chapter_seqio.tex:421: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:421: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:448: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:448: 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'CODE' [] ./Tutorial/chapter_seqio.tex:540: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:540: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:540: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:540: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:550: Warning: line too long ./Tutorial/chapter_seqio.tex:560: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:560: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:564: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:564: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:565: Warning: Undefined label: 'sec:seqio_todict' ./Tutorial/chapter_seqio.tex:566: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_seqio.tex:566: Warning: Undefined block in text mode: 'CODE' [] 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./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1612: Warning: Undefined label: 'sec:pairwise-affine-gapscores' ./Tutorial/chapter_align.tex:1613: Warning: Undefined label: 'sec:pairwise-general-gapscores' ./Tutorial/chapter_align.tex:1613: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1613: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1623: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1623: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1623: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1623: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1636: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1636: Warning: Undefined 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'CODE' [] ./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1722: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1722: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1729: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1729: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1729: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1729: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1730: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1730: Warning: Undefined block in 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./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:1908: Warning: Undefined label: 'sec:pairwise-examples' ./Tutorial/chapter_align.tex:1910: Warning: Undefined block in 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./Tutorial/chapter_align.tex:2164: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2164: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2166: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2181: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2192: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2192: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2203: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2203: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2295: Warning: line too long ./Tutorial/chapter_align.tex:2311: Warning: line too long ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2392: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2392: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2392: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2392: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2411: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2411: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2411: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2411: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2412: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2412: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2418: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2424: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2424: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2424: Warning: Undefined citation: 'kent2002' ./Tutorial/chapter_align.tex:2428: Warning: line too long ./Tutorial/chapter_align.tex:2431: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2431: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2433: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2433: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2434: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2434: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2435: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2435: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2479: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2479: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2479: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2479: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2485: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2485: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2493: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2493: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2496: Warning: Multiple definitions for label: sec:pairwise-general-gapscores ./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2519: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2519: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2519: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2519: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2612: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2612: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2612: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2612: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2698: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2698: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2698: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2698: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2725: Warning: Undefined citation: 'schneider2005' ./Tutorial/chapter_align.tex:2725: Warning: Undefined label: 'sec:substitution_matrices' ./Tutorial/chapter_align.tex:2758: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2758: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2758: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2758: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2864: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2864: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2932: Warning: '_' occurring outside math mode ./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2938: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2938: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2951: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2951: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2958: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2958: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2975: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2975: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2993: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2993: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2993: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:2993: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3007: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3007: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3030: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3030: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3049: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3049: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3070: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3070: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3119: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3119: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3119: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3119: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3217: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3217: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3217: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3217: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3263: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3263: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3282: Warning: Undefined citation: 'altschul1990' ./Tutorial/chapter_align.tex:3282: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3282: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3302: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3302: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3315: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3315: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3315: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3315: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3350: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3350: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3354: Warning: Undefined citation: 'henikoff1992' ./Tutorial/chapter_align.tex:3354: Warning: Undefined citation: 'dayhoff1978' ./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3369: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3369: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3379: Warning: Undefined citation: 'schneider2005' ./Tutorial/chapter_align.tex:3391: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3391: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3391: Warning: Undefined label: 'sec:pairwise' ./Tutorial/chapter_align.tex:3393: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3393: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3396: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3396: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3400: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3400: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3416: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3416: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3425: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3425: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3429: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3429: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3442: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3442: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3443: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3443: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3448: Warning: line too long ./Tutorial/chapter_align.tex:3450: Warning: line too long ./Tutorial/chapter_align.tex:3468: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3468: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3491: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3491: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3508: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3508: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3511: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3511: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3528: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3528: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3529: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3529: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3552: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3552: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3565: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3565: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3572: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_align.tex:3572: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:1: Warning: line too long 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./Tutorial/chapter_blast.tex:202: Warning: '_' occurring outside math mode ./Tutorial/chapter_blast.tex:202: Warning: '_' occurring outside math mode ./Tutorial/chapter_blast.tex:206: Warning: Undefined label: 'sec:alignment-tools' ./Tutorial/chapter_blast.tex:225: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:225: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:236: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:236: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:238: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:238: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:240: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:240: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_blast.tex:241: Warning: Undefined label: 'sec:parsing-blast' 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'CODE' [] ./Tutorial/chapter_entrez.tex:890: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:899: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:899: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:904: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:904: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:904: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:904: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:940: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:947: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:947: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:951: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:951: Warning: Undefined block in text 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'CODE' [] ./Tutorial/chapter_entrez.tex:1038: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1046: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1046: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1046: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1046: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1060: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1060: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1060: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1060: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1060: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1060: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1067: Warning: Undefined 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./Tutorial/chapter_entrez.tex:1349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1349: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1349: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_entrez.tex:1373: Warning: Undefined label: 'sec:entrez-guidelines' ./Tutorial/chapter_entrez.tex:1374: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_entrez.tex:1393: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1393: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1434: Warning: Undefined label: 'sec:entrez-search-fetch-genbank' ./Tutorial/chapter_entrez.tex:1435: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1435: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1436: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1436: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1442: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1442: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1443: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1443: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1456: Warning: Undefined label: 'sec:entrez_example_genbank' ./Tutorial/chapter_entrez.tex:1456: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1456: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1456: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1456: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1478: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1478: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1545: Warning: Undefined label: 'sec:entrez-and-medline' ./Tutorial/chapter_entrez.tex:1545: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1545: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_entrez.tex:1550: Warning: Undefined label: 'sec:elink' ./Tutorial/chapter_entrez.tex:1575: Warning: Undefined label: 'sec:entrez-webenv' ./Tutorial/chapter_uniprot.tex:1: Warning: line too long ./Tutorial/chapter_uniprot.tex:8: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:8: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:12: Warning: Undefined label: 'sec:SeqIO_ExPASy_and_SwissProt' ./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:12: Warning: Undefined 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text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:47: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:47: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:53: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:53: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:77: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:77: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:80: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:80: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:80: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:80: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:80: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:80: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:82: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:82: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:89: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:89: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:123: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:123: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:138: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_uniprot.tex:138: Warning: Undefined 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text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1534: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_motifs.tex:1565: Warning: '_' occurring outside math mode ./Tutorial/chapter_motifs.tex:1566: Warning: '_' occurring outside math mode ./Tutorial/chapter_motifs.tex:1566: Warning: '_' occurring outside math mode ./Tutorial/chapter_motifs.tex:1567: Warning: '_' occurring outside math mode ./Tutorial/chapter_cluster.tex:6: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:6: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:6: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:6: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:6: Warning: Undefined citation: 'dehoon2004' ./Tutorial/chapter_cluster.tex:8: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:8: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 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text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:553: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:555: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:555: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:555: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:555: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:556: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:559: 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./Tutorial/chapter_cluster.tex:588: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:589: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:589: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:600: Warning: Undefined citation: 'kohonen1997' ./Tutorial/chapter_cluster.tex:600: Warning: Undefined citation: 'tamayo1999' ./Tutorial/chapter_cluster.tex:607: Warning: Cannot output that numerical entity: U+00B7 ./Tutorial/chapter_cluster.tex:611: Warning: Cannot output that numerical entity: U+00B7 ./Tutorial/chapter_cluster.tex:616: Warning: Cannot output that numerical entity: U+00B7 ./Tutorial/chapter_cluster.tex:623: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:623: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:625: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:625: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:632: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:632: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:634: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:634: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:634: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:634: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:636: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:636: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:636: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:636: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:637: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:637: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:637: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:637: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:638: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:638: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:638: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:638: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:639: Warning: 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./Tutorial/chapter_cluster.tex:643: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:643: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:644: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:644: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:644: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:644: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:646: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:646: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:646: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:646: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:647: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:650: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:650: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:652: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:652: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:654: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:654: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:660: Warning: Undefined citation: 'yeung2001' ./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:668: Warning: Undefined citation: 'golub1971' ./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:670: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:670: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:675: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:675: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:677: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:677: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:678: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:678: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:679: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:679: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:680: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:680: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:681: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:681: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:683: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:683: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:686: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:686: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:686: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:686: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:690: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:690: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:692: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:692: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:692: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:692: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:711: Warning: line too long ./Tutorial/chapter_cluster.tex:714: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:714: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:716: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:716: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:716: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:716: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:749: Warning: overfull line in array : array too wide ./Tutorial/chapter_cluster.tex:749: Warning: line too long ./Tutorial/chapter_cluster.tex:749: Warning: line too long ./Tutorial/chapter_cluster.tex:755: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:755: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:758: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:758: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:761: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:761: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:764: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:764: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:767: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:767: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:768: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:768: Warning: Undefined block in 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./Tutorial/chapter_cluster.tex:782: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:783: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:783: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:783: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:783: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:785: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:785: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:789: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:789: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:789: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:789: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:799: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:799: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:799: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:799: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:801: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:801: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:801: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:801: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:802: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:805: Warning: Undefined label: 'sec:distancematrix' ./Tutorial/chapter_cluster.tex:815: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:815: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:815: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:815: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:816: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:816: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:817: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:817: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:817: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:817: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:818: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:818: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:818: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:818: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:819: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:819: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:819: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:819: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cluster.tex:820: Warning: 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./Tutorial/chapter_learning.tex:273: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:273: Warning: Undefined label: 'sec:LogisticRegression' ./Tutorial/chapter_learning.tex:277: Warning: Undefined label: 'table:training' ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined label: 'sec:LogisticRegressionTraining' ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_learning.tex:285: Warning: 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./Tutorial/chapter_graphics.tex:16: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:18: Warning: Undefined citation: 'pritchard2006' ./Tutorial/chapter_graphics.tex:28: Warning: Undefined citation: 'toth2006' ./Tutorial/chapter_graphics.tex:31: Warning: Undefined citation: 'vanderauwera2009' ./Tutorial/chapter_graphics.tex:34: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:34: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:35: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:35: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:36: Warning: Undefined label: 'chapter:seq_annot' ./Tutorial/chapter_graphics.tex:36: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode 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'CODE' [] ./Tutorial/chapter_graphics.tex:132: Warning: Image in text ./Tutorial/chapter_graphics.tex:132: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:144: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:144: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:163: Warning: Image in text ./Tutorial/chapter_graphics.tex:163: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:212: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:212: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:212: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:212: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:217: 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./Tutorial/chapter_graphics.tex:352: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:396: Warning: Image in text ./Tutorial/chapter_graphics.tex:396: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:409: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:409: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:430: Warning: Image in text ./Tutorial/chapter_graphics.tex:430: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:430: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:430: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:459: Warning: Image in text ./Tutorial/chapter_graphics.tex:459: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:459: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:459: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:473: 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./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: 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./Tutorial/chapter_graphics.tex:876: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:890: Warning: Image in text ./Tutorial/chapter_graphics.tex:890: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:890: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:914: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:914: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:923: Warning: Image in text ./Tutorial/chapter_graphics.tex:923: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:923: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:953: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:953: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:954: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:954: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:1004: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:1004: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:1006: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:1006: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:1011: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:1011: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:1012: Warning: Undefined citation: 'jupe2012' ./Tutorial/chapter_graphics.tex:1035: Warning: line too long ./Tutorial/chapter_graphics.tex:1036: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:1036: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:1057: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:1057: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_graphics.tex:1110: Warning: Image in text ./Tutorial/chapter_graphics.tex:1110: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:1125: Warning: line too long ./Tutorial/chapter_graphics.tex:1190: Warning: Image in text ./Tutorial/chapter_graphics.tex:1190: Warning: '_' occurring outside math mode ./Tutorial/chapter_kegg.tex:1: Warning: line too long ./Tutorial/chapter_kegg.tex:1: Warning: line too long ./Tutorial/chapter_kegg.tex:1: Warning: line too long ./Tutorial/chapter_kegg.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_kegg.tex:10: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_kegg.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_kegg.tex:23: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phenotype.tex:5: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phenotype.tex:5: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phenotype.tex:10: Warning: '_' occurring outside math mode ./Tutorial/chapter_phenotype.tex:16: Warning: '_' occurring outside math mode ./Tutorial/chapter_phenotype.tex:30: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phenotype.tex:30: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_phenotype.tex:32: Warning: '_' occurring outside math mode ./Tutorial/chapter_phenotype.tex:231: Warning: Optional argument to \item in itemize environment ./Tutorial/chapter_phenotype.tex:233: Warning: Optional argument to \item in itemize environment ./Tutorial/chapter_phenotype.tex:235: Warning: Optional argument to \item in itemize environment ./Tutorial/chapter_cookbook.tex:1: Warning: line too long ./Tutorial/chapter_cookbook.tex:1: Warning: line too long ./Tutorial/chapter_cookbook.tex:1: Warning: line too long ./Tutorial/chapter_cookbook.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:22: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:22: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_cookbook.tex:55: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:55: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:55: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:55: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:58: Warning: Undefined label: 'sec:low-level-fasta-fastq' ./Tutorial/chapter_cookbook.tex:60: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:60: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:103: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:105: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:105: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:105: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:105: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:114: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:115: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:115: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:116: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:116: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:125: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:125: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:126: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:126: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:126: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:126: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:145: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:145: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:146: Warning: Undefined label: 'sec:Bio.SeqIO-and-StringIO' ./Tutorial/chapter_cookbook.tex:201: Warning: Undefined label: 'sec:translation' ./Tutorial/chapter_cookbook.tex:201: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:201: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:202: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:202: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:202: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:202: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:205: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:205: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:206: Warning: Undefined label: 'sec:SeqIO-reverse-complement' ./Tutorial/chapter_cookbook.tex:207: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:207: Warning: Undefined block in text mode: 'CODE' [] ./Tutorial/chapter_cookbook.tex:208: Warning: 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(./_minted-Tutorial/EEEF4ABAD66CE989F67C9E27EEDE95CCBD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:seqio-todict-functionkey' on page 53 undefined on input line 804. (./_minted-Tutorial/F6AFF5A59B0706E4973BC1656FBD2D669543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/C4099CB0613585FCCD5EA7D8198704CEBD02851C2FB632864165FCA4920 46548.pygtex [53]) Overfull \hbox (9.93459pt too wide) in paragraph at lines 848--853 \OT1/cmr/m/n/10 FTP site ([][]$\OT1/cmtt/m/n/10 ftp : / / ftp . uniprot . org / pub / databases / uniprot / current _ release / knowledgebase / complete / (./_minted-Tutorial/D52DA4EEEEE2BF0FBE89EE253714929DBD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:SeqIO-sort' on page 54 undefined on input line 86 6. Overfull \hbox (4.48064pt too wide) in paragraph at lines 891--894 []\OT1/cmr/m/n/10 As of Gen-Bank re-lease $210$, there are $38$ files mak-ing u p the vi-ral se-quences, \OT1/cmtt/m/n/10 gbvrl1.seq\OT1/cmr/m/n/10 , ..., \OT1 /cmtt/m/n/10 gbvrl38.seq\OT1/cmr/m/n/10 , (./_minted-Tutorial/D41A88D88AB398F0C3B719A5C7D017C144BBF456F55B5DC060035246D76 9EADB.pygtex [54]) (./_minted-Tutorial/B4D970E8C81930851D8639D77EC3E41044BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/7C4E0944FB13EC4E75DD6FC64900395ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C68CC3C9B3A505FB972706356D7F336FBD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:seqio-index-getraw' on page 55 undefined on input line 948. 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(./_minted-Tutorial/4EBA0A67E686E73FAA1A0EB27C260028BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C06224D76A18C126B27DFE55444AA3FDBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E381FF526AC999B71717F178C997F6B2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5F05AD4A17978E60C531612707D8F26ABD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:SeqIO-translate' on page 60 undefined on input li ne 1311. [60] (./_minted-Tutorial/D19467E367634413AE9EE17A62E5D9EA9543DFECA235A69AE23006BA05B 4EB70.pygtex) LaTeX Warning: Reference `sec:SeqRecord-format' on page 61 undefined on input l ine 1331. (./_minted-Tutorial/EDF3737891061C33EDE0FBFD16CCC63B9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/D1EAD55A1F8AD3DEAB82383A4F020F539543DFECA235A69AE23006BA05B 4EB70.pygtex) Overfull \hbox (19.46596pt too wide) in paragraph at lines 1349--1351 \OT1/cmr/m/n/10 Making a sin-gle call to [][]\OT1/cmtt/m/n/10 SeqIO.write(...) []\OT1/cmr/m/n/10 is also much quicker than mul-ti-ple calls to the [][]\OT1/cm tt/m/n/10 SeqRecord.format(...) [61] (./_minted-Tutorial/2F337ECD1F936D416FF9C5C6F41A02D7BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3337CD054623BAC21B6021E996EE0DFD9543DFECA235A69AE23006BA05B 4EB70.pygtex) Overfull \hbox (21.32593pt too wide) in paragraph at lines 1393--1397 []\OT1/cmr/m/n/10 Likewise, when pars-ing FASTQ files, in-ter-nally [][]\OT1/cm tt/m/n/10 Bio.SeqIO.parse() []\OT1/cmr/m/n/10 calls the low-level [][]\OT1/cmtt /m/n/10 FastqGeneralIterator (./_minted-Tutorial/D3AF6542680CA390CDA8C8DF87C693D3BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `chapter:cookbook' on page 62 undefined on input line 1412. (./_minted-Tutorial/D749A84299CF58E876E9A899069830DB9543DFECA235A69AE23006BA05B 4EB70.pygtex)) [62] (./Tutorial/chapter_align.tex Chapter 6. LaTeX Warning: Reference `sec:appendix-handles' on page 63 undefined on input l ine 31. 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(./_minted-Tutorial/FC96AF22EDD72BC4AC2EE47EBAA6B045BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E941CFC951CAE25312D9A5CAC9B27425BD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (8.40039pt too wide) in paragraph at lines 1126--1130 []\OT1/cmr/m/n/10 By de-fault MUS-CLE will out-put the align-ment as a FASTA fi le (us-ing gapped se-quences). 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LaTeX Warning: Float too large for page by 32.27644pt on input line 481. ) [128] [129 <./images/BlastRecord.png>] [130 <./images/PSIBlastRecord.png>] (./Tutorial/chapter_searchio.tex Chapter 8. (./_minted-Tutorial/6D0EADF658E662CBA394834EFAC7346E669566ECC2CFEDC7429F829576A D0DC6.pygtex) [131] Overfull \hbox (2.9019pt too wide) in paragraph at lines 85--93 [][][]\OT1/cmtt/m/n/10 HSPFragment[]\OT1/cmr/m/n/10 , to rep-re-sent a sin-gle con-tigu-ous align-ment be-tween query and hit se-quences. 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Overfull \hbox (27.24287pt too wide) in paragraph at lines 743--745 []\OT1/cmr/m/n/10 It should not sur-prise you now that the [][]\OT1/cmtt/m/n/10 HSP []\OT1/cmr/m/n/10 ob-ject has an [][]\OT1/cmtt/m/n/10 alignment []\OT1/cmr /m/n/10 prop-erty which is a [][]\OT1/cmtt/m/n/10 MultipleSeqAlignment (./_minted-Tutorial/338C616C7128C3DB7FFD516F5C2BDA12BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1195D6861E887568107FA7F463EA9BBABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/31F43A46088F6D2E63B39857A3536909BD02851C2FB632864165FCA4920 46548.pygtex [141]) (./_minted-Tutorial/16771935702D6A2A9762A80A621013D8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/046FE550C51B323D1E952A27E126FE19BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A55E467518B2E0F936A232F0970B1037BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6D69D310788199FBA6E8A5BF5CAB2021BD02851C2FB632864165FCA4920 46548.pygtex [142]) (./_minted-Tutorial/2C71B4AE1F4F9990447491C6C291ABC2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/FD7ECFDD9D017B829A54C995FEE42EEDBD02851C2FB632864165FCA4920 46548.pygtex [143]) (./_minted-Tutorial/3AD8335853E972C8E62AAF79CF0A3D33BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/758BAC7574A59544686354199D20892CBD02851C2FB632864165FCA4920 46548.pygtex) [144] (./_minted-Tutorial/7A63CB5E786CCE052981F7DD10653DA9BD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (14.20721pt too wide) in paragraph at lines 1055--1059 \OT1/cmr/m/n/10 func-tion re-turns a gen-er-a-tor ob-ject that yields a [][]\OT 1/cmtt/m/n/10 QueryResult []\OT1/cmr/m/n/10 ob-ject in each it-er-a-tion. 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[212] (./_minted-Tutorial/7A6D5A10ECC42BAFEE724455549BCB15BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D5B0F5228C1E7FAD0C7AB40AEFF6B6A9BD02851C2FB632864165FCA4920 46548.pygtex [213]) (./_minted-Tutorial/2810A7579DC6FE011D31E2F074471A74BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D9D0B8746EBF14CF4BE7DA480D9ECD5DBD02851C2FB632864165FCA4920 46548.pygtex) [214] LaTeX Warning: Citation `hamelryck2003b' on page 215 undefined on input line 18 61. LaTeX Warning: Citation `majumdar2005' on page 215 undefined on input line 1862 . ) [215] (./Tutorial/chapter_popgen.tex Chapter 12. (./_minted-Tutorial/E5F1866C3CBB485B8C06B62764ACFBB29543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/331BEE386F268F55DE217F54E27EAB6B9543DFECA235A69AE23006BA05B 4EB70.pygtex) [216] (./_minted-Tutorial/6CD64A1F591B16F512F7EB6B68E5B3FC9543DFECA235A69AE23006BA05B 4EB70.pygtex)) [217] (./Tutorial/chapter_phylo.tex Chapter 13. 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[224 <./images/phylo-draw-example.p ng>] Overfull \hbox (19.85507pt too wide) in paragraph at lines 479--486 \OT1/cmr/m/n/10 For ex-am-ple, in a tree with clade names Foo1, Foo2 and Foo3, [][]\OT1/cmtt/m/n/10 tree.find_clades({"name": "Foo1"}) [225] Overfull \hbox (13.48741pt too wide) in paragraph at lines 534--537 []\OT1/cmr/m/n/10 Find each clade con-tain-ing a match-ing el-e-ment. That is, find each el-e-ment as with [][]\OT1/cmtt/m/n/10 find_elements[]\OT1/cmr/m/n/10 , [226] (./_minted-Tutorial/6AAB725DBD2E5B7C5FD79A9A16536BF69543DFECA235A69AE23006BA05B 4EB70.pygtex) [227] Overfull \hbox (15.04868pt too wide) in paragraph at lines 703--707 []\OT1/cmr/m/n/10 Below is an ex-am-ple on how to use a python script to in-ter -act with PhyML ([][]$\OT1/cmtt/m/n/10 http : / / www . atgc-[]montpellier . 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LaTeX Warning: Citation `dehoon2004' on page 258 undefined on input line 6. LaTeX Warning: Citation `lecuyer1988' on page 258 undefined on input line 30. LaTeX Warning: Citation `kachitvichyanukul1988' on page 258 undefined on input line 30. [258] [259] [260] LaTeX Warning: Citation `snedecor1989' on page 261 undefined on input line 154. [261] (./_minted-Tutorial/C7B59059E3AE6CDE790EFE6EB0ED4140BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Reference `sec:distancefunctions' on page 262 undefined on input line 183. 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[278] Overfull \hbox (106.77225pt too wide) in paragraph at lines 929--931 \OT1/cmr/m/n/10 An ar-ray with di-men-sions $[]$ if rows are be-ing clus-tered, or $[]$ (./_minted-Tutorial/A39469F362670EDC6C7E8FD9FDF412C4BD02851C2FB632864165FCA4920 46548.pygtex) LaTeX Warning: Citation `hihara2001' on page 279 undefined on input line 954. (./_minted-Tutorial/12B5F20EFF78F0E8FE505D45A9786D70BD02851C2FB632864165FCA4920 46548.pygtex [279]) (./_minted-Tutorial/E6C8D570402CFDDB43A6AE5A198BCF58BD02851C2FB632864165FCA4920 46548.pygtex)) Overfull \hbox (26.21434pt too wide) in paragraph at lines 986--116 []\OT1/cmr/m/n/10 This will cre-ate the files [][]\OT1/cmtt/m/n/10 cyano_result _K_G2_A2.cdt[]\OT1/cmr/m/n/10 , [][]\OT1/cmtt/m/n/10 cyano_result_K_G2.kgg[]\OT 1/cmr/m/n/10 , and [][]\OT1/cmtt/m/n/10 cyano_result_K_A2.kag[]\OT1/cmr/m/n/10 . [280] (./Tutorial/chapter_learning.tex Chapter 16. [281] LaTeX Warning: Reference `eq:OP' on page 282 undefined on input line 40. 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(./_minted-Tutorial/A2465D4E8908256A31684D5DDE7DA1119543DFECA235A69AE23006BA05B 4EB70.pygtex [306 <./images/three_track_simple.png>]) (./_minted-Tutorial/347EB36A3001532221DDF6C29AA04AFB9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/F46F39DD7A8EC7B20CD42ACF6EFD18409543DFECA235A69AE23006BA05B 4EB70.pygtex [307]) (./_minted-Tutorial/2CF2D2FC7E96B3F426F22452724A4C289543DFECA235A69AE23006BA05B 4EB70.pygtex) Overfull \hbox (2.65141pt too wide) in paragraph at lines 873--879 []\OT1/cmr/m/n/10 There are sev-eral im-por-tant pieces to this code. First the [][]\OT1/cmtt/m/n/10 GenomeDiagram []\OT1/cmr/m/n/10 ob-ject has a [][]\OT1/cm tt/m/n/10 cross_track_links Excluding 'htmlonly' comment. LaTeX Warning: Reference `fig:three_track_cl' on page 308 undefined on input li ne 894. LaTeX Warning: Reference `sec:gd_cross_links' on page 308 undefined on input li ne 901. LaTeX Warning: Reference `sec:gd_cross_links' on page 308 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/AB16E58608A2F17CC79E6929557208879543DFECA235A69AE23006BA05B 4EB70.pygtex [330]) Overfull \hbox (4.57849pt too wide) in paragraph at lines 475--477 \OT1/cmr/m/n/10 That should find $13819$ reads from \OT1/cmtt/m/n/10 SRR014849. fastq \OT1/cmr/m/n/10 and save them to a new FASTQ file, \OT1/cmtt/m/n/10 with[ ]primer.fastq\OT1/cmr/m/n/10 . LaTeX Warning: Reference `sec:SeqRecord-slicing' on page 331 undefined on input line 480. 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(./_minted-Tutorial/415024C641C8DA7A09117B3DFE240C78BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/487DCC9F44A2539C9B32C0122AEF4065BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5098CD053449CEC3C9C30C90A007A364BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/EEEF4ABAD66CE989F67C9E27EEDE95CCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F6AFF5A59B0706E4973BC1656FBD2D669543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/C4099CB0613585FCCD5EA7D8198704CEBD02851C2FB632864165FCA4920 46548.pygtex [60]) Overfull \hbox (9.93459pt too wide) in paragraph at lines 848--853 \OT1/cmr/m/n/10 FTP site ([][]$\OT1/cmtt/m/n/10 ftp : / / ftp . uniprot . org / pub / databases / uniprot / current _ release / knowledgebase / complete / (./_minted-Tutorial/D52DA4EEEEE2BF0FBE89EE253714929DBD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (4.48064pt too wide) in paragraph at lines 891--894 []\OT1/cmr/m/n/10 As of Gen-Bank re-lease $210$, there are $38$ files mak-ing u p the vi-ral se-quences, \OT1/cmtt/m/n/10 gbvrl1.seq\OT1/cmr/m/n/10 , ..., \OT1 /cmtt/m/n/10 gbvrl38.seq\OT1/cmr/m/n/10 , (./_minted-Tutorial/D41A88D88AB398F0C3B719A5C7D017C144BBF456F55B5DC060035246D76 9EADB.pygtex [61]) (./_minted-Tutorial/B4D970E8C81930851D8639D77EC3E41044BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/7C4E0944FB13EC4E75DD6FC64900395ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C68CC3C9B3A505FB972706356D7F336FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/61AD507889ED86CFCEFC880BAF2A2777BD02851C2FB632864165FCA4920 46548.pygtex) [62] (./_minted-Tutorial/DC5117490176932EFB8A7F0E0DA450F6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/657D43328835FC01F9133F8BC964475D44BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/82CBCD9B9F23373D67D9D0D7D2CA363FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/36F8D0FD2B4ADF57AC4203A0C80C6471BD02851C2FB632864165FCA4920 46548.pygtex) [63] (./_minted-Tutorial/9CEF7BF9B2634ACBC930BA5EB6DD73429543DFECA235A69AE23006BA05B 4EB70.pygtex [64]) (./_minted-Tutorial/AC02E3950380715FC960C04EF317D69F9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/1C65F538FA7F22F7BB5183FC1553A0C6669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/935F773BF84C3BF326F4BA093FEC79D4669566ECC2CFEDC7429F829576A D0DC6.pygtex [65]) (./_minted-Tutorial/C194E2231D844AE7D0223173D2A899919543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/10CB116B7358444BA68AFA046B5B84D59543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/29D12D495374A5A8C37AEB7083851DEABD02851C2FB632864165FCA4920 46548.pygtex) [66] (./_minted-Tutorial/920133226A22EEB682D854077D7FB78FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4EBA0A67E686E73FAA1A0EB27C260028BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C06224D76A18C126B27DFE55444AA3FDBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E381FF526AC999B71717F178C997F6B2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5F05AD4A17978E60C531612707D8F26ABD02851C2FB632864165FCA4920 46548.pygtex) [67] (./_minted-Tutorial/D19467E367634413AE9EE17A62E5D9EA9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/EDF3737891061C33EDE0FBFD16CCC63B9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/D1EAD55A1F8AD3DEAB82383A4F020F539543DFECA235A69AE23006BA05B 4EB70.pygtex) Overfull \hbox (19.46596pt too wide) in paragraph at lines 1349--1351 \OT1/cmr/m/n/10 Making a sin-gle call to [][]\OT1/cmtt/m/n/10 SeqIO.write(...) []\OT1/cmr/m/n/10 is also much quicker than mul-ti-ple calls to the [][]\OT1/cm tt/m/n/10 SeqRecord.format(...) [68] (./_minted-Tutorial/2F337ECD1F936D416FF9C5C6F41A02D7BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3337CD054623BAC21B6021E996EE0DFD9543DFECA235A69AE23006BA05B 4EB70.pygtex) Overfull \hbox (21.32593pt too wide) in paragraph at lines 1393--1397 []\OT1/cmr/m/n/10 Likewise, when pars-ing FASTQ files, in-ter-nally [][]\OT1/cm tt/m/n/10 Bio.SeqIO.parse() []\OT1/cmr/m/n/10 calls the low-level [][]\OT1/cmtt /m/n/10 FastqGeneralIterator (./_minted-Tutorial/D3AF6542680CA390CDA8C8DF87C693D3BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D749A84299CF58E876E9A899069830DB9543DFECA235A69AE23006BA05B 4EB70.pygtex)) [69] (./Tutorial/chapter_align.tex Chapter 6. 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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/9776F24C4F96F850E549BEF997E4D18CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D8256B42DA32121F3B83617DD03F4024BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DA108466F70572EEAE2D54AEA4C156A1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8FD10ACD641F4427B35E96F33B44479F669566ECC2CFEDC7429F829576A D0DC6.pygtex [78]) (./_minted-Tutorial/ACC9FF1F2F025F77815D96DC3115B7DFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7E530BB128C8AE6BCF7BCE91DD4AF189669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/C17F8CD5F33DB6EB328532E02ADD1FE6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C02EB78C9555A4FEE4954D77162ACF99669566ECC2CFEDC7429F829576A D0DC6.pygtex [79]) (./_minted-Tutorial/74D8F602592BD3646F12A04951B2C44CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CB14E2060AF38515C129AB5808537F169543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/E78F5A80C222A5B2777910FED4F43F56669566ECC2CFEDC7429F829576A D0DC6.pygtex [80]) (./_minted-Tutorial/4D0AF4A40C449D27FF181EC477C63CE6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/2590B11C695B984E246A0A91734F786CBD02851C2FB632864165FCA4920 46548.pygtex) [81] (./_minted-Tutorial/508710FC1759BFFED598544DEC99BC0DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/886094CE2C1CAC714387144709D5A47ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6DC12DBE1D4FD44E7395C66258B5EAC9BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CAC16111FAD8C2E739F6D7C04A986BF0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A4149E9BEF55B5853014A59A3CBBFBE5BD02851C2FB632864165FCA4920 46548.pygtex [82]) (./_minted-Tutorial/8327145320A3BCB412D977F6683B71A2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1E096B06E33D157FFE18E045579F838CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C7331D522D75BB7830A1364BC3B71692BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C45FE25766D82D1C4A245CBB9A77DB00BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C0937EED558D842CEA8E3DB9514C6E59BD02851C2FB632864165FCA4920 46548.pygtex [83]) (./_minted-Tutorial/8EC03E9C8500D05C6439AC85123A9253BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/AE857C14E4731CC6F6EBA53051460097BD02851C2FB632864165FCA4920 46548.pygtex) [84] (./_minted-Tutorial/F88E003F9A4A95A929AA549FA710239CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/523928538FA511A925EC995B1803BD16BD02851C2FB632864165FCA4920 46548.pygtex) [85] (./_minted-Tutorial/CD47D1913C82182C164BD47DA4715282BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E7AA94166BAA5F4CBB44EF4336F3E893BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B49F47BF4F2EB4093BDE51E631C63064BD02851C2FB632864165FCA4920 46548.pygtex) [86] (./_minted-Tutorial/230B4706E315BD2F2A44F2EBCB37A442BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C11A66992B6C74B61F5A0BE7757AF3BCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/EAE190D91CC491562308EE568F986368BD02851C2FB632864165FCA4920 46548.pygtex [87]) (./_minted-Tutorial/6256254C5A7DFD21185291C77133BFDFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/FC96AF22EDD72BC4AC2EE47EBAA6B045BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E941CFC951CAE25312D9A5CAC9B27425BD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (8.40039pt too wide) in paragraph at lines 1126--1130 []\OT1/cmr/m/n/10 By de-fault MUS-CLE will out-put the align-ment as a FASTA fi le (us-ing gapped se-quences). The [][]\OT1/cmtt/m/n/10 Bio.AlignIO (./_minted-Tutorial/EA6A02999040945446E72AC6A00E56D8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/106ED62B0CFC10E7D5BC6CFC9CE003BDBD02851C2FB632864165FCA4920 46548.pygtex [88]) (./_minted-Tutorial/4D75AC9EDD74C466535F1EC4944833F7BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/14F1F3BAF80772F5999B0773C02432E7BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A261B9E9E2D4EB3C1DF5131C6F739998BD02851C2FB632864165FCA4920 46548.pygtex [89]) (./_minted-Tutorial/E2B86D066966C8BA13EEEF614D3E7454BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E87BDA1F176DA567A757DBA0231BC5BABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6BF1884F2D94AF8D067A2A20A9A41E2CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F551ABCEBB0043257A807C76B9D81B5CBD02851C2FB632864165FCA4920 46548.pygtex [90]) (./_minted-Tutorial/37B6E52C66902FA821D4B0E80172CE74BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0BA045AD7DFE0F0F3DD972F3E2C40BA1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/482576AF06E80D82290535FF7857A240BD02851C2FB632864165FCA4920 46548.pygtex) [91] (./_minted-Tutorial/5D3CCD84BC2EC46BF5FD98E7A3FC7266669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/D9565472E525C9F2B734FC37A70D258E669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/39152F199CEBB3375366F2E947824519BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/256B036DA9C3EDBC9EE41E2E52FDE1ADBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DC6CF8B5CDDD2C32E2052C03AF385674BD02851C2FB632864165FCA4920 46548.pygtex [92]) (./_minted-Tutorial/CEE035FF629B69F7D6B6351C1DCE2493BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DF151703751D72BD556402B910190A87BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/004029547AAB1172AF2684D2CA89EA88BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/554024580088332FAF0EA9296BACE82EBD02851C2FB632864165FCA4920 46548.pygtex) [93] (./_minted-Tutorial/419ECEB266819C8DCC38EB3E1DC3E361BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/143B9D317680E51D3A6E5641208720CABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6CCC707502EDD92E9C355854215BF885BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0A4B1939051DE630E53C7151447C8DD4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/2B6197C314840AD3EC15C56F366120C5BD02851C2FB632864165FCA4920 46548.pygtex [94]) (./_minted-Tutorial/E5E00F47BD7A0C8BC5F8818526283868BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/52B42D5819C8EC5D57A21AE60D28F6CEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5F566D907B2F88621EC4175F1F17AE04BD02851C2FB632864165FCA4920 46548.pygtex) [95] (./_minted-Tutorial/0FE96E337A3BA73D52896D46E2E233DCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/434D41043E1630324FA64E8B55B90BD5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/48453D528762FF183499778647AF218BBD02851C2FB632864165FCA4920 46548.pygtex [96]) (./_minted-Tutorial/BD86EE3248811DE8FD9DE8ED02397A39BD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (76.42714pt too wide) in paragraph at lines 1707--1711 []\OT1/cmr/m/n/10 By de-fault, [][]\OT1/cmtt/m/n/10 aligner.substitution_matrix []\OT1/cmr/m/n/10 is [][]\OT1/cmtt/m/n/10 None[]\OT1/cmr/m/n/10 . The at-tribu tes [][]\OT1/cmtt/m/n/10 aligner.match_score []\OT1/cmr/m/n/10 and [][]\OT1/cmt t/m/n/10 aligner.mismatch_score Overfull \hbox (47.73264pt too wide) in paragraph at lines 1707--1711 []\OT1/cmr/m/n/10 are ig-nored if [][]\OT1/cmtt/m/n/10 aligner.substitution_mat rix []\OT1/cmr/m/n/10 is not [][]\OT1/cmtt/m/n/10 None[]\OT1/cmr/m/n/10 . Set-t ing [][]\OT1/cmtt/m/n/10 aligner.match_score []\OT1/cmr/m/n/10 or [][]\OT1/cmtt /m/n/10 aligner.mismatch_score LaTeX Warning: `h' float specifier changed to `ht'. 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Overfull \hbox (5.71313pt too wide) in paragraph at lines 45--46 []\OT1/cmr/m/n/10 NCBI guide-lines, from [][]$\OT1/cmtt/m/n/10 https : / / blas t . ncbi . nlm . nih . gov / Blast . cgi ? 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Excluding 'htmlonly' comment. LaTeX Warning: Float too large for page by 32.27644pt on input line 481. ) [135] [136 <./images/BlastRecord.png>] [137 <./images/PSIBlastRecord.png>] (./Tutorial/chapter_searchio.tex Chapter 8. (./_minted-Tutorial/6D0EADF658E662CBA394834EFAC7346E669566ECC2CFEDC7429F829576A D0DC6.pygtex) [138] Overfull \hbox (2.9019pt too wide) in paragraph at lines 85--93 [][][]\OT1/cmtt/m/n/10 HSPFragment[]\OT1/cmr/m/n/10 , to rep-re-sent a sin-gle con-tigu-ous align-ment be-tween query and hit se-quences. [][]\OT1/cmtt/m/n/10 HSPFragment Overfull \hbox (8.43927pt too wide) in paragraph at lines 105--107 [][][]\OT1/cmtt/m/n/10 parse []\OT1/cmr/m/n/10 is used for search out-put files with mul-ti-ple queries and re-turns a gen-er-a-tor that yields [][]\OT1/cmtt/ m/n/10 QueryResult (./_minted-Tutorial/0EF47CD31A1F702FF10BD5C95E6D18FCBD02851C2FB632864165FCA4920 46548.pygtex [139]) (./_minted-Tutorial/BCDD1F95C8585B3C70DE9C1280B51955BD02851C2FB632864165FCA4920 46548.pygtex [140]) (./_minted-Tutorial/7A12FEF8445FE62A62C651C8B4EC163FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/362861C831165FEA5413E0240053CD89BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/40227DD719AAD22E8DC2923BF43CE327BD02851C2FB632864165FCA4920 46548.pygtex [141]) (./_minted-Tutorial/FD9C81C098491598DBFB6208173BB575BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/87D36F7AE3CBC4EDC6FCCFDE0173412CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CA24D00985B075C56E7C71A246E439FFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DE8A481953AA0F7BD7A99C0E281AD1A0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E7AA701BE1D007CE77D402E8CBFC777ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/906546E8B6F7831A0E7C5FC93AA56A03BD02851C2FB632864165FCA4920 46548.pygtex) [142] (./_minted-Tutorial/0B914838010D3E86EC368E1702EB7253BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E4688DCAB619DBEB784ED0D836D1E619BD02851C2FB632864165FCA4920 46548.pygtex [143]) (./_minted-Tutorial/DDECA9EB99D9FA38003A52C176593072BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/578CBF904F35965EECFEC1FA694F0752BD02851C2FB632864165FCA4920 46548.pygtex [144]) (./_minted-Tutorial/C0EB7D270F64704BA5AF848A21AACD64BD02851C2FB632864165FCA4920 46548.pygtex) [145] (./_minted-Tutorial/84848AABE250EF05E85067B2CD3275B8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A2EA3A12F7596A64ECEE374A9C53499ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E7A6E47CCC64E8FADF02D1CDC6246863BD02851C2FB632864165FCA4920 46548.pygtex) [146] (./_minted-Tutorial/A3385B945E43CC076FFA693B27681F05BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DAAFD2AAF126ED8D7284764B561B5E2BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4B4824DE2ED3215F02082987EE573577BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/61406D58E5F7C40FD0A0280DCAA66B46BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/BF77764978D907008BC936FD2A5FCD95BD02851C2FB632864165FCA4920 46548.pygtex [147]) (./_minted-Tutorial/CE618F26D70602D511E57E53CD880444BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DE23F71CD74CF7717D38AD01C1E1C787BD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (27.24287pt too wide) in paragraph at lines 743--745 []\OT1/cmr/m/n/10 It should not sur-prise you now that the [][]\OT1/cmtt/m/n/10 HSP []\OT1/cmr/m/n/10 ob-ject has an [][]\OT1/cmtt/m/n/10 alignment []\OT1/cmr /m/n/10 prop-erty which is a [][]\OT1/cmtt/m/n/10 MultipleSeqAlignment (./_minted-Tutorial/338C616C7128C3DB7FFD516F5C2BDA12BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1195D6861E887568107FA7F463EA9BBABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/31F43A46088F6D2E63B39857A3536909BD02851C2FB632864165FCA4920 46548.pygtex [148]) (./_minted-Tutorial/16771935702D6A2A9762A80A621013D8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/046FE550C51B323D1E952A27E126FE19BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A55E467518B2E0F936A232F0970B1037BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6D69D310788199FBA6E8A5BF5CAB2021BD02851C2FB632864165FCA4920 46548.pygtex [149]) (./_minted-Tutorial/2C71B4AE1F4F9990447491C6C291ABC2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/FD7ECFDD9D017B829A54C995FEE42EEDBD02851C2FB632864165FCA4920 46548.pygtex [150]) (./_minted-Tutorial/3AD8335853E972C8E62AAF79CF0A3D33BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/758BAC7574A59544686354199D20892CBD02851C2FB632864165FCA4920 46548.pygtex) [151] (./_minted-Tutorial/7A63CB5E786CCE052981F7DD10653DA9BD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (14.20721pt too wide) in paragraph at lines 1055--1059 \OT1/cmr/m/n/10 func-tion re-turns a gen-er-a-tor ob-ject that yields a [][]\OT 1/cmtt/m/n/10 QueryResult []\OT1/cmr/m/n/10 ob-ject in each it-er-a-tion. Like [][]\OT1/cmtt/m/n/10 Bio.SearchIO.read[]\OT1/cmr/m/n/10 , (./_minted-Tutorial/DC4E434DA5B851CF1E22BD3608A311F4BD02851C2FB632864165FCA4920 46548.pygtex) [152] Overfull \hbox (20.13245pt too wide) in paragraph at lines 1087--1092 []\OT1/cmr/m/n/10 In this case, the ideal choice would be to in-dex the file us -ing [][]\OT1/cmtt/m/n/10 Bio.SearchIO.index []\OT1/cmr/m/n/10 or [][]\OT1/cmtt /m/n/10 Bio.SearchIO.index_db[]\OT1/cmr/m/n/10 . (./_minted-Tutorial/0AB25750C7D89E832295045C60D6B8C4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DFACFE04880AE0CA2E8E32ABDC9E9868BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/51F256FC56FFFAE1F1E84A4EFC5BAE55BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5BCEFFE3DBB7A0AE4FD5D950731D72DEBD02851C2FB632864165FCA4920 46548.pygtex) [153] Overfull \hbox (11.82602pt too wide) in paragraph at lines 1167--1170 []\OT1/cmr/m/n/10 Finally, [][]\OT1/cmtt/m/n/10 Bio.SearchIO []\OT1/cmr/m/n/10 also pro-vides a [][]\OT1/cmtt/m/n/10 convert []\OT1/cmr/m/n/10 func-tion, whic h is sim-ply a short-cut for [][]\OT1/cmtt/m/n/10 Bio.SearchIO.parse (./_minted-Tutorial/BDE985FA3ADA6B0D37013C3D5F37C176BD02851C2FB632864165FCA4920 46548.pygtex)) [154] (./Tutorial/chapter_entrez.tex Chapter 9. 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Use \OT1/cmtt/m/n/10 structure[]rebuild[]test$$ (./_minted-Tutorial/BD4323A41DFED2A7E4CD261AA65F95EDBD02851C2FB632864165FCA4920 46548.pygtex) [210] (./_minted-Tutorial/6395F38A139598C6CC297CDBA73A8A43BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/21D2C13C2AA9395E0B1E4F1DDC801798BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/12E711A2CBFD0B046AA026208A117C1E9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/813FE78A3F8D8E46F06FF71539F000E69543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/CD78F368EB103F71947A3184BB62B46F9543DFECA235A69AE23006BA05B 4EB70.pygtex [211]) (./_minted-Tutorial/8E34478E945971E05C77F0A0E8C1B9D89543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/0D3FBB23D21A6A468370D56058193010BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/BBA5405CCC4A3178ADA49DA358246C819543DFECA235A69AE23006BA05B 4EB70.pygtex [212]) (./_minted-Tutorial/DE601B1883F045FBEE1B28168CFF0CCABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/AAF43F15691D49893FAEEAB7B7693A1D9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/0ABBC5325B76EBCC5687BB33E7595F219543DFECA235A69AE23006BA05B 4EB70.pygtex) Excluding 'htmlonly' comment. [213 <./images/1a8o-ca-plot.png>] Overfull \hbox (15.27203pt too wide) in paragraph at lines 1292--1295 []\OT1/cmr/m/n/10 This work uses equa-tions de-vel-oped by Blue, the Hedronome- ter, dis-cussed in [][]$\OT1/cmtt/m/n/10 https : / / math . stackexchange . Overfull \hbox (116.15723pt too wide) in paragraph at lines 1292--1295 \OT1/cmtt/m/n/10 com / a / 49340 / 409$[][] \OT1/cmr/m/n/10 and fur-ther in [][ ]$\OT1/cmtt/m/n/10 http : / / daylateanddollarshort . com / mathdocs / Heron-[] like-[]Results-[]for-[]Tetrahedral-[]Volume . 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(./_minted-Tutorial/6C5156DAD460519324A5B7657B301B5DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1836031BC83AA94C8906762F613E6CBABD02851C2FB632864165FCA4920 46548.pygtex) [226] (./_minted-Tutorial/D0A75FB8C1C791E4AA80420B93F216A8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/FEC6C2CB5FA0AFCFE00D995BD3642FF2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/2B435DC3041611A5D6A663B437ADB1ADBD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (25.13162pt too wide) in paragraph at lines 182--185 []\OT1/cmr/m/n/10 Let's tar-get the most re-cent com-mon an-ces-tor (MRCA) of t he nodes named ``E'' and ``F''. The [][]\OT1/cmtt/m/n/10 common_ancestor (./_minted-Tutorial/29624A9666C9430AABADF395148BBF27BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D0F05D42BA0A9BC594EEDB16319A972DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/87517FEF82BFE1AB8D89A83F4DC5E8B9BD02851C2FB632864165FCA4920 46548.pygtex [227 <./images/phylo-simple-draw.png>]) Excluding 'htmlonly' comment. 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[231 <./images/phylo-draw-example.p ng>] Overfull \hbox (19.85507pt too wide) in paragraph at lines 479--486 \OT1/cmr/m/n/10 For ex-am-ple, in a tree with clade names Foo1, Foo2 and Foo3, [][]\OT1/cmtt/m/n/10 tree.find_clades({"name": "Foo1"}) [232] Overfull \hbox (13.48741pt too wide) in paragraph at lines 534--537 []\OT1/cmr/m/n/10 Find each clade con-tain-ing a match-ing el-e-ment. That is, find each el-e-ment as with [][]\OT1/cmtt/m/n/10 find_elements[]\OT1/cmr/m/n/10 , [233] (./_minted-Tutorial/6AAB725DBD2E5B7C5FD79A9A16536BF69543DFECA235A69AE23006BA05B 4EB70.pygtex) [234] Overfull \hbox (15.04868pt too wide) in paragraph at lines 703--707 []\OT1/cmr/m/n/10 Below is an ex-am-ple on how to use a python script to in-ter -act with PhyML ([][]$\OT1/cmtt/m/n/10 http : / / www . atgc-[]montpellier . 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[265] [266] [267] [268] (./_minted-Tutorial/C7B59059E3AE6CDE790EFE6EB0ED4140BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C2B72A7408C7DF74DFCEBE0485997287BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/425EDAA643B5AA9589F3EEE601735827BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/50B5971EFCF22FCC4E1302DB2D0A25009543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/293084E63EA5C0E01F325A4DD59469C0BD02851C2FB632864165FCA4920 46548.pygtex [269]) Overfull \hbox (78.60634pt too wide) in paragraph at lines 245--246 \OT1/cmr/m/n/10 men-sions of these ar-rays are $[]$ if [][]\OT1/cmtt/m/n/10 tra nspose []\OT1/cmr/m/n/10 is [][]\OT1/cmtt/m/n/10 0[]\OT1/cmr/m/n/10 , or $[]$ (./_minted-Tutorial/05DC01C08B8EDF71F86E3C3A9C28EB34BD02851C2FB632864165FCA4920 46548.pygtex) [270] [271] (./_minted-Tutorial/A4A28B5A443208DEAB3B4D76AA3B762EBD02851C2FB632864165FCA4920 46548.pygtex) [272] (./_minted-Tutorial/C286E2777B917B774560CBDC7CF92626BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D04E097D8E8C4C039FEC20FA103CED189543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/36EF8931044EF448BC70F722AFADB43D9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/805B33438269C932AC54C0DAB5A3D7AC9543DFECA235A69AE23006BA05B 4EB70.pygtex) [273] [274] Overfull \hbox (16.73593pt too wide) in paragraph at lines 423--424 [][]\OT1/cmtt/m/n/10 distance []\OT1/cmr/m/n/10 is the dis-tance be-tween them. 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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/AB16E58608A2F17CC79E6929557208879543DFECA235A69AE23006BA05B 4EB70.pygtex [337]) Overfull \hbox (4.57849pt too wide) in paragraph at lines 475--477 \OT1/cmr/m/n/10 That should find $13819$ reads from \OT1/cmtt/m/n/10 SRR014849. fastq \OT1/cmr/m/n/10 and save them to a new FASTQ file, \OT1/cmtt/m/n/10 with[ ]primer.fastq\OT1/cmr/m/n/10 . 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Overfull \hbox (4.00363pt too wide) in paragraph at lines 1117--1120 []\OT1/cmr/m/it/10 Tip: \OT1/cmr/m/n/10 Rather than us-ing [][]\OT1/cmtt/m/n/10 pylab.show() []\OT1/cmr/m/n/10 to show the plot in a win-dow, you can also use [][]\OT1/cmtt/m/n/10 pylab.savefig(...) (./_minted-Tutorial/798776F436EA559BACD9C305C09973919543DFECA235A69AE23006BA05B 4EB70.pygtex [347 <./images/hist_plot.png>]) (./_minted-Tutorial/CB78AD94DFE82ADBAF348C0EC1D261CD9543DFECA235A69AE23006BA05B 4EB70.pygtex) Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. [348 <./images/gc_plot.png>] (./_minted-Tutorial/6E0DA723E11A7B9CA8E2353A984B5DF79543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/80A47C8780CE3021D53829563E8166569543DFECA235A69AE23006BA05B 4EB70.pygtex [349 <./images/dot_plot.png>]) (./_minted-Tutorial/9574E55C4A182E2A0201DF18689F52F49543DFECA235A69AE23006BA05B 4EB70.pygtex) Excluding 'htmlonly' comment. 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For ex-am-ple, [][]\OT1/cmtt/m/n/10 expec ted_frequencies[^^MD^^M, ^^ME^^M] (./_minted-Tutorial/40ECF2E139F38209730D3B02B624EF74BD02851C2FB632864165FCA4920 46548.pygtex [357]) (./_minted-Tutorial/8965C8E87A0A43ECCE216C12F7DE7A4FBD02851C2FB632864165FCA4920 46548.pygtex)) [358] (./Tutorial/chapter_testing.tex Chapter 21. 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(./_minted-Tutorial/415024C641C8DA7A09117B3DFE240C78BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/487DCC9F44A2539C9B32C0122AEF4065BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5098CD053449CEC3C9C30C90A007A364BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/EEEF4ABAD66CE989F67C9E27EEDE95CCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F6AFF5A59B0706E4973BC1656FBD2D669543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/C4099CB0613585FCCD5EA7D8198704CEBD02851C2FB632864165FCA4920 46548.pygtex [60]) Overfull \hbox (9.93459pt too wide) in paragraph at lines 848--853 \OT1/cmr/m/n/10 FTP site ([][]$\OT1/cmtt/m/n/10 ftp : / / ftp . uniprot . org / pub / databases / uniprot / current _ release / knowledgebase / complete / (./_minted-Tutorial/D52DA4EEEEE2BF0FBE89EE253714929DBD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (4.48064pt too wide) in paragraph at lines 891--894 []\OT1/cmr/m/n/10 As of Gen-Bank re-lease $210$, there are $38$ files mak-ing u p the vi-ral se-quences, \OT1/cmtt/m/n/10 gbvrl1.seq\OT1/cmr/m/n/10 , ..., \OT1 /cmtt/m/n/10 gbvrl38.seq\OT1/cmr/m/n/10 , (./_minted-Tutorial/D41A88D88AB398F0C3B719A5C7D017C144BBF456F55B5DC060035246D76 9EADB.pygtex [61]) (./_minted-Tutorial/B4D970E8C81930851D8639D77EC3E41044BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/7C4E0944FB13EC4E75DD6FC64900395ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C68CC3C9B3A505FB972706356D7F336FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/61AD507889ED86CFCEFC880BAF2A2777BD02851C2FB632864165FCA4920 46548.pygtex) [62] (./_minted-Tutorial/DC5117490176932EFB8A7F0E0DA450F6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/657D43328835FC01F9133F8BC964475D44BBF456F55B5DC060035246D76 9EADB.pygtex) (./_minted-Tutorial/82CBCD9B9F23373D67D9D0D7D2CA363FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/36F8D0FD2B4ADF57AC4203A0C80C6471BD02851C2FB632864165FCA4920 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(./_minted-Tutorial/E381FF526AC999B71717F178C997F6B2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5F05AD4A17978E60C531612707D8F26ABD02851C2FB632864165FCA4920 46548.pygtex) [67] (./_minted-Tutorial/D19467E367634413AE9EE17A62E5D9EA9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/EDF3737891061C33EDE0FBFD16CCC63B9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/D1EAD55A1F8AD3DEAB82383A4F020F539543DFECA235A69AE23006BA05B 4EB70.pygtex) Overfull \hbox (19.46596pt too wide) in paragraph at lines 1349--1351 \OT1/cmr/m/n/10 Making a sin-gle call to [][]\OT1/cmtt/m/n/10 SeqIO.write(...) []\OT1/cmr/m/n/10 is also much quicker than mul-ti-ple calls to the [][]\OT1/cm tt/m/n/10 SeqRecord.format(...) [68] (./_minted-Tutorial/2F337ECD1F936D416FF9C5C6F41A02D7BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/3337CD054623BAC21B6021E996EE0DFD9543DFECA235A69AE23006BA05B 4EB70.pygtex) Overfull \hbox (21.32593pt too wide) in paragraph at lines 1393--1397 []\OT1/cmr/m/n/10 Likewise, when pars-ing FASTQ files, in-ter-nally [][]\OT1/cm tt/m/n/10 Bio.SeqIO.parse() []\OT1/cmr/m/n/10 calls the low-level [][]\OT1/cmtt /m/n/10 FastqGeneralIterator (./_minted-Tutorial/D3AF6542680CA390CDA8C8DF87C693D3BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D749A84299CF58E876E9A899069830DB9543DFECA235A69AE23006BA05B 4EB70.pygtex)) [69] (./Tutorial/chapter_align.tex Chapter 6. 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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/9776F24C4F96F850E549BEF997E4D18CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D8256B42DA32121F3B83617DD03F4024BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DA108466F70572EEAE2D54AEA4C156A1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/8FD10ACD641F4427B35E96F33B44479F669566ECC2CFEDC7429F829576A D0DC6.pygtex [78]) (./_minted-Tutorial/ACC9FF1F2F025F77815D96DC3115B7DFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/7E530BB128C8AE6BCF7BCE91DD4AF189669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/C17F8CD5F33DB6EB328532E02ADD1FE6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C02EB78C9555A4FEE4954D77162ACF99669566ECC2CFEDC7429F829576A D0DC6.pygtex [79]) (./_minted-Tutorial/74D8F602592BD3646F12A04951B2C44CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CB14E2060AF38515C129AB5808537F169543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/E78F5A80C222A5B2777910FED4F43F56669566ECC2CFEDC7429F829576A D0DC6.pygtex [80]) (./_minted-Tutorial/4D0AF4A40C449D27FF181EC477C63CE6BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/2590B11C695B984E246A0A91734F786CBD02851C2FB632864165FCA4920 46548.pygtex) [81] (./_minted-Tutorial/508710FC1759BFFED598544DEC99BC0DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/886094CE2C1CAC714387144709D5A47ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6DC12DBE1D4FD44E7395C66258B5EAC9BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CAC16111FAD8C2E739F6D7C04A986BF0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A4149E9BEF55B5853014A59A3CBBFBE5BD02851C2FB632864165FCA4920 46548.pygtex [82]) (./_minted-Tutorial/8327145320A3BCB412D977F6683B71A2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1E096B06E33D157FFE18E045579F838CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C7331D522D75BB7830A1364BC3B71692BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C45FE25766D82D1C4A245CBB9A77DB00BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C0937EED558D842CEA8E3DB9514C6E59BD02851C2FB632864165FCA4920 46548.pygtex [83]) (./_minted-Tutorial/8EC03E9C8500D05C6439AC85123A9253BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/AE857C14E4731CC6F6EBA53051460097BD02851C2FB632864165FCA4920 46548.pygtex) [84] (./_minted-Tutorial/F88E003F9A4A95A929AA549FA710239CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/523928538FA511A925EC995B1803BD16BD02851C2FB632864165FCA4920 46548.pygtex) [85] (./_minted-Tutorial/CD47D1913C82182C164BD47DA4715282BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E7AA94166BAA5F4CBB44EF4336F3E893BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/B49F47BF4F2EB4093BDE51E631C63064BD02851C2FB632864165FCA4920 46548.pygtex) [86] (./_minted-Tutorial/230B4706E315BD2F2A44F2EBCB37A442BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C11A66992B6C74B61F5A0BE7757AF3BCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/EAE190D91CC491562308EE568F986368BD02851C2FB632864165FCA4920 46548.pygtex [87]) (./_minted-Tutorial/6256254C5A7DFD21185291C77133BFDFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/FC96AF22EDD72BC4AC2EE47EBAA6B045BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E941CFC951CAE25312D9A5CAC9B27425BD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (8.40039pt too wide) in paragraph at lines 1126--1130 []\OT1/cmr/m/n/10 By de-fault MUS-CLE will out-put the align-ment as a FASTA fi le (us-ing gapped se-quences). The [][]\OT1/cmtt/m/n/10 Bio.AlignIO (./_minted-Tutorial/EA6A02999040945446E72AC6A00E56D8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/106ED62B0CFC10E7D5BC6CFC9CE003BDBD02851C2FB632864165FCA4920 46548.pygtex [88]) (./_minted-Tutorial/4D75AC9EDD74C466535F1EC4944833F7BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/14F1F3BAF80772F5999B0773C02432E7BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A261B9E9E2D4EB3C1DF5131C6F739998BD02851C2FB632864165FCA4920 46548.pygtex [89]) (./_minted-Tutorial/E2B86D066966C8BA13EEEF614D3E7454BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E87BDA1F176DA567A757DBA0231BC5BABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6BF1884F2D94AF8D067A2A20A9A41E2CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/F551ABCEBB0043257A807C76B9D81B5CBD02851C2FB632864165FCA4920 46548.pygtex [90]) (./_minted-Tutorial/37B6E52C66902FA821D4B0E80172CE74BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0BA045AD7DFE0F0F3DD972F3E2C40BA1BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/482576AF06E80D82290535FF7857A240BD02851C2FB632864165FCA4920 46548.pygtex) [91] (./_minted-Tutorial/5D3CCD84BC2EC46BF5FD98E7A3FC7266669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/D9565472E525C9F2B734FC37A70D258E669566ECC2CFEDC7429F829576A D0DC6.pygtex) (./_minted-Tutorial/39152F199CEBB3375366F2E947824519BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/256B036DA9C3EDBC9EE41E2E52FDE1ADBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DC6CF8B5CDDD2C32E2052C03AF385674BD02851C2FB632864165FCA4920 46548.pygtex [92]) (./_minted-Tutorial/CEE035FF629B69F7D6B6351C1DCE2493BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DF151703751D72BD556402B910190A87BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/004029547AAB1172AF2684D2CA89EA88BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/554024580088332FAF0EA9296BACE82EBD02851C2FB632864165FCA4920 46548.pygtex) [93] (./_minted-Tutorial/419ECEB266819C8DCC38EB3E1DC3E361BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/143B9D317680E51D3A6E5641208720CABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6CCC707502EDD92E9C355854215BF885BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/0A4B1939051DE630E53C7151447C8DD4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/2B6197C314840AD3EC15C56F366120C5BD02851C2FB632864165FCA4920 46548.pygtex [94]) (./_minted-Tutorial/E5E00F47BD7A0C8BC5F8818526283868BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/52B42D5819C8EC5D57A21AE60D28F6CEBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5F566D907B2F88621EC4175F1F17AE04BD02851C2FB632864165FCA4920 46548.pygtex) [95] (./_minted-Tutorial/0FE96E337A3BA73D52896D46E2E233DCBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/434D41043E1630324FA64E8B55B90BD5BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/48453D528762FF183499778647AF218BBD02851C2FB632864165FCA4920 46548.pygtex [96]) (./_minted-Tutorial/BD86EE3248811DE8FD9DE8ED02397A39BD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (76.42714pt too wide) in paragraph at lines 1707--1711 []\OT1/cmr/m/n/10 By de-fault, [][]\OT1/cmtt/m/n/10 aligner.substitution_matrix []\OT1/cmr/m/n/10 is [][]\OT1/cmtt/m/n/10 None[]\OT1/cmr/m/n/10 . The at-tribu tes [][]\OT1/cmtt/m/n/10 aligner.match_score []\OT1/cmr/m/n/10 and [][]\OT1/cmt t/m/n/10 aligner.mismatch_score Overfull \hbox (47.73264pt too wide) in paragraph at lines 1707--1711 []\OT1/cmr/m/n/10 are ig-nored if [][]\OT1/cmtt/m/n/10 aligner.substitution_mat rix []\OT1/cmr/m/n/10 is not [][]\OT1/cmtt/m/n/10 None[]\OT1/cmr/m/n/10 . Set-t ing [][]\OT1/cmtt/m/n/10 aligner.match_score []\OT1/cmr/m/n/10 or [][]\OT1/cmtt /m/n/10 aligner.mismatch_score LaTeX Warning: `h' float specifier changed to `ht'. 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Overfull \hbox (5.71313pt too wide) in paragraph at lines 45--46 []\OT1/cmr/m/n/10 NCBI guide-lines, from [][]$\OT1/cmtt/m/n/10 https : / / blas t . ncbi . nlm . nih . gov / Blast . cgi ? 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Excluding 'htmlonly' comment. LaTeX Warning: Float too large for page by 32.27644pt on input line 481. ) [135] [136 <./images/BlastRecord.png>] [137 <./images/PSIBlastRecord.png>] (./Tutorial/chapter_searchio.tex Chapter 8. (./_minted-Tutorial/6D0EADF658E662CBA394834EFAC7346E669566ECC2CFEDC7429F829576A D0DC6.pygtex) [138] Overfull \hbox (2.9019pt too wide) in paragraph at lines 85--93 [][][]\OT1/cmtt/m/n/10 HSPFragment[]\OT1/cmr/m/n/10 , to rep-re-sent a sin-gle con-tigu-ous align-ment be-tween query and hit se-quences. [][]\OT1/cmtt/m/n/10 HSPFragment Overfull \hbox (8.43927pt too wide) in paragraph at lines 105--107 [][][]\OT1/cmtt/m/n/10 parse []\OT1/cmr/m/n/10 is used for search out-put files with mul-ti-ple queries and re-turns a gen-er-a-tor that yields [][]\OT1/cmtt/ m/n/10 QueryResult (./_minted-Tutorial/0EF47CD31A1F702FF10BD5C95E6D18FCBD02851C2FB632864165FCA4920 46548.pygtex [139]) (./_minted-Tutorial/BCDD1F95C8585B3C70DE9C1280B51955BD02851C2FB632864165FCA4920 46548.pygtex [140]) (./_minted-Tutorial/7A12FEF8445FE62A62C651C8B4EC163FBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/362861C831165FEA5413E0240053CD89BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/40227DD719AAD22E8DC2923BF43CE327BD02851C2FB632864165FCA4920 46548.pygtex [141]) (./_minted-Tutorial/FD9C81C098491598DBFB6208173BB575BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/87D36F7AE3CBC4EDC6FCCFDE0173412CBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/CA24D00985B075C56E7C71A246E439FFBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DE8A481953AA0F7BD7A99C0E281AD1A0BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E7AA701BE1D007CE77D402E8CBFC777ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/906546E8B6F7831A0E7C5FC93AA56A03BD02851C2FB632864165FCA4920 46548.pygtex) [142] (./_minted-Tutorial/0B914838010D3E86EC368E1702EB7253BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E4688DCAB619DBEB784ED0D836D1E619BD02851C2FB632864165FCA4920 46548.pygtex [143]) (./_minted-Tutorial/DDECA9EB99D9FA38003A52C176593072BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/578CBF904F35965EECFEC1FA694F0752BD02851C2FB632864165FCA4920 46548.pygtex [144]) (./_minted-Tutorial/C0EB7D270F64704BA5AF848A21AACD64BD02851C2FB632864165FCA4920 46548.pygtex) [145] (./_minted-Tutorial/84848AABE250EF05E85067B2CD3275B8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A2EA3A12F7596A64ECEE374A9C53499ABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/E7A6E47CCC64E8FADF02D1CDC6246863BD02851C2FB632864165FCA4920 46548.pygtex) [146] (./_minted-Tutorial/A3385B945E43CC076FFA693B27681F05BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DAAFD2AAF126ED8D7284764B561B5E2BBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/4B4824DE2ED3215F02082987EE573577BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/61406D58E5F7C40FD0A0280DCAA66B46BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/BF77764978D907008BC936FD2A5FCD95BD02851C2FB632864165FCA4920 46548.pygtex [147]) (./_minted-Tutorial/CE618F26D70602D511E57E53CD880444BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DE23F71CD74CF7717D38AD01C1E1C787BD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (27.24287pt too wide) in paragraph at lines 743--745 []\OT1/cmr/m/n/10 It should not sur-prise you now that the [][]\OT1/cmtt/m/n/10 HSP []\OT1/cmr/m/n/10 ob-ject has an [][]\OT1/cmtt/m/n/10 alignment []\OT1/cmr /m/n/10 prop-erty which is a [][]\OT1/cmtt/m/n/10 MultipleSeqAlignment (./_minted-Tutorial/338C616C7128C3DB7FFD516F5C2BDA12BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1195D6861E887568107FA7F463EA9BBABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/31F43A46088F6D2E63B39857A3536909BD02851C2FB632864165FCA4920 46548.pygtex [148]) (./_minted-Tutorial/16771935702D6A2A9762A80A621013D8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/046FE550C51B323D1E952A27E126FE19BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/A55E467518B2E0F936A232F0970B1037BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/6D69D310788199FBA6E8A5BF5CAB2021BD02851C2FB632864165FCA4920 46548.pygtex [149]) (./_minted-Tutorial/2C71B4AE1F4F9990447491C6C291ABC2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/FD7ECFDD9D017B829A54C995FEE42EEDBD02851C2FB632864165FCA4920 46548.pygtex [150]) (./_minted-Tutorial/3AD8335853E972C8E62AAF79CF0A3D33BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/758BAC7574A59544686354199D20892CBD02851C2FB632864165FCA4920 46548.pygtex) [151] (./_minted-Tutorial/7A63CB5E786CCE052981F7DD10653DA9BD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (14.20721pt too wide) in paragraph at lines 1055--1059 \OT1/cmr/m/n/10 func-tion re-turns a gen-er-a-tor ob-ject that yields a [][]\OT 1/cmtt/m/n/10 QueryResult []\OT1/cmr/m/n/10 ob-ject in each it-er-a-tion. Like [][]\OT1/cmtt/m/n/10 Bio.SearchIO.read[]\OT1/cmr/m/n/10 , (./_minted-Tutorial/DC4E434DA5B851CF1E22BD3608A311F4BD02851C2FB632864165FCA4920 46548.pygtex) [152] Overfull \hbox (20.13245pt too wide) in paragraph at lines 1087--1092 []\OT1/cmr/m/n/10 In this case, the ideal choice would be to in-dex the file us -ing [][]\OT1/cmtt/m/n/10 Bio.SearchIO.index []\OT1/cmr/m/n/10 or [][]\OT1/cmtt /m/n/10 Bio.SearchIO.index_db[]\OT1/cmr/m/n/10 . (./_minted-Tutorial/0AB25750C7D89E832295045C60D6B8C4BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/DFACFE04880AE0CA2E8E32ABDC9E9868BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/51F256FC56FFFAE1F1E84A4EFC5BAE55BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/5BCEFFE3DBB7A0AE4FD5D950731D72DEBD02851C2FB632864165FCA4920 46548.pygtex) [153] Overfull \hbox (11.82602pt too wide) in paragraph at lines 1167--1170 []\OT1/cmr/m/n/10 Finally, [][]\OT1/cmtt/m/n/10 Bio.SearchIO []\OT1/cmr/m/n/10 also pro-vides a [][]\OT1/cmtt/m/n/10 convert []\OT1/cmr/m/n/10 func-tion, whic h is sim-ply a short-cut for [][]\OT1/cmtt/m/n/10 Bio.SearchIO.parse (./_minted-Tutorial/BDE985FA3ADA6B0D37013C3D5F37C176BD02851C2FB632864165FCA4920 46548.pygtex)) [154] (./Tutorial/chapter_entrez.tex Chapter 9. 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Use \OT1/cmtt/m/n/10 structure[]rebuild[]test$$ (./_minted-Tutorial/BD4323A41DFED2A7E4CD261AA65F95EDBD02851C2FB632864165FCA4920 46548.pygtex) [210] (./_minted-Tutorial/6395F38A139598C6CC297CDBA73A8A43BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/21D2C13C2AA9395E0B1E4F1DDC801798BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/12E711A2CBFD0B046AA026208A117C1E9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/813FE78A3F8D8E46F06FF71539F000E69543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/CD78F368EB103F71947A3184BB62B46F9543DFECA235A69AE23006BA05B 4EB70.pygtex [211]) (./_minted-Tutorial/8E34478E945971E05C77F0A0E8C1B9D89543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/0D3FBB23D21A6A468370D56058193010BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/BBA5405CCC4A3178ADA49DA358246C819543DFECA235A69AE23006BA05B 4EB70.pygtex [212]) (./_minted-Tutorial/DE601B1883F045FBEE1B28168CFF0CCABD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/AAF43F15691D49893FAEEAB7B7693A1D9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/0ABBC5325B76EBCC5687BB33E7595F219543DFECA235A69AE23006BA05B 4EB70.pygtex) Excluding 'htmlonly' comment. [213 <./images/1a8o-ca-plot.png>] Overfull \hbox (15.27203pt too wide) in paragraph at lines 1292--1295 []\OT1/cmr/m/n/10 This work uses equa-tions de-vel-oped by Blue, the Hedronome- ter, dis-cussed in [][]$\OT1/cmtt/m/n/10 https : / / math . stackexchange . Overfull \hbox (116.15723pt too wide) in paragraph at lines 1292--1295 \OT1/cmtt/m/n/10 com / a / 49340 / 409$[][] \OT1/cmr/m/n/10 and fur-ther in [][ ]$\OT1/cmtt/m/n/10 http : / / daylateanddollarshort . com / mathdocs / Heron-[] like-[]Results-[]for-[]Tetrahedral-[]Volume . 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(./_minted-Tutorial/6C5156DAD460519324A5B7657B301B5DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/1836031BC83AA94C8906762F613E6CBABD02851C2FB632864165FCA4920 46548.pygtex) [226] (./_minted-Tutorial/D0A75FB8C1C791E4AA80420B93F216A8BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/FEC6C2CB5FA0AFCFE00D995BD3642FF2BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/2B435DC3041611A5D6A663B437ADB1ADBD02851C2FB632864165FCA4920 46548.pygtex) Overfull \hbox (25.13162pt too wide) in paragraph at lines 182--185 []\OT1/cmr/m/n/10 Let's tar-get the most re-cent com-mon an-ces-tor (MRCA) of t he nodes named ``E'' and ``F''. The [][]\OT1/cmtt/m/n/10 common_ancestor (./_minted-Tutorial/29624A9666C9430AABADF395148BBF27BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D0F05D42BA0A9BC594EEDB16319A972DBD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/87517FEF82BFE1AB8D89A83F4DC5E8B9BD02851C2FB632864165FCA4920 46548.pygtex [227 <./images/phylo-simple-draw.png>]) Excluding 'htmlonly' comment. 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[231 <./images/phylo-draw-example.p ng>] Overfull \hbox (19.85507pt too wide) in paragraph at lines 479--486 \OT1/cmr/m/n/10 For ex-am-ple, in a tree with clade names Foo1, Foo2 and Foo3, [][]\OT1/cmtt/m/n/10 tree.find_clades({"name": "Foo1"}) [232] Overfull \hbox (13.48741pt too wide) in paragraph at lines 534--537 []\OT1/cmr/m/n/10 Find each clade con-tain-ing a match-ing el-e-ment. That is, find each el-e-ment as with [][]\OT1/cmtt/m/n/10 find_elements[]\OT1/cmr/m/n/10 , [233] (./_minted-Tutorial/6AAB725DBD2E5B7C5FD79A9A16536BF69543DFECA235A69AE23006BA05B 4EB70.pygtex) [234] Overfull \hbox (15.04868pt too wide) in paragraph at lines 703--707 []\OT1/cmr/m/n/10 Below is an ex-am-ple on how to use a python script to in-ter -act with PhyML ([][]$\OT1/cmtt/m/n/10 http : / / www . atgc-[]montpellier . 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[265] [266] [267] [268] (./_minted-Tutorial/C7B59059E3AE6CDE790EFE6EB0ED4140BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/C2B72A7408C7DF74DFCEBE0485997287BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/425EDAA643B5AA9589F3EEE601735827BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/50B5971EFCF22FCC4E1302DB2D0A25009543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/293084E63EA5C0E01F325A4DD59469C0BD02851C2FB632864165FCA4920 46548.pygtex [269]) Overfull \hbox (78.60634pt too wide) in paragraph at lines 245--246 \OT1/cmr/m/n/10 men-sions of these ar-rays are $[]$ if [][]\OT1/cmtt/m/n/10 tra nspose []\OT1/cmr/m/n/10 is [][]\OT1/cmtt/m/n/10 0[]\OT1/cmr/m/n/10 , or $[]$ (./_minted-Tutorial/05DC01C08B8EDF71F86E3C3A9C28EB34BD02851C2FB632864165FCA4920 46548.pygtex) [270] [271] (./_minted-Tutorial/A4A28B5A443208DEAB3B4D76AA3B762EBD02851C2FB632864165FCA4920 46548.pygtex) [272] (./_minted-Tutorial/C286E2777B917B774560CBDC7CF92626BD02851C2FB632864165FCA4920 46548.pygtex) (./_minted-Tutorial/D04E097D8E8C4C039FEC20FA103CED189543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/36EF8931044EF448BC70F722AFADB43D9543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/805B33438269C932AC54C0DAB5A3D7AC9543DFECA235A69AE23006BA05B 4EB70.pygtex) [273] [274] Overfull \hbox (16.73593pt too wide) in paragraph at lines 423--424 [][]\OT1/cmtt/m/n/10 distance []\OT1/cmr/m/n/10 is the dis-tance be-tween them. 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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/AB16E58608A2F17CC79E6929557208879543DFECA235A69AE23006BA05B 4EB70.pygtex [337]) Overfull \hbox (4.57849pt too wide) in paragraph at lines 475--477 \OT1/cmr/m/n/10 That should find $13819$ reads from \OT1/cmtt/m/n/10 SRR014849. fastq \OT1/cmr/m/n/10 and save them to a new FASTQ file, \OT1/cmtt/m/n/10 with[ ]primer.fastq\OT1/cmr/m/n/10 . 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Overfull \hbox (4.00363pt too wide) in paragraph at lines 1117--1120 []\OT1/cmr/m/it/10 Tip: \OT1/cmr/m/n/10 Rather than us-ing [][]\OT1/cmtt/m/n/10 pylab.show() []\OT1/cmr/m/n/10 to show the plot in a win-dow, you can also use [][]\OT1/cmtt/m/n/10 pylab.savefig(...) (./_minted-Tutorial/798776F436EA559BACD9C305C09973919543DFECA235A69AE23006BA05B 4EB70.pygtex [347 <./images/hist_plot.png>]) (./_minted-Tutorial/CB78AD94DFE82ADBAF348C0EC1D261CD9543DFECA235A69AE23006BA05B 4EB70.pygtex) Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. [348 <./images/gc_plot.png>] (./_minted-Tutorial/6E0DA723E11A7B9CA8E2353A984B5DF79543DFECA235A69AE23006BA05B 4EB70.pygtex) (./_minted-Tutorial/80A47C8780CE3021D53829563E8166569543DFECA235A69AE23006BA05B 4EB70.pygtex [349 <./images/dot_plot.png>]) (./_minted-Tutorial/9574E55C4A182E2A0201DF18689F52F49543DFECA235A69AE23006BA05B 4EB70.pygtex) Excluding 'htmlonly' comment. 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For ex-am-ple, [][]\OT1/cmtt/m/n/10 expec ted_frequencies[^^MD^^M, ^^ME^^M] (./_minted-Tutorial/40ECF2E139F38209730D3B02B624EF74BD02851C2FB632864165FCA4920 46548.pygtex [357]) (./_minted-Tutorial/8965C8E87A0A43ECCE216C12F7DE7A4FBD02851C2FB632864165FCA4920 46548.pygtex)) [358] (./Tutorial/chapter_testing.tex Chapter 21. 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LaTeX Warning: There were multiply-defined labels. ) (see the transcript file for additional information) < /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb> Output written on Tutorial.pdf (374 pages, 3024630 bytes). Transcript written on Tutorial.log. pdflatex biopdb_faq.tex This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./biopdb_faq.tex LaTeX2e <2023-06-01> patch level 1 L3 programming layer <2023-08-29> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2023/05/17 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/bookman.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pbk.fd)) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def)) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/generic/iftex/ifvtex.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty)) (/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty))) (/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 56. (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf)) (/usr/share/texlive/texmf-dist/tex/generic/babel/locale/en/babel-english.tex) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) No file biopdb_faq.aux. *geometry* driver: auto-detecting *geometry* detected driver: pdftex *geometry* verbose mode - [ preamble ] result: * driver: pdftex * paper: a4paper * layout: * layoutoffset:(h,v)=(0.0pt,0.0pt) * modes: * h-part:(L,W,R)=(89.62709pt, 418.25368pt, 89.6271pt) * v-part:(T,H,B)=(56.9055pt, 731.23584pt, 56.9055pt) * \paperwidth=597.50787pt * \paperheight=845.04684pt * \textwidth=418.25368pt * \textheight=731.23584pt * \oddsidemargin=17.3571pt * \evensidemargin=17.3571pt * \topmargin=-52.36449pt * \headheight=12.0pt * \headsep=25.0pt * \topskip=10.0pt * \footskip=30.0pt * \marginparwidth=65.0pt * \marginparsep=11.0pt * \columnsep=10.0pt * \skip\footins=9.0pt plus 4.0pt minus 2.0pt * \hoffset=0.0pt * \voffset=0.0pt * \mag=1000 * \@twocolumnfalse * \@twosidefalse * \@mparswitchfalse * \@reversemarginfalse * (1in=72.27pt=25.4mm, 1cm=28.453pt) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) Overfull \hbox (40.90678pt too wide) in paragraph at lines 112--119 []\T1/pbk/l/n/10 However, the [][]\T1/pcr/m/n/10 Bio.PDB.mmCIF.MMCIFlex []\T1/p bk/l/n/10 mod-ule (used in-ter-nally by [][]\T1/pcr/m/n/10 Bio.PDB.MMCIFParser [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}{/usr/share/texlive/texmf- dist/fonts/enc/dvips/base/8r.enc}] (/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 1345--1353 []\T1/pbk/l/n/10 THE CON-TRIB-U-TORS AND COPY-RIGHT HOLD-ERS OF THIS SOFT-WARE DIS-CLAIM [15] (./biopdb_faq.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. Package rerunfilecheck Warning: File `biopdb_faq.out' has changed. 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Transcript written on biopdb_faq.log. pdflatex biopdb_faq.tex This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./biopdb_faq.tex LaTeX2e <2023-06-01> patch level 1 L3 programming layer <2023-08-29> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2023/05/17 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/bookman.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pbk.fd)) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def)) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/generic/iftex/ifvtex.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty)) (/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty))) (/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 56. (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf)) (/usr/share/texlive/texmf-dist/tex/generic/babel/locale/en/babel-english.tex) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./biopdb_faq.aux) *geometry* driver: auto-detecting *geometry* detected driver: pdftex *geometry* verbose mode - [ preamble ] result: * driver: pdftex * paper: a4paper * layout: * layoutoffset:(h,v)=(0.0pt,0.0pt) * modes: * h-part:(L,W,R)=(89.62709pt, 418.25368pt, 89.6271pt) * v-part:(T,H,B)=(56.9055pt, 731.23584pt, 56.9055pt) * \paperwidth=597.50787pt * \paperheight=845.04684pt * \textwidth=418.25368pt * \textheight=731.23584pt * \oddsidemargin=17.3571pt * \evensidemargin=17.3571pt * \topmargin=-52.36449pt * \headheight=12.0pt * \headsep=25.0pt * \topskip=10.0pt * \footskip=30.0pt * \marginparwidth=65.0pt * \marginparsep=11.0pt * \columnsep=10.0pt * \skip\footins=9.0pt plus 4.0pt minus 2.0pt * \hoffset=0.0pt * \voffset=0.0pt * \mag=1000 * \@twocolumnfalse * \@twosidefalse * \@mparswitchfalse * \@reversemarginfalse * (1in=72.27pt=25.4mm, 1cm=28.453pt) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx)) (./biopdb_faq.out) (./biopdb_faq.out) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) Overfull \hbox (40.90678pt too wide) in paragraph at lines 112--119 []\T1/pbk/l/n/10 However, the [][]\T1/pcr/m/n/10 Bio.PDB.mmCIF.MMCIFlex []\T1/p bk/l/n/10 mod-ule (used in-ter-nally by [][]\T1/pcr/m/n/10 Bio.PDB.MMCIFParser [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}{/usr/share/texlive/texmf- dist/fonts/enc/dvips/base/8r.enc}] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pbk.fd) [2] Overfull \hbox (21.75009pt too wide) in paragraph at lines 271--276 \T1/pbk/l/n/10 file to their val-ues. If there are mul-ti-ple val-ues (like in the case of tag \T1/pcr/m/n/10 _atom_site.Cartn_y\T1/pbk/l/n/10 , [3] Overfull \hbox (13.9754pt too wide) in paragraph at lines 312--318 \T1/pbk/l/n/10 The avail-able keys are \T1/pcr/m/n/10 name, head, deposition_-d ate, release_-date, structure_- Overfull \hbox (11.71707pt too wide) in paragraph at lines 312--318 \T1/pcr/m/n/10 method, resolution, structure_-reference \T1/pbk/l/n/10 (maps to a list of ref-er-ences), \T1/pcr/m/n/10 journal_- [4] [5] [6] [7 <./images/smcra.png (PNG copy)>] [8] [9] [10] Overfull \hbox (45.08351pt too wide) in paragraph at lines 1012--1016 \T1/pbk/l/n/10 Note that in the above case only model 0 of the struc-ture is co n-sid-ered by \T1/pcr/m/n/10 PolypeptideBuilder\T1/pbk/l/n/10 . Overfull \hbox (10.80998pt too wide) in paragraph at lines 1020--1024 \T1/pbk/l/n/10 try). The se-quence of each polypep-tide can then eas-ily be ob- tained from the \T1/pcr/m/n/10 Polypeptide [11] [12] Overfull \hbox (87.74638pt too wide) in paragraph at lines 1148--1149 []\T1/pcr/m/n/10 # Calculate classical coordination number exp_fs=hse.calc_fs_e xposure(model) Overfull \hbox (20.6135pt too wide) in paragraph at lines 1169--1174 \T1/pcr/m/n/10 Atom \T1/pbk/l/n/10 ob-jects re-turn a \T1/pcr/m/n/10 Vector \T1 /pbk/l/n/10 ob-ject rep-re-sen-ta-tion of the co-or-di-nates with the \T1/pcr/m /n/10 get_vector [13] [14] Overfull \hbox (1.21811pt too wide) in paragraph at lines 1345--1353 []\T1/pbk/l/n/10 THE CON-TRIB-U-TORS AND COPY-RIGHT HOLD-ERS OF THIS SOFT-WARE DIS-CLAIM [15] (./biopdb_faq.aux) ) (see the transcript file for additional information) Output written on biopdb_faq.pdf (15 pages, 165504 bytes). Transcript written on biopdb_faq.log. pdflatex biopdb_faq.tex This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./biopdb_faq.tex LaTeX2e <2023-06-01> patch level 1 L3 programming layer <2023-08-29> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2023/05/17 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/bookman.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pbk.fd)) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def)) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/generic/iftex/ifvtex.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty)) (/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty))) (/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 56. (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf)) (/usr/share/texlive/texmf-dist/tex/generic/babel/locale/en/babel-english.tex) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./biopdb_faq.aux) *geometry* driver: auto-detecting *geometry* detected driver: pdftex *geometry* verbose mode - [ preamble ] result: * driver: pdftex * paper: a4paper * layout: * layoutoffset:(h,v)=(0.0pt,0.0pt) * modes: * h-part:(L,W,R)=(89.62709pt, 418.25368pt, 89.6271pt) * v-part:(T,H,B)=(56.9055pt, 731.23584pt, 56.9055pt) * \paperwidth=597.50787pt * \paperheight=845.04684pt * \textwidth=418.25368pt * \textheight=731.23584pt * \oddsidemargin=17.3571pt * \evensidemargin=17.3571pt * \topmargin=-52.36449pt * \headheight=12.0pt * \headsep=25.0pt * \topskip=10.0pt * \footskip=30.0pt * \marginparwidth=65.0pt * \marginparsep=11.0pt * \columnsep=10.0pt * \skip\footins=9.0pt plus 4.0pt minus 2.0pt * \hoffset=0.0pt * \voffset=0.0pt * \mag=1000 * \@twocolumnfalse * \@twosidefalse * \@mparswitchfalse * \@reversemarginfalse * (1in=72.27pt=25.4mm, 1cm=28.453pt) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx)) (./biopdb_faq.out) (./biopdb_faq.out) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) Overfull \hbox (40.90678pt too wide) in paragraph at lines 112--119 []\T1/pbk/l/n/10 However, the [][]\T1/pcr/m/n/10 Bio.PDB.mmCIF.MMCIFlex []\T1/p bk/l/n/10 mod-ule (used in-ter-nally by [][]\T1/pcr/m/n/10 Bio.PDB.MMCIFParser [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}{/usr/share/texlive/texmf- dist/fonts/enc/dvips/base/8r.enc}] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pbk.fd) [2] Overfull \hbox (21.75009pt too wide) in paragraph at lines 271--276 \T1/pbk/l/n/10 file to their val-ues. If there are mul-ti-ple val-ues (like in the case of tag \T1/pcr/m/n/10 _atom_site.Cartn_y\T1/pbk/l/n/10 , [3] Overfull \hbox (13.9754pt too wide) in paragraph at lines 312--318 \T1/pbk/l/n/10 The avail-able keys are \T1/pcr/m/n/10 name, head, deposition_-d ate, release_-date, structure_- Overfull \hbox (11.71707pt too wide) in paragraph at lines 312--318 \T1/pcr/m/n/10 method, resolution, structure_-reference \T1/pbk/l/n/10 (maps to a list of ref-er-ences), \T1/pcr/m/n/10 journal_- [4] [5] [6] [7 <./images/smcra.png (PNG copy)>] [8] [9] [10] Overfull \hbox (45.08351pt too wide) in paragraph at lines 1012--1016 \T1/pbk/l/n/10 Note that in the above case only model 0 of the struc-ture is co n-sid-ered by \T1/pcr/m/n/10 PolypeptideBuilder\T1/pbk/l/n/10 . Overfull \hbox (10.80998pt too wide) in paragraph at lines 1020--1024 \T1/pbk/l/n/10 try). The se-quence of each polypep-tide can then eas-ily be ob- tained from the \T1/pcr/m/n/10 Polypeptide [11] [12] Overfull \hbox (87.74638pt too wide) in paragraph at lines 1148--1149 []\T1/pcr/m/n/10 # Calculate classical coordination number exp_fs=hse.calc_fs_e xposure(model) Overfull \hbox (20.6135pt too wide) in paragraph at lines 1169--1174 \T1/pcr/m/n/10 Atom \T1/pbk/l/n/10 ob-jects re-turn a \T1/pcr/m/n/10 Vector \T1 /pbk/l/n/10 ob-ject rep-re-sen-ta-tion of the co-or-di-nates with the \T1/pcr/m /n/10 get_vector [13] [14] Overfull \hbox (1.21811pt too wide) in paragraph at lines 1345--1353 []\T1/pbk/l/n/10 THE CON-TRIB-U-TORS AND COPY-RIGHT HOLD-ERS OF THIS SOFT-WARE DIS-CLAIM [15] (./biopdb_faq.aux) ) (see the transcript file for additional information) Output written on biopdb_faq.pdf (15 pages, 165504 bytes). Transcript written on biopdb_faq.log. make[2]: Leaving directory '/<>/Doc' make[1]: Leaving directory '/<>' rm -f debian/python3-biopython.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/<>' 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 GraphicsBitmaps 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 "3.12 3.11" --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:310: set -e; \ mkdir -p /<>/.pybuild/cpython3_3.12/build/home; \ mkdir -p /<>/.pybuild/cpython3_3.12/build/Doc/examples; \ cp -a Doc/Tutorial.tex /<>/.pybuild/cpython3_3.12/build/Doc; \ cp -a Doc/Tutorial /<>/.pybuild/cpython3_3.12/build/Doc; \ cp -a Doc/examples /<>/.pybuild/cpython3_3.12/build/Doc; \ cp -a Tests /<>/.pybuild/cpython3_3.12/build; \ cd /<>/.pybuild/cpython3_3.12/build/Tests; \ env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=/<>/.pybuild/cpython3_3.12/build/home python3.12 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_Align_Alignment ... ok test_Align_a2m ... ok test_Align_bed ... ok test_Align_bigbed ... ok test_Align_bigmaf ... ok test_Align_bigpsl ... ok test_Align_clustal ... ok test_Align_emboss ... ok test_Align_exonerate ... ok test_Align_fasta ... ok test_Align_hhr ... ok test_Align_maf ... ok test_Align_mauve ... ok test_Align_msf ... ok test_Align_nexus ... ok test_Align_phylip ... ok test_Align_psl ... ok test_Align_sam ... ok test_Align_stockholm ... ok test_Align_tabular ... 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_Dialign_tool ... ok test_EMBL_unittest ... ok test_Emboss ... /<>/.pybuild/cpython3_3.12/build/Bio/SeqIO/InsdcIO.py:1241: BiopythonWarning: Non-standard molecule type: mRNA warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning) ok test_EmbossPrimer ... ok test_Entrez ... /<>/.pybuild/cpython3_3.12/build/Bio/Entrez/__init__.py:694: UserWarning: Email address is not specified. To make use of NCBI's E-utilities, NCBI requires you to specify your email address with each request. As an example, if your email address is A.N.Other@example.com, you can specify it as follows: from Bio import Entrez Entrez.email = 'A.N.Other@example.com' In case of excessive usage of the E-utilities, NCBI will attempt to contact a user at the email address provided before blocking access to the E-utilities. warnings.warn( FAIL test_Entrez_online ... skipping. internet not available test_Entrez_parser ... ok test_Enzyme ... ok test_ExPASy ... skipping. internet not available test_Fasttree_tool ... ok test_File ... ok test_GenBank ... /<>/.pybuild/cpython3_3.12/build/Bio/SeqIO/InsdcIO.py:1241: BiopythonWarning: Non-standard molecule type: genomic DNA warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning) ok test_GenomeDiagram ... ok 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 ... ok test_Medline ... ok test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. test_NCBITextParser ... ok test_NCBIXML ... ok test_NCBI_BLAST_tools ... 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_CEAligner ... ok test_PDB_DSSP ... 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_PSEA ... skipping. Download and install psea from ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/. Make sure that psea is on path test_PDB_Polypeptide ... ok test_PDB_QCSuperimposer ... ok test_PDB_SASA ... ok test_PDB_SMCRA ... ok test_PDB_Selection ... 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_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 ... /<>/.pybuild/cpython3_3.12/build/Bio/GenBank/Scanner.py:303: BiopythonParserWarning: Non-standard feature line wrapping (didn't break on comma)? warnings.warn( /<>/.pybuild/cpython3_3.12/build/Bio/SeqIO/InsdcIO.py:1241: BiopythonWarning: Non-standard molecule type: mRNA warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning) /<>/.pybuild/cpython3_3.12/build/Bio/SeqIO/InsdcIO.py:1241: BiopythonWarning: Non-standard molecule type: unassigned DNA warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning) /<>/.pybuild/cpython3_3.12/build/Bio/SeqIO/InsdcIO.py:1241: BiopythonWarning: Non-standard molecule type: genomic DNA warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning) ok test_SeqIO_NibIO ... ok test_SeqIO_PdbIO ... ok test_SeqIO_QualityIO ... ok test_SeqIO_SeqXML ... ok test_SeqIO_SnapGene ... ok test_SeqIO_TwoBitIO ... ok test_SeqIO_Xdna ... ok test_SeqIO_features ... /<>/.pybuild/cpython3_3.12/build/Bio/SeqIO/InsdcIO.py:1241: BiopythonWarning: Non-standard molecule type: unassigned DNA warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning) /<>/.pybuild/cpython3_3.12/build/Bio/SeqIO/InsdcIO.py:1241: BiopythonWarning: Non-standard molecule type: genomic DNA warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning) /<>/.pybuild/cpython3_3.12/build/Bio/SeqIO/InsdcIO.py:1241: BiopythonWarning: Non-standard molecule type: mRNA warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning) /<>/.pybuild/cpython3_3.12/build/Bio/SeqIO/InsdcIO.py:549: BiopythonWarning: Annotation 'swissprot: locus SCX3_BUTOC, accession P01485; class: standard. created: Jul 21, 1986. sequence updated: Jul 21, 1986. annotation updated: Oct 16, 2001. xrefs: gi: gi: 69530 xrefs (non-sequence databases): HSSP P01484, InterPro IPR003614, InterPro IPR002061, InterPro IPR001219, Pfam PF00537, PRINTS PR00284, ProDom PD000908, SMART SM00505' too long for 'DBSOURCE' line warnings.warn( 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_SwissProt ... ok test_TCoffee_tool ... ok test_TogoWS ... skipping. internet not available test_TreeConstruction ... ok test_Tutorial ... /<>/.pybuild/cpython3_3.12/build/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module. warnings.warn( 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 ... /<>/.pybuild/cpython3_3.12/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( /<>/.pybuild/cpython3_3.12/build/Bio/Seq.py:2779: 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( /<>/.pybuild/cpython3_3.12/build/Bio/codonalign/__init__.py:612: BiopythonWarning: start codon of pro1 (S 0) does not correspond to pro1 (TCA) warnings.warn( /<>/.pybuild/cpython3_3.12/build/Bio/codonalign/__init__.py:678: BiopythonWarning: start codon of pro2(S 0) does not correspond to pro2(TCA) warnings.warn( ok test_geo ... ok test_kNN ... ok test_motifs ... ok test_motifs_online ... skipping. internet not available test_pairwise2 ... ok test_pairwise2_no_C ... ok test_pairwise_aligner ... ok test_pairwise_alignment_map ... 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_prosite ... ok test_samtools_tool ... ok test_seq ... 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.a2m docstring test ... ok Bio.Align.bed docstring test ... ok Bio.Align.bigbed docstring test ... ok Bio.Align.bigmaf docstring test ... ok Bio.Align.bigpsl docstring test ... ok Bio.Align.clustal docstring test ... ok Bio.Align.emboss docstring test ... ok Bio.Align.exonerate docstring test ... ok Bio.Align.fasta docstring test ... ok Bio.Align.hhr docstring test ... ok Bio.Align.interfaces docstring test ... ok Bio.Align.maf docstring test ... ok Bio.Align.mauve docstring test ... ok Bio.Align.msf docstring test ... ok Bio.Align.nexus docstring test ... ok Bio.Align.phylip docstring test ... ok Bio.Align.psl docstring test ... ok Bio.Align.sam docstring test ... ok Bio.Align.stockholm docstring test ... ok Bio.Align.substitution_matrices docstring test ... ok Bio.Align.tabular 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.Data docstring test ... ok Bio.Data.CodonTable docstring test ... ok Bio.Data.IUPACData docstring test ... ok Bio.Data.PDBData 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.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.SASA 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.ccealign docstring test ... ok Bio.PDB.cealign 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.qcprot 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.TwoBitIO docstring test ... ok Bio.SeqIO.UniprotIO docstring test ... ok Bio.SeqIO.XdnaIO docstring test ... ok Bio.SeqIO._index docstring test ... ok Bio.SeqIO._twoBitIO 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.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.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_construct_cgi_epost2 (test_Entrez.TestURLConstruction.test_construct_cgi_epost2) ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/.pybuild/cpython3_3.12/build/Tests/test_Entrez.py", line 212, in test_construct_cgi_epost2 check_request_ids(self, query, variables["id"]) File "/<>/.pybuild/cpython3_3.12/build/Tests/test_Entrez.py", line 129, in check_request_ids testcase.assertEquals(len(params["id"]), 1) ^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'TestURLConstruction' object has no attribute 'assertEquals'. Did you mean: 'assertEqual'? ---------------------------------------------------------------------- Ran 551 tests in 365.648 seconds FAILED (failures = 1) Skipping any tests requiring internet access Python version: 3.12.0 (main, Oct 4 2023, 06:27:34) [GCC 13.2.0] Operating system: posix linux E: pybuild pybuild:395: test: plugin custom failed with: exit code=1: set -e; \ mkdir -p /<>/.pybuild/cpython3_3.12/build/home; \ mkdir -p /<>/.pybuild/cpython3_3.12/build/Doc/examples; \ cp -a Doc/Tutorial.tex /<>/.pybuild/cpython3_3.12/build/Doc; \ cp -a Doc/Tutorial /<>/.pybuild/cpython3_3.12/build/Doc; \ cp -a Doc/examples /<>/.pybuild/cpython3_3.12/build/Doc; \ cp -a Tests /<>/.pybuild/cpython3_3.12/build; \ cd /<>/.pybuild/cpython3_3.12/build/Tests; \ env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=/<>/.pybuild/cpython3_3.12/build/home python3.12 run_tests.py --offline I: pybuild base:310: set -e; \ mkdir -p /<>/.pybuild/cpython3_3.11/build/home; \ mkdir -p /<>/.pybuild/cpython3_3.11/build/Doc/examples; \ cp -a Doc/Tutorial.tex /<>/.pybuild/cpython3_3.11/build/Doc; \ cp -a Doc/Tutorial /<>/.pybuild/cpython3_3.11/build/Doc; \ cp -a Doc/examples /<>/.pybuild/cpython3_3.11/build/Doc; \ cp -a Tests /<>/.pybuild/cpython3_3.11/build; \ cd /<>/.pybuild/cpython3_3.11/build/Tests; \ env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=/<>/.pybuild/cpython3_3.11/build/home python3.11 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_Align_Alignment ... ok test_Align_a2m ... ok test_Align_bed ... ok test_Align_bigbed ... ok test_Align_bigmaf ... ok test_Align_bigpsl ... ok test_Align_clustal ... ok test_Align_emboss ... ok test_Align_exonerate ... ok test_Align_fasta ... ok test_Align_hhr ... ok test_Align_maf ... ok test_Align_mauve ... ok test_Align_msf ... ok test_Align_nexus ... ok test_Align_phylip ... ok test_Align_psl ... ok test_Align_sam ... ok test_Align_stockholm ... ok test_Align_tabular ... 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_Dialign_tool ... ok test_EMBL_unittest ... ok test_Emboss ... /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py:1241: BiopythonWarning: Non-standard molecule type: mRNA warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning) ok test_EmbossPrimer ... ok test_Entrez ... /<>/.pybuild/cpython3_3.11/build/Bio/Entrez/__init__.py:694: UserWarning: Email address is not specified. To make use of NCBI's E-utilities, NCBI requires you to specify your email address with each request. As an example, if your email address is A.N.Other@example.com, you can specify it as follows: from Bio import Entrez Entrez.email = 'A.N.Other@example.com' In case of excessive usage of the E-utilities, NCBI will attempt to contact a user at the email address provided before blocking access to the E-utilities. warnings.warn( ok test_Entrez_online ... skipping. internet not available test_Entrez_parser ... ok test_Enzyme ... ok test_ExPASy ... skipping. internet not available test_Fasttree_tool ... ok test_File ... ok test_GenBank ... /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py:1241: BiopythonWarning: Non-standard molecule type: genomic DNA warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning) ok test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' ok 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 ... ok test_Medline ... ok test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. test_NCBITextParser ... ok test_NCBIXML ... ok test_NCBI_BLAST_tools ... 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_CEAligner ... ok test_PDB_DSSP ... 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_PSEA ... skipping. Download and install psea from ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/. Make sure that psea is on path test_PDB_Polypeptide ... ok test_PDB_QCSuperimposer ... ok test_PDB_SASA ... ok test_PDB_SMCRA ... ok test_PDB_Selection ... 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_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 ... /<>/.pybuild/cpython3_3.11/build/Bio/GenBank/Scanner.py:303: BiopythonParserWarning: Non-standard feature line wrapping (didn't break on comma)? warnings.warn( /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py:1241: BiopythonWarning: Non-standard molecule type: mRNA warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning) /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py:1241: BiopythonWarning: Non-standard molecule type: unassigned DNA warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning) /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py:1241: BiopythonWarning: Non-standard molecule type: genomic DNA warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning) ok test_SeqIO_NibIO ... ok test_SeqIO_PdbIO ... ok test_SeqIO_QualityIO ... ok test_SeqIO_SeqXML ... ok test_SeqIO_SnapGene ... ok test_SeqIO_TwoBitIO ... ok test_SeqIO_Xdna ... ok test_SeqIO_features ... /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py:1241: BiopythonWarning: Non-standard molecule type: unassigned DNA warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning) /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py:1241: BiopythonWarning: Non-standard molecule type: genomic DNA warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning) /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py:1241: BiopythonWarning: Non-standard molecule type: mRNA warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning) /<>/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py:549: BiopythonWarning: Annotation 'swissprot: locus SCX3_BUTOC, accession P01485; class: standard. created: Jul 21, 1986. sequence updated: Jul 21, 1986. annotation updated: Oct 16, 2001. xrefs: gi: gi: 69530 xrefs (non-sequence databases): HSSP P01484, InterPro IPR003614, InterPro IPR002061, InterPro IPR001219, Pfam PF00537, PRINTS PR00284, ProDom PD000908, SMART SM00505' too long for 'DBSOURCE' line warnings.warn( 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_SwissProt ... ok test_TCoffee_tool ... ok test_TogoWS ... skipping. internet not available test_TreeConstruction ... ok test_Tutorial ... /<>/.pybuild/cpython3_3.11/build/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module. warnings.warn( 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 ... /<>/.pybuild/cpython3_3.11/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( /<>/.pybuild/cpython3_3.11/build/Bio/Seq.py:2779: 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( /<>/.pybuild/cpython3_3.11/build/Bio/codonalign/__init__.py:612: BiopythonWarning: start codon of pro1 (S 0) does not correspond to pro1 (TCA) warnings.warn( /<>/.pybuild/cpython3_3.11/build/Bio/codonalign/__init__.py:678: BiopythonWarning: start codon of pro2(S 0) does not correspond to pro2(TCA) warnings.warn( ok test_geo ... ok test_kNN ... ok test_motifs ... ok test_motifs_online ... skipping. internet not available test_pairwise2 ... ok test_pairwise2_no_C ... ok test_pairwise_aligner ... ok test_pairwise_alignment_map ... 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_prosite ... ok test_samtools_tool ... ok test_seq ... 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.a2m docstring test ... ok Bio.Align.bed docstring test ... ok Bio.Align.bigbed docstring test ... ok Bio.Align.bigmaf docstring test ... ok Bio.Align.bigpsl docstring test ... ok Bio.Align.clustal docstring test ... ok Bio.Align.emboss docstring test ... ok Bio.Align.exonerate docstring test ... ok Bio.Align.fasta docstring test ... ok Bio.Align.hhr docstring test ... ok Bio.Align.interfaces docstring test ... ok Bio.Align.maf docstring test ... ok Bio.Align.mauve docstring test ... ok Bio.Align.msf docstring test ... ok Bio.Align.nexus docstring test ... ok Bio.Align.phylip docstring test ... ok Bio.Align.psl docstring test ... ok Bio.Align.sam docstring test ... ok Bio.Align.stockholm docstring test ... ok Bio.Align.substitution_matrices docstring test ... ok Bio.Align.tabular 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.Data docstring test ... ok Bio.Data.CodonTable docstring test ... ok Bio.Data.IUPACData docstring test ... ok Bio.Data.PDBData 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.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.SASA 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.ccealign docstring test ... ok Bio.PDB.cealign 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.qcprot 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.TwoBitIO docstring test ... ok Bio.SeqIO.UniprotIO docstring test ... ok Bio.SeqIO.XdnaIO docstring test ... ok Bio.SeqIO._index docstring test ... ok Bio.SeqIO._twoBitIO 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.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.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 ---------------------------------------------------------------------- Ran 551 tests in 389.096 seconds Skipping any tests requiring internet access Python version: 3.11.6 (main, Oct 8 2023, 05:06:43) [GCC 13.2.0] Operating system: posix linux rm -fr -- /tmp/dh-xdg-rundir-yViEOhdw dh_auto_test: error: pybuild --test -i python{version} -p "3.12 3.11" --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:86: override_dh_auto_test] Error 25 make[1]: Leaving directory '/<>' make: *** [debian/rules:42: binary-arch] Error 2 dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2023-11-07T11:37:52Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build Type: any Build-Space: 359980 Build-Time: 944 Distribution: noble-proposed Fail-Stage: build Host Architecture: armhf Install-Time: 240 Job: python-biopython_1.81+dfsg-1build1.dsc Machine Architecture: arm64 Package: python-biopython Package-Time: 1186 Source-Version: 1.81+dfsg-1build1 Space: 359980 Status: attempted Version: 1.81+dfsg-1build1 -------------------------------------------------------------------------------- Finished at 2023-11-07T11:37:52Z Build needed 00:19:46, 359980k disk space E: Build failure (dpkg-buildpackage died) RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-26951322 Scanning for processes to kill in build PACKAGEBUILD-26951322