https://launchpad.net/ubuntu/+archive/test-rebuild-20200925-groovy/+build/20043692 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-072 4.15.0-118-generic #119-Ubuntu SMP Tue Sep 8 12:21:56 UTC 2020 aarch64 Buildd toolchain package versions: launchpad-buildd_193~468~ubuntu18.04.1 python3-lpbuildd_193~468~ubuntu18.04.1 sbuild_0.75.0-1ubuntu1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu16.04.1 bzr_2.7.0+bzr6622-10 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu18.04.1 git_1:2.17.1-1ubuntu0.7 dpkg-dev_1.19.0.5ubuntu2.3 python-debian_0.1.32 python3-debian_0.1.32. Syncing the system clock with the buildd NTP service... 1 Oct 03:24:57 ntpdate[1627]: adjust time server 10.211.37.1 offset 0.043447 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=groovy --arch=arm64 PACKAGEBUILD-20043692 --image-type chroot /home/buildd/filecache-default/3ff5711ac2503d035c89289b694a465e92f31811 Creating target for build PACKAGEBUILD-20043692 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=groovy --arch=arm64 PACKAGEBUILD-20043692 Starting target for build PACKAGEBUILD-20043692 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=groovy --arch=arm64 PACKAGEBUILD-20043692 'deb http://ftpmaster.internal/ubuntu groovy main universe' Overriding sources.list in build-PACKAGEBUILD-20043692 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=groovy --arch=arm64 PACKAGEBUILD-20043692 Updating target for build PACKAGEBUILD-20043692 Get:1 http://ftpmaster.internal/ubuntu groovy InRelease [267 kB] Get:2 http://ftpmaster.internal/ubuntu groovy/main arm64 Packages [1344 kB] Get:3 http://ftpmaster.internal/ubuntu groovy/main Translation-en [507 kB] Get:4 http://ftpmaster.internal/ubuntu groovy/universe arm64 Packages [12.3 MB] Get:5 http://ftpmaster.internal/ubuntu groovy/universe Translation-en [5260 kB] Fetched 19.7 MB in 6s (3038 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libffi7 libjson-c4 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libffi8ubuntu1 libgssapi-krb5-2 libjson-c5 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libnsl-dev libnsl2 libnss-nis libnss-nisplus libtirpc-common libtirpc-dev libtirpc3 rpcsvc-proto The following packages will be upgraded: apt base-files binutils binutils-aarch64-linux-gnu binutils-common bsdutils build-essential ca-certificates coreutils cpp cpp-10 debianutils dpkg dpkg-dev g++ g++-10 gcc gcc-10 gcc-10-base libapparmor1 libapt-pkg6.0 libasan6 libatomic1 libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap2 libcc1-0 libcryptsetup12 libctf-nobfd0 libctf0 libdb5.3 libdpkg-perl libgcc-10-dev libgcc-s1 libgdbm-compat4 libgdbm6 libgmp10 libgnutls30 libgomp1 libip4tc2 libitm1 liblsan0 liblzma5 libmount1 libmpc3 libmpfr6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpng16-16 libselinux1 libsemanage-common libsemanage1 libsmartcols1 libsqlite3-0 libssl1.1 libstdc++-10-dev libstdc++6 libsystemd0 libtsan0 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev mount openssl sensible-utils systemd systemd-sysv systemd-timesyncd util-linux xz-utils zlib1g 82 upgraded, 15 newly installed, 0 to remove and 0 not upgraded. Need to get 60.9 MB of archives. After this operation, 3470 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu groovy/main arm64 libkrb5support0 arm64 1.17-10 [30.2 kB] Get:2 http://ftpmaster.internal/ubuntu groovy/main arm64 libk5crypto3 arm64 1.17-10 [80.3 kB] Get:3 http://ftpmaster.internal/ubuntu groovy/main arm64 libkeyutils1 arm64 1.6.1-2ubuntu1 [9932 B] Get:4 http://ftpmaster.internal/ubuntu groovy/main arm64 libssl1.1 arm64 1.1.1f-1ubuntu4 [1160 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/main arm64 libkrb5-3 arm64 1.17-10 [312 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main arm64 libgssapi-krb5-2 arm64 1.17-10 [113 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/main arm64 libtirpc-common all 1.2.6-1build1 [7472 B] Get:8 http://ftpmaster.internal/ubuntu groovy/main arm64 libtirpc3 arm64 1.2.6-1build1 [73.5 kB] Get:9 http://ftpmaster.internal/ubuntu groovy/main arm64 libnsl2 arm64 1.3.0-0ubuntu3 [37.0 kB] Get:10 http://ftpmaster.internal/ubuntu groovy/main arm64 libnss-nis arm64 3.1-0ubuntu4 [23.8 kB] Get:11 http://ftpmaster.internal/ubuntu groovy/main arm64 libnss-nisplus arm64 1.3-0ubuntu4 [20.7 kB] Get:12 http://ftpmaster.internal/ubuntu groovy/main arm64 libc6 arm64 2.32-0ubuntu3 [2252 kB] Get:13 http://ftpmaster.internal/ubuntu groovy/main arm64 libc-dev-bin arm64 2.32-0ubuntu3 [28.7 kB] Get:14 http://ftpmaster.internal/ubuntu groovy/main arm64 libc6-dev arm64 2.32-0ubuntu3 [1726 kB] Get:15 http://ftpmaster.internal/ubuntu groovy/main arm64 rpcsvc-proto arm64 1.4.2-0ubuntu3 [59.8 kB] Get:16 http://ftpmaster.internal/ubuntu groovy/main arm64 libtirpc-dev arm64 1.2.6-1build1 [185 kB] Get:17 http://ftpmaster.internal/ubuntu groovy/main arm64 libnsl-dev arm64 1.3.0-0ubuntu3 [65.6 kB] Get:18 http://ftpmaster.internal/ubuntu groovy/main arm64 libc-bin arm64 2.32-0ubuntu3 [504 kB] Get:19 http://ftpmaster.internal/ubuntu groovy/main arm64 linux-libc-dev arm64 5.8.0-20.21 [1135 kB] Get:20 http://ftpmaster.internal/ubuntu groovy/main arm64 libcc1-0 arm64 10.2.0-11ubuntu1 [37.0 kB] Get:21 http://ftpmaster.internal/ubuntu groovy/main arm64 libctf0 arm64 2.35.1-1ubuntu1 [44.0 kB] Get:22 http://ftpmaster.internal/ubuntu groovy/main arm64 libctf-nobfd0 arm64 2.35.1-1ubuntu1 [44.8 kB] Get:23 http://ftpmaster.internal/ubuntu groovy/main arm64 binutils-aarch64-linux-gnu arm64 2.35.1-1ubuntu1 [2026 kB] Get:24 http://ftpmaster.internal/ubuntu groovy/main arm64 libbinutils arm64 2.35.1-1ubuntu1 [484 kB] Get:25 http://ftpmaster.internal/ubuntu groovy/main arm64 binutils-common arm64 2.35.1-1ubuntu1 [212 kB] Get:26 http://ftpmaster.internal/ubuntu groovy/main arm64 binutils arm64 2.35.1-1ubuntu1 [3356 B] Get:27 http://ftpmaster.internal/ubuntu groovy/main arm64 gcc-10-base arm64 10.2.0-11ubuntu1 [19.5 kB] Get:28 http://ftpmaster.internal/ubuntu groovy/main arm64 libgcc-s1 arm64 10.2.0-11ubuntu1 [34.6 kB] Get:29 http://ftpmaster.internal/ubuntu groovy/main arm64 libgomp1 arm64 10.2.0-11ubuntu1 [94.1 kB] Get:30 http://ftpmaster.internal/ubuntu groovy/main arm64 libitm1 arm64 10.2.0-11ubuntu1 [24.3 kB] Get:31 http://ftpmaster.internal/ubuntu groovy/main arm64 libatomic1 arm64 10.2.0-11ubuntu1 [9888 B] Get:32 http://ftpmaster.internal/ubuntu groovy/main arm64 libasan6 arm64 10.2.0-11ubuntu1 [319 kB] Get:33 http://ftpmaster.internal/ubuntu groovy/main arm64 liblsan0 arm64 10.2.0-11ubuntu1 [130 kB] Get:34 http://ftpmaster.internal/ubuntu groovy/main arm64 libtsan0 arm64 10.2.0-11ubuntu1 [303 kB] Get:35 http://ftpmaster.internal/ubuntu groovy/main arm64 libubsan1 arm64 10.2.0-11ubuntu1 [127 kB] Get:36 http://ftpmaster.internal/ubuntu groovy/main arm64 g++-10 arm64 10.2.0-11ubuntu1 [8097 kB] Get:37 http://ftpmaster.internal/ubuntu groovy/main arm64 libstdc++-10-dev arm64 10.2.0-11ubuntu1 [1719 kB] Get:38 http://ftpmaster.internal/ubuntu groovy/main arm64 libgcc-10-dev arm64 10.2.0-11ubuntu1 [910 kB] Get:39 http://ftpmaster.internal/ubuntu groovy/main arm64 gcc-10 arm64 10.2.0-11ubuntu1 [14.6 MB] Get:40 http://ftpmaster.internal/ubuntu groovy/main arm64 cpp-10 arm64 10.2.0-11ubuntu1 [7141 kB] Get:41 http://ftpmaster.internal/ubuntu groovy/main arm64 libstdc++6 arm64 10.2.0-11ubuntu1 [464 kB] Get:42 http://ftpmaster.internal/ubuntu groovy/main arm64 zlib1g arm64 1:1.2.11.dfsg-2ubuntu2 [51.1 kB] Get:43 http://ftpmaster.internal/ubuntu groovy/main arm64 libgmp10 arm64 2:6.2.0+dfsg-6ubuntu1 [216 kB] Get:44 http://ftpmaster.internal/ubuntu groovy/main arm64 libmpfr6 arm64 4.1.0-3 [216 kB] Get:45 http://ftpmaster.internal/ubuntu groovy/main arm64 libmpc3 arm64 1.2.0~rc1-1 [42.5 kB] Get:46 http://ftpmaster.internal/ubuntu groovy/main arm64 libzstd1 arm64 1.4.5+dfsg-4 [269 kB] Get:47 http://ftpmaster.internal/ubuntu groovy/main arm64 base-files arm64 11ubuntu13 [60.4 kB] Get:48 http://ftpmaster.internal/ubuntu groovy/main arm64 bsdutils arm64 1:2.36-3ubuntu1 [82.8 kB] Get:49 http://ftpmaster.internal/ubuntu groovy/main arm64 libselinux1 arm64 3.1-2 [64.9 kB] Get:50 http://ftpmaster.internal/ubuntu groovy/main arm64 coreutils arm64 8.32-3ubuntu1 [1257 kB] Get:51 http://ftpmaster.internal/ubuntu groovy/main arm64 debianutils arm64 4.11.1 [85.2 kB] Get:52 http://ftpmaster.internal/ubuntu groovy/main arm64 dpkg arm64 1.20.5ubuntu2 [1156 kB] Get:53 http://ftpmaster.internal/ubuntu groovy/main arm64 util-linux arm64 2.36-3ubuntu1 [1028 kB] Get:54 http://ftpmaster.internal/ubuntu groovy/main arm64 liblzma5 arm64 5.2.4-1ubuntu1 [87.9 kB] Get:55 http://ftpmaster.internal/ubuntu groovy/main arm64 libffi8ubuntu1 arm64 3.4~20200819gead65ca871-0ubuntu3 [17.4 kB] Get:56 http://ftpmaster.internal/ubuntu groovy/main arm64 libp11-kit0 arm64 0.23.21-2build1 [182 kB] Get:57 http://ftpmaster.internal/ubuntu groovy/main arm64 libgnutls30 arm64 3.6.15-4ubuntu2 [698 kB] Get:58 http://ftpmaster.internal/ubuntu groovy/main arm64 systemd-sysv arm64 246.6-1ubuntu1 [10.3 kB] Get:59 http://ftpmaster.internal/ubuntu groovy/main arm64 systemd-timesyncd arm64 246.6-1ubuntu1 [26.3 kB] Get:60 http://ftpmaster.internal/ubuntu groovy/main arm64 libapparmor1 arm64 3.0.0~beta1-0ubuntu6 [35.4 kB] Get:61 http://ftpmaster.internal/ubuntu groovy/main arm64 libaudit-common all 1:2.8.5-3ubuntu1 [4076 B] Get:62 http://ftpmaster.internal/ubuntu groovy/main arm64 libaudit1 arm64 1:2.8.5-3ubuntu1 [38.3 kB] Get:63 http://ftpmaster.internal/ubuntu groovy/main arm64 libcap2 arm64 1:2.43-1 [17.2 kB] Get:64 http://ftpmaster.internal/ubuntu groovy/main arm64 libjson-c5 arm64 0.15-1 [29.9 kB] Get:65 http://ftpmaster.internal/ubuntu groovy/main arm64 libblkid1 arm64 2.36-3ubuntu1 [126 kB] Get:66 http://ftpmaster.internal/ubuntu groovy/main arm64 libuuid1 arm64 2.36-3ubuntu1 [21.2 kB] Get:67 http://ftpmaster.internal/ubuntu groovy/main arm64 libcryptsetup12 arm64 2:2.3.3-1ubuntu6 [176 kB] Get:68 http://ftpmaster.internal/ubuntu groovy/main arm64 libip4tc2 arm64 1.8.5-3ubuntu1 [18.7 kB] Get:69 http://ftpmaster.internal/ubuntu groovy/main arm64 libmount1 arm64 2.36-3ubuntu1 [139 kB] Get:70 http://ftpmaster.internal/ubuntu groovy/main arm64 libpam0g arm64 1.3.1-5ubuntu6 [54.6 kB] Get:71 http://ftpmaster.internal/ubuntu groovy/main arm64 mount arm64 2.36-3ubuntu1 [117 kB] Get:72 http://ftpmaster.internal/ubuntu groovy/main arm64 systemd arm64 246.6-1ubuntu1 [3840 kB] Get:73 http://ftpmaster.internal/ubuntu groovy/main arm64 libsystemd0 arm64 246.6-1ubuntu1 [252 kB] Get:74 http://ftpmaster.internal/ubuntu groovy/main arm64 libudev1 arm64 246.6-1ubuntu1 [62.4 kB] Get:75 http://ftpmaster.internal/ubuntu groovy/main arm64 libapt-pkg6.0 arm64 2.1.10 [768 kB] Get:76 http://ftpmaster.internal/ubuntu groovy/main arm64 apt arm64 2.1.10 [1247 kB] Get:77 http://ftpmaster.internal/ubuntu groovy/main arm64 libpam-modules-bin arm64 1.3.1-5ubuntu6 [35.9 kB] Get:78 http://ftpmaster.internal/ubuntu groovy/main arm64 libpam-modules arm64 1.3.1-5ubuntu6 [242 kB] Get:79 http://ftpmaster.internal/ubuntu groovy/main arm64 libdb5.3 arm64 5.3.28+dfsg1-0.6ubuntu3 [620 kB] Get:80 http://ftpmaster.internal/ubuntu groovy/main arm64 libpam-runtime all 1.3.1-5ubuntu6 [37.3 kB] Get:81 http://ftpmaster.internal/ubuntu groovy/main arm64 libsemanage-common all 3.1-1 [10.2 kB] Get:82 http://ftpmaster.internal/ubuntu groovy/main arm64 libsemanage1 arm64 3.1-1 [80.6 kB] Get:83 http://ftpmaster.internal/ubuntu groovy/main arm64 libsmartcols1 arm64 2.36-3ubuntu1 [90.7 kB] Get:84 http://ftpmaster.internal/ubuntu groovy/main arm64 sensible-utils all 0.0.13 [15.1 kB] Get:85 http://ftpmaster.internal/ubuntu groovy/main arm64 openssl arm64 1.1.1f-1ubuntu4 [600 kB] Get:86 http://ftpmaster.internal/ubuntu groovy/main arm64 ca-certificates all 20200601 [147 kB] Get:87 http://ftpmaster.internal/ubuntu groovy/main arm64 libsqlite3-0 arm64 3.33.0-1 [540 kB] Get:88 http://ftpmaster.internal/ubuntu groovy/main arm64 xz-utils arm64 5.2.4-1ubuntu1 [81.2 kB] Get:89 http://ftpmaster.internal/ubuntu groovy/main arm64 libgdbm6 arm64 1.18.1-5.1 [26.6 kB] Get:90 http://ftpmaster.internal/ubuntu groovy/main arm64 libpng16-16 arm64 1.6.37-3 [175 kB] Get:91 http://ftpmaster.internal/ubuntu groovy/main arm64 g++ arm64 4:10.2.0-1ubuntu1 [1592 B] Get:92 http://ftpmaster.internal/ubuntu groovy/main arm64 gcc arm64 4:10.2.0-1ubuntu1 [5228 B] Get:93 http://ftpmaster.internal/ubuntu groovy/main arm64 cpp arm64 4:10.2.0-1ubuntu1 [27.7 kB] Get:94 http://ftpmaster.internal/ubuntu groovy/main arm64 dpkg-dev all 1.20.5ubuntu2 [758 kB] Get:95 http://ftpmaster.internal/ubuntu groovy/main arm64 libdpkg-perl all 1.20.5ubuntu2 [232 kB] Get:96 http://ftpmaster.internal/ubuntu groovy/main arm64 build-essential arm64 12.8ubuntu3 [4636 B] Get:97 http://ftpmaster.internal/ubuntu groovy/main arm64 libgdbm-compat4 arm64 1.18.1-5.1 [6044 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 60.9 MB in 3s (24.1 MB/s) Selecting previously unselected package libkrb5support0:arm64. (Reading database ... 12777 files and directories currently installed.) Preparing to unpack .../libkrb5support0_1.17-10_arm64.deb ... Unpacking libkrb5support0:arm64 (1.17-10) ... Setting up libkrb5support0:arm64 (1.17-10) ... Selecting previously unselected package libk5crypto3:arm64. (Reading database ... 12782 files and directories currently installed.) Preparing to unpack .../libk5crypto3_1.17-10_arm64.deb ... Unpacking libk5crypto3:arm64 (1.17-10) ... Setting up libk5crypto3:arm64 (1.17-10) ... Selecting previously unselected package libkeyutils1:arm64. (Reading database ... 12787 files and directories currently installed.) Preparing to unpack .../libkeyutils1_1.6.1-2ubuntu1_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.1-2ubuntu1) ... Setting up libkeyutils1:arm64 (1.6.1-2ubuntu1) ... (Reading database ... 12792 files and directories currently installed.) Preparing to unpack .../libssl1.1_1.1.1f-1ubuntu4_arm64.deb ... 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RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-20043692 arm64 groovy -c chroot:build-PACKAGEBUILD-20043692 --arch=arm64 --dist=groovy --nolog python-biopython_1.76+dfsg-1.dsc Initiating build PACKAGEBUILD-20043692 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-118-generic #119-Ubuntu SMP Tue Sep 8 12:21:56 UTC 2020 aarch64 sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on bos02-arm64-072.buildd +==============================================================================+ | python-biopython 1.76+dfsg-1 (arm64) Thu, 01 Oct 2020 03:25:58 +0000 | +==============================================================================+ Package: python-biopython Version: 1.76+dfsg-1 Source Version: 1.76+dfsg-1 Distribution: groovy Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-20043692/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- python-biopython_1.76+dfsg-1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/python-biopython-qlvf3h/python-biopython-1.76+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/python-biopython-qlvf3h' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-7TnpY9/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-7TnpY9/apt_archive ./ InRelease Get:2 copy:/<>/resolver-7TnpY9/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-7TnpY9/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-7TnpY9/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-7TnpY9/apt_archive ./ Packages [432 B] Fetched 1738 B in 0s (47.9 kB/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libffi7 libjson-c4 Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 856 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-7TnpY9/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [856 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 856 B in 0s (64.2 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 13027 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_arm64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (arm64 included in any all) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), dh-python, python3-all-dev, python3-numpy, flex, python3-reportlab, hevea, texlive-latex-base, texlive-latex-extra, texlive-fonts-recommended, bwa, clustalo, clustalw, dialign, dssp, emboss, fasttree, mafft, muscle, ncbi-blast+, phylip, prank, probcons, python3-networkx, python3-mysqldb, python3-matplotlib, python3-pil, python3-rdflib, python3-renderpm, python3-psycopg2, python3-scipy, python3-setuptools, python3-unittest2, samtools, t-coffee, wise, python3-pygments Filtered Build-Depends: debhelper-compat (= 12), dh-python, python3-all-dev, python3-numpy, flex, python3-reportlab, hevea, texlive-latex-base, texlive-latex-extra, texlive-fonts-recommended, bwa, clustalo, clustalw, dialign, dssp, emboss, fasttree, mafft, muscle, ncbi-blast+, phylip, prank, probcons, python3-networkx, python3-mysqldb, python3-matplotlib, python3-pil, python3-rdflib, python3-renderpm, python3-psycopg2, python3-scipy, python3-setuptools, python3-unittest2, samtools, t-coffee, wise, python3-pygments dpkg-deb: building package 'sbuild-build-depends-python-biopython-dummy' in '/<>/resolver-7TnpY9/apt_archive/sbuild-build-depends-python-biopython-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-python-biopython-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-7TnpY9/apt_archive ./ InRelease Get:2 copy:/<>/resolver-7TnpY9/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-7TnpY9/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-7TnpY9/apt_archive ./ Sources [750 B] Get:5 copy:/<>/resolver-7TnpY9/apt_archive ./ Packages [801 B] Fetched 2514 B in 0s (70.3 kB/s) Reading package lists... Reading package lists... Install python-biopython build dependencies (apt-based resolver) ---------------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libffi7 libjson-c4 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils bwa clustalo clustalw debhelper dh-autoreconf dh-python dh-strip-nondeterminism dialign dssp dwz emboss emboss-data emboss-lib fasttree file flex fontconfig-config fonts-dejavu-core fonts-lmodern fonts-lyx fonts-urw-base35 gettext gettext-base ghostscript groff-base hevea intltool-debian libapache-pom-java libarchive-zip-perl libargtable2-0 libasn1-8-heimdal libavahi-client3 libavahi-common-data libavahi-common3 libblas3 libboost-program-options1.71.0 libboost-thread1.71.0 libbrotli1 libbsd0 libcairo2 libcommons-logging-java libcommons-parent-java libcroco3 libcups2 libcurl3-gnutls libdbus-1-3 libdebhelper-perl libdeflate0 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfreetype6 libgd3 libgfortran5 libglib2.0-0 libgraphite2-3 libgs9 libgs9-common libgssapi3-heimdal libharfbuzz0b libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhpdf-2.3.0 libhts3 libhx509-5-heimdal libice6 libicu67 libidn11 libijs-0.35 libimagequant0 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libkpathsea6 libkrb5-26-heimdal liblapack3 liblbfgsb0 liblcms2-2 libldap-2.4-2 liblmdb0 libmagic-mgc libmagic1 libmbedcrypto3 libmbedtls12 libmbedx509-0 libmysqlclient21 libnetpbm10 libnghttp2-14 libopenjp2-7 libpaper-utils libpaper1 libpdfbox-java libpipeline1 libpixman-1-0 libpq5 libpsl5 libptexenc1 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.8 libpython3.8-dev libpython3.8-minimal libpython3.8-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libssh-4 libsub-override-perl libsynctex2 libteckit0 libtexlua53 libtiff5 libtool libuchardet0 libwebp6 libwebpdemux2 libwebpmux3 libwind0-heimdal libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxt6 libzzip-0-13 m4 mafft man-db mime-support muscle mysql-common ncbi-blast+ ncbi-data netpbm node-jquery phylip po-debconf poppler-data prank preview-latex-style probcons python-matplotlib-data python3 python3-all python3-all-dev python3-cycler python3-dateutil python3-decorator python3-dev python3-distutils python3-isodate python3-kiwisolver python3-lib2to3 python3-linecache2 python3-matplotlib python3-minimal python3-mysqldb python3-networkx python3-numpy python3-pil python3-pkg-resources python3-psycopg2 python3-pygments python3-pyparsing python3-rdflib python3-renderpm python3-reportlab python3-reportlab-accel python3-scipy python3-setuptools python3-six python3-traceback2 python3-unittest2 python3.8 python3.8-dev python3.8-minimal samtools t-coffee t1utils tex-common texlive-base texlive-binaries texlive-fonts-recommended texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures ttf-bitstream-vera ucf wise wise-data x11-common xdg-utils zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc clustalx seaview dh-make emboss-doc emboss-test embassy bison flex-doc fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre gettext-doc libasprintf-dev libgettextpo-dev ghostscript-x groff hevea-doc libavalon-framework-java libcommons-logging-java-doc libexcalibur-logkit-java liblog4j1.2-java cups-common libgd-tools libjs-jquery-ui-docs liblcms2-utils libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser phylip-doc libmail-box-perl poppler-utils fonts-japanese-mincho | fonts-ipafont-mincho fonts-japanese-gothic | fonts-ipafont-gothic fonts-arphic-ukai fonts-arphic-uming fonts-nanum probcons-extra python3-doc python3-tk python3-venv python-cycler-doc dvipng ffmpeg gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-nose python3-pyqt5 python3-sip python3-tornado texlive-extra-utils ttf-staypuft default-mysql-server | virtual-mysql-server python3-mysqldb-dbg python-networkx-doc python3-gdal python3-pydot python3-pygraphviz gfortran python-numpy-doc python3-pytest python3-numpy-dbg python-pil-doc python3-pil-dbg python-psycopg2-doc python-pygments-doc python-pyparsing-doc python-rdflib-doc python3-renderpm-dbg pdf-viewer python3-egenix-mxtexttools python-reportlab-doc python-scipy-doc python-setuptools-doc python3.8-venv python3.8-doc binfmt-support cwltool boxshade t-coffee-examples perl-tk xpdf | pdf-viewer xzdec texlive-fonts-recommended-doc texlive-latex-base-doc icc-profiles libfile-which-perl libspreadsheet-parseexcel-perl texlive-latex-extra-doc texlive-latex-recommended-doc texlive-luatex texlive-pstricks dot2tex prerex ruby-tcltk | libtcltk-ruby texlive-pictures-doc vprerex wise-doc Recommended packages: primer3 libfl-dev curl | wget | lynx dbus libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs fonts-droid-fallback javascript-common libldap-common publicsuffix libsasl2-modules libltdl-dev blast2 libwww-perl lynx ruby libmail-sendmail-perl python3-tk python3-yaml python3-olefile python3-sparqlwrapper python3-html5lib amap-align dialign-tx fsa kalign libsoap-lite-perl libxml-simple-perl mustang poa proda tm-align lmodern dvisvgm tex-gyre tipa texlive-plain-generic ruby | ruby-interpreter tk libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils bwa clustalo clustalw debhelper dh-autoreconf dh-python dh-strip-nondeterminism dialign dssp dwz emboss emboss-data emboss-lib fasttree file flex fontconfig-config fonts-dejavu-core fonts-lmodern fonts-lyx fonts-urw-base35 gettext gettext-base ghostscript groff-base hevea intltool-debian libapache-pom-java libarchive-zip-perl libargtable2-0 libasn1-8-heimdal libavahi-client3 libavahi-common-data libavahi-common3 libblas3 libboost-program-options1.71.0 libboost-thread1.71.0 libbrotli1 libbsd0 libcairo2 libcommons-logging-java libcommons-parent-java libcroco3 libcups2 libcurl3-gnutls libdbus-1-3 libdebhelper-perl libdeflate0 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfreetype6 libgd3 libgfortran5 libglib2.0-0 libgraphite2-3 libgs9 libgs9-common libgssapi3-heimdal libharfbuzz0b libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhpdf-2.3.0 libhts3 libhx509-5-heimdal libice6 libicu67 libidn11 libijs-0.35 libimagequant0 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libkpathsea6 libkrb5-26-heimdal liblapack3 liblbfgsb0 liblcms2-2 libldap-2.4-2 liblmdb0 libmagic-mgc libmagic1 libmbedcrypto3 libmbedtls12 libmbedx509-0 libmysqlclient21 libnetpbm10 libnghttp2-14 libopenjp2-7 libpaper-utils libpaper1 libpdfbox-java libpipeline1 libpixman-1-0 libpq5 libpsl5 libptexenc1 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.8 libpython3.8-dev libpython3.8-minimal libpython3.8-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libssh-4 libsub-override-perl libsynctex2 libteckit0 libtexlua53 libtiff5 libtool libuchardet0 libwebp6 libwebpdemux2 libwebpmux3 libwind0-heimdal libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxt6 libzzip-0-13 m4 mafft man-db mime-support muscle mysql-common ncbi-blast+ ncbi-data netpbm node-jquery phylip po-debconf poppler-data prank preview-latex-style probcons python-matplotlib-data python3 python3-all python3-all-dev python3-cycler python3-dateutil python3-decorator python3-dev python3-distutils python3-isodate python3-kiwisolver python3-lib2to3 python3-linecache2 python3-matplotlib python3-minimal python3-mysqldb python3-networkx python3-numpy python3-pil python3-pkg-resources python3-psycopg2 python3-pygments python3-pyparsing python3-rdflib python3-renderpm python3-reportlab python3-reportlab-accel python3-scipy python3-setuptools python3-six python3-traceback2 python3-unittest2 python3.8 python3.8-dev python3.8-minimal samtools sbuild-build-depends-python-biopython-dummy t-coffee t1utils tex-common texlive-base texlive-binaries texlive-fonts-recommended texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures ttf-bitstream-vera ucf wise wise-data x11-common xdg-utils zlib1g-dev 0 upgraded, 220 newly installed, 0 to remove and 0 not upgraded. Need to get 241 MB of archives. After this operation, 1216 MB of additional disk space will be used. 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http://ftpmaster.internal/ubuntu groovy/main arm64 mysql-common all 5.8+1.0.5ubuntu2 [7496 B] Get:84 http://ftpmaster.internal/ubuntu groovy/main arm64 libmysqlclient21 arm64 8.0.21-1 [1191 kB] Get:85 http://ftpmaster.internal/ubuntu groovy/main arm64 libroken18-heimdal arm64 7.7.0+dfsg-2 [39.4 kB] Get:86 http://ftpmaster.internal/ubuntu groovy/main arm64 libasn1-8-heimdal arm64 7.7.0+dfsg-2 [150 kB] Get:87 http://ftpmaster.internal/ubuntu groovy/main arm64 libheimbase1-heimdal arm64 7.7.0+dfsg-2 [27.9 kB] Get:88 http://ftpmaster.internal/ubuntu groovy/main arm64 libhcrypto4-heimdal arm64 7.7.0+dfsg-2 [84.8 kB] Get:89 http://ftpmaster.internal/ubuntu groovy/main arm64 libwind0-heimdal arm64 7.7.0+dfsg-2 [47.2 kB] Get:90 http://ftpmaster.internal/ubuntu groovy/main arm64 libhx509-5-heimdal arm64 7.7.0+dfsg-2 [98.6 kB] Get:91 http://ftpmaster.internal/ubuntu groovy/main arm64 libkrb5-26-heimdal arm64 7.7.0+dfsg-2 [192 kB] Get:92 http://ftpmaster.internal/ubuntu groovy/main arm64 libheimntlm0-heimdal arm64 7.7.0+dfsg-2 [14.8 kB] Get:93 http://ftpmaster.internal/ubuntu groovy/main arm64 libgssapi3-heimdal arm64 7.7.0+dfsg-2 [88.4 kB] Get:94 http://ftpmaster.internal/ubuntu groovy/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-2 [15.1 kB] Get:95 http://ftpmaster.internal/ubuntu groovy/main arm64 libsasl2-2 arm64 2.1.27+dfsg-2 [48.4 kB] Get:96 http://ftpmaster.internal/ubuntu groovy/main arm64 libldap-2.4-2 arm64 2.4.53+dfsg-1ubuntu1 [148 kB] Get:97 http://ftpmaster.internal/ubuntu groovy/main arm64 libpq5 arm64 12.4-1 [107 kB] Get:98 http://ftpmaster.internal/ubuntu groovy/universe arm64 emboss-lib arm64 6.6.0+dfsg-7ubuntu2 [2546 kB] Get:99 http://ftpmaster.internal/ubuntu groovy/universe arm64 emboss-data all 6.6.0+dfsg-7ubuntu2 [61.0 MB] Get:100 http://ftpmaster.internal/ubuntu groovy/universe arm64 emboss arm64 6.6.0+dfsg-7ubuntu2 [942 kB] Get:101 http://ftpmaster.internal/ubuntu groovy/universe arm64 fonts-lmodern all 2.004.5-6 [4532 kB] Get:102 http://ftpmaster.internal/ubuntu groovy/universe arm64 fonts-lyx all 2.3.5.2-1 [154 kB] Get:103 http://ftpmaster.internal/ubuntu groovy/main arm64 fonts-urw-base35 all 20170801.1-3 [6333 kB] Get:104 http://ftpmaster.internal/ubuntu groovy/main arm64 libgs9-common all 9.52~dfsg-1ubuntu2 [689 kB] Get:105 http://ftpmaster.internal/ubuntu groovy/main arm64 libavahi-common-data arm64 0.8-3ubuntu1 [25.1 kB] Get:106 http://ftpmaster.internal/ubuntu groovy/main arm64 libavahi-common3 arm64 0.8-3ubuntu1 [20.6 kB] Get:107 http://ftpmaster.internal/ubuntu groovy/main arm64 libavahi-client3 arm64 0.8-3ubuntu1 [24.2 kB] Get:108 http://ftpmaster.internal/ubuntu groovy/main arm64 libcups2 arm64 2.3.3-3ubuntu1 [218 kB] Get:109 http://ftpmaster.internal/ubuntu groovy/main arm64 libidn11 arm64 1.33-2.4 [46.1 kB] Get:110 http://ftpmaster.internal/ubuntu groovy/main arm64 libijs-0.35 arm64 0.35-15 [15.1 kB] Get:111 http://ftpmaster.internal/ubuntu groovy/main arm64 libjbig2dec0 arm64 0.18+20200417-1 [57.6 kB] Get:112 http://ftpmaster.internal/ubuntu groovy/main arm64 liblcms2-2 arm64 2.9-4 [131 kB] Get:113 http://ftpmaster.internal/ubuntu groovy/main arm64 libopenjp2-7 arm64 2.3.1-1ubuntu4 [131 kB] Get:114 http://ftpmaster.internal/ubuntu groovy/main arm64 libpaper1 arm64 1.1.28 [12.7 kB] Get:115 http://ftpmaster.internal/ubuntu groovy/main arm64 libgs9 arm64 9.52~dfsg-1ubuntu2 [2008 kB] Get:116 http://ftpmaster.internal/ubuntu groovy/main arm64 ghostscript arm64 9.52~dfsg-1ubuntu2 [52.0 kB] Get:117 http://ftpmaster.internal/ubuntu groovy/universe arm64 libnetpbm10 arm64 2:10.0-15.3build1 [50.7 kB] Get:118 http://ftpmaster.internal/ubuntu groovy/universe arm64 netpbm arm64 2:10.0-15.3build1 [927 kB] Get:119 http://ftpmaster.internal/ubuntu groovy/main arm64 libpaper-utils arm64 1.1.28 [8328 B] Get:120 http://ftpmaster.internal/ubuntu groovy/main arm64 libkpathsea6 arm64 2020.20200327.54578-4build1 [54.8 kB] Get:121 http://ftpmaster.internal/ubuntu groovy/main arm64 libptexenc1 arm64 2020.20200327.54578-4build1 [34.8 kB] Get:122 http://ftpmaster.internal/ubuntu groovy/main arm64 libsynctex2 arm64 2020.20200327.54578-4build1 [52.6 kB] Get:123 http://ftpmaster.internal/ubuntu groovy/main arm64 libtexlua53 arm64 2020.20200327.54578-4build1 [101 kB] Get:124 http://ftpmaster.internal/ubuntu groovy/main arm64 t1utils arm64 1.41-4 [53.5 kB] Get:125 http://ftpmaster.internal/ubuntu groovy/main arm64 libpixman-1-0 arm64 0.38.4-0ubuntu1 [130 kB] Get:126 http://ftpmaster.internal/ubuntu groovy/main arm64 libxcb-render0 arm64 1.14-2 [14.7 kB] Get:127 http://ftpmaster.internal/ubuntu groovy/main arm64 libxcb-shm0 arm64 1.14-2 [5560 B] Get:128 http://ftpmaster.internal/ubuntu groovy/main arm64 libxrender1 arm64 1:0.9.10-1 [16.1 kB] Get:129 http://ftpmaster.internal/ubuntu groovy/main arm64 libcairo2 arm64 1.16.0-4ubuntu1 [538 kB] Get:130 http://ftpmaster.internal/ubuntu groovy/main arm64 libgraphite2-3 arm64 1.3.14-1 [67.8 kB] Get:131 http://ftpmaster.internal/ubuntu groovy/main arm64 libharfbuzz0b arm64 2.6.4-1ubuntu5 [306 kB] Get:132 http://ftpmaster.internal/ubuntu groovy/universe arm64 libteckit0 arm64 2.5.8+ds2-5ubuntu2 [291 kB] Get:133 http://ftpmaster.internal/ubuntu groovy/main arm64 x11-common all 1:7.7+19ubuntu14 [22.3 kB] Get:134 http://ftpmaster.internal/ubuntu groovy/main arm64 libice6 arm64 2:1.0.10-1 [37.2 kB] Get:135 http://ftpmaster.internal/ubuntu groovy/main arm64 libsm6 arm64 2:1.2.3-1 [15.1 kB] Get:136 http://ftpmaster.internal/ubuntu groovy/main arm64 libxt6 arm64 1:1.2.0-1 [147 kB] Get:137 http://ftpmaster.internal/ubuntu groovy/main arm64 libxmu6 arm64 2:1.1.3-0ubuntu1 [42.9 kB] Get:138 http://ftpmaster.internal/ubuntu groovy/main arm64 libxaw7 arm64 2:1.0.13-1 [137 kB] Get:139 http://ftpmaster.internal/ubuntu groovy/main arm64 libxi6 arm64 2:1.7.10-1 [28.2 kB] Get:140 http://ftpmaster.internal/ubuntu groovy/universe arm64 libzzip-0-13 arm64 0.13.62-3.2ubuntu1 [25.7 kB] Get:141 http://ftpmaster.internal/ubuntu groovy/universe arm64 texlive-binaries arm64 2020.20200327.54578-4build1 [7528 kB] Get:142 http://ftpmaster.internal/ubuntu groovy/main arm64 xdg-utils all 1.1.3-2ubuntu1 [61.6 kB] Get:143 http://ftpmaster.internal/ubuntu groovy/universe arm64 texlive-base all 2020.20200804-2 [21.4 MB] Get:144 http://ftpmaster.internal/ubuntu groovy/universe arm64 hevea arm64 2.34-2build2 [2101 kB] Get:145 http://ftpmaster.internal/ubuntu groovy/universe arm64 libapache-pom-java all 18-1 [4720 B] Get:146 http://ftpmaster.internal/ubuntu groovy/main arm64 libblas3 arm64 3.9.0-3ubuntu1 [89.3 kB] Get:147 http://ftpmaster.internal/ubuntu groovy/universe arm64 libcommons-parent-java all 43-1 [10.8 kB] Get:148 http://ftpmaster.internal/ubuntu groovy/universe arm64 libcommons-logging-java all 1.2-2 [60.3 kB] Get:149 http://ftpmaster.internal/ubuntu groovy/main arm64 libnghttp2-14 arm64 1.41.0-3 [64.6 kB] Get:150 http://ftpmaster.internal/ubuntu groovy/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2build2 [53.1 kB] Get:151 http://ftpmaster.internal/ubuntu groovy/main arm64 libssh-4 arm64 0.9.4-1ubuntu3 [161 kB] Get:152 http://ftpmaster.internal/ubuntu groovy/main arm64 libcurl3-gnutls arm64 7.68.0-1ubuntu4 [211 kB] Get:153 http://ftpmaster.internal/ubuntu groovy/universe arm64 libdeflate0 arm64 1.6-1 [51.1 kB] Get:154 http://ftpmaster.internal/ubuntu groovy/main arm64 libexpat1-dev arm64 2.2.9-1build1 [103 kB] Get:155 http://ftpmaster.internal/ubuntu groovy/main arm64 libgfortran5 arm64 10.2.0-11ubuntu1 [345 kB] Get:156 http://ftpmaster.internal/ubuntu groovy/universe arm64 libhts3 arm64 1.10.2-5 [300 kB] Get:157 http://ftpmaster.internal/ubuntu groovy/main arm64 libimagequant0 arm64 2.12.2-1.1 [29.3 kB] Get:158 http://ftpmaster.internal/ubuntu groovy/main arm64 node-jquery all 3.5.1+dfsg-4 [309 kB] Get:159 http://ftpmaster.internal/ubuntu groovy/main arm64 libjs-jquery all 3.5.1+dfsg-4 [2308 B] Get:160 http://ftpmaster.internal/ubuntu groovy/universe arm64 libjs-jquery-ui all 1.12.1+dfsg-6 [231 kB] Get:161 http://ftpmaster.internal/ubuntu groovy/main arm64 liblapack3 arm64 3.9.0-3ubuntu1 [1528 kB] Get:162 http://ftpmaster.internal/ubuntu groovy/universe arm64 liblbfgsb0 arm64 3.0+dfsg.3-9 [24.5 kB] Get:163 http://ftpmaster.internal/ubuntu groovy/universe arm64 libmbedcrypto3 arm64 2.16.5-1ubuntu1 [144 kB] Get:164 http://ftpmaster.internal/ubuntu groovy/universe arm64 libmbedx509-0 arm64 2.16.5-1ubuntu1 [41.5 kB] Get:165 http://ftpmaster.internal/ubuntu groovy/universe arm64 libmbedtls12 arm64 2.16.5-1ubuntu1 [64.5 kB] Get:166 http://ftpmaster.internal/ubuntu groovy/main arm64 libpython3.8 arm64 3.8.6-1 [1480 kB] Get:167 http://ftpmaster.internal/ubuntu groovy/main arm64 libpython3.8-dev arm64 3.8.6-1 [3349 kB] Get:168 http://ftpmaster.internal/ubuntu groovy/main arm64 libpython3-dev arm64 3.8.2-0ubuntu2 [7236 B] Get:169 http://ftpmaster.internal/ubuntu groovy/main arm64 libpython3-all-dev arm64 3.8.2-0ubuntu2 [1116 B] Get:170 http://ftpmaster.internal/ubuntu groovy/main arm64 libwebpdemux2 arm64 0.6.1-2 [8868 B] Get:171 http://ftpmaster.internal/ubuntu groovy/main arm64 libwebpmux3 arm64 0.6.1-2 [17.3 kB] Get:172 http://ftpmaster.internal/ubuntu groovy/universe arm64 mafft arm64 7.471-1 [880 kB] Get:173 http://ftpmaster.internal/ubuntu groovy/universe arm64 muscle arm64 1:3.8.1551-2build1 [228 kB] Get:174 http://ftpmaster.internal/ubuntu groovy/universe arm64 ncbi-data all 6.1.20170106+dfsg1-8 [3518 kB] Get:175 http://ftpmaster.internal/ubuntu groovy/universe arm64 ncbi-blast+ arm64 2.10.1-2 [10.1 MB] Get:176 http://ftpmaster.internal/ubuntu groovy/universe arm64 phylip arm64 1:3.697+dfsg-2 [848 kB] Get:177 http://ftpmaster.internal/ubuntu groovy/universe arm64 prank arm64 0.0.170427+dfsg-2build1 [323 kB] Get:178 http://ftpmaster.internal/ubuntu groovy/universe arm64 preview-latex-style all 11.91-2ubuntu2 [184 kB] Get:179 http://ftpmaster.internal/ubuntu groovy/universe arm64 probcons arm64 1.12-12build1 [111 kB] Get:180 http://ftpmaster.internal/ubuntu groovy/universe arm64 python-matplotlib-data all 3.3.0-3 [3803 kB] Get:181 http://ftpmaster.internal/ubuntu groovy/main arm64 python3-all arm64 3.8.2-0ubuntu2 [1104 B] Get:182 http://ftpmaster.internal/ubuntu groovy/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2ubuntu2 [154 kB] Get:183 http://ftpmaster.internal/ubuntu groovy/main arm64 python3.8-dev arm64 3.8.6-1 [515 kB] Get:184 http://ftpmaster.internal/ubuntu groovy/main arm64 python3-dev arm64 3.8.2-0ubuntu2 [1212 B] Get:185 http://ftpmaster.internal/ubuntu groovy/main arm64 python3-all-dev arm64 3.8.2-0ubuntu2 [1112 B] Get:186 http://ftpmaster.internal/ubuntu groovy/main arm64 python3-six all 1.15.0-1 [12.0 kB] Get:187 http://ftpmaster.internal/ubuntu groovy/universe arm64 python3-cycler all 0.10.0-3 [8132 B] Get:188 http://ftpmaster.internal/ubuntu groovy/main arm64 python3-dateutil all 2.8.1-4 [79.8 kB] Get:189 http://ftpmaster.internal/ubuntu groovy/main arm64 python3-decorator all 4.4.2-0ubuntu1 [10.3 kB] Get:190 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2.8.5-1 [106 kB] Get:200 http://ftpmaster.internal/ubuntu groovy/main arm64 python3-pygments all 2.3.1+dfsg-4 [581 kB] Get:201 http://ftpmaster.internal/ubuntu groovy/universe arm64 python3-rdflib all 4.2.2-5 [241 kB] Get:202 http://ftpmaster.internal/ubuntu groovy/main arm64 python3-renderpm arm64 3.5.47-1 [54.7 kB] Get:203 http://ftpmaster.internal/ubuntu groovy/main arm64 python3-reportlab-accel arm64 3.5.47-1 [18.9 kB] Get:204 http://ftpmaster.internal/ubuntu groovy/main arm64 python3-reportlab all 3.5.47-1 [550 kB] Get:205 http://ftpmaster.internal/ubuntu groovy/main arm64 python3-setuptools all 49.3.1-2 [453 kB] Get:206 http://ftpmaster.internal/ubuntu groovy/main arm64 python3-traceback2 all 1.4.0-6 [16.6 kB] Get:207 http://ftpmaster.internal/ubuntu groovy/main arm64 python3-unittest2 all 1.1.0-7 [75.5 kB] Get:208 http://ftpmaster.internal/ubuntu groovy/universe arm64 samtools arm64 1.10-4 [474 kB] Get:209 http://ftpmaster.internal/ubuntu groovy/universe arm64 t-coffee arm64 13.41.0.28bdc39+dfsg-4 [898 kB] Get:210 http://ftpmaster.internal/ubuntu groovy/universe arm64 texlive-fonts-recommended all 2020.20200804-2 [4974 kB] Get:211 http://ftpmaster.internal/ubuntu groovy/universe arm64 texlive-latex-base all 2020.20200804-2 [1036 kB] Get:212 http://ftpmaster.internal/ubuntu groovy/universe arm64 libfontbox-java all 1:1.8.16-2 [207 kB] Get:213 http://ftpmaster.internal/ubuntu groovy/universe arm64 libpdfbox-java all 1:1.8.16-2 [5199 kB] Get:214 http://ftpmaster.internal/ubuntu groovy/universe arm64 texlive-latex-recommended all 2020.20200804-2 [14.5 MB] Get:215 http://ftpmaster.internal/ubuntu groovy/universe arm64 texlive-pictures all 2020.20200804-2 [4655 kB] Get:216 http://ftpmaster.internal/ubuntu groovy/universe arm64 texlive-latex-extra all 2020.20200804-3 [12.8 MB] Get:217 http://ftpmaster.internal/ubuntu groovy/universe arm64 wise-data all 2.4.1-23 [76.8 kB] Get:218 http://ftpmaster.internal/ubuntu groovy/universe arm64 wise arm64 2.4.1-23 [964 kB] Get:219 http://ftpmaster.internal/ubuntu groovy/universe arm64 fasttree arm64 2.1.11-1 [162 kB] Get:220 http://ftpmaster.internal/ubuntu groovy/universe arm64 python3-scipy arm64 1.5.2-2 [10.6 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 241 MB in 12s (19.9 MB/s) Selecting previously unselected package libpython3.8-minimal:arm64. 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Setting up libfile-stripnondeterminism-perl (1.9.0-1) ... Setting up libpaper1:arm64 (1.1.28) ... Creating config file /etc/papersize with new version Setting up libice6:arm64 (2:1.0.10-1) ... Setting up libxdmcp6:arm64 (1:1.1.3-0ubuntu1) ... Setting up liblapack3:arm64 (3.9.0-3ubuntu1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libxcb1:arm64 (1.14-2) ... Setting up libpdfbox-java (1:1.8.16-2) ... Setting up libtool (2.4.6-14) ... Setting up libxcb-render0:arm64 (1.14-2) ... Setting up libmbedx509-0:arm64 (2.16.5-1ubuntu1) ... Setting up fontconfig-config (2.13.1-2ubuntu3) ... Setting up wise (2.4.1-23) ... Setting up libwebpdemux2:arm64 (0.6.1-2) ... Setting up libasn1-8-heimdal:arm64 (7.7.0+dfsg-2) ... Setting up libcommons-parent-java (43-1) ... Setting up libmbedtls12:arm64 (2.16.5-1ubuntu1) ... Setting up libavahi-common3:arm64 (0.8-3ubuntu1) ... Setting up libcommons-logging-java (1.2-2) ... Setting up m4 (1.4.18-4) ... Setting up python3 (3.8.2-0ubuntu2) ... Setting up libxcb-shm0:arm64 (1.14-2) ... Setting up libpaper-utils (1.1.28) ... Setting up clustalo (1.2.4-4build1) ... Setting up dssp (3.0.0-3build1) ... Setting up libhcrypto4-heimdal:arm64 (7.7.0+dfsg-2) ... Setting up ncbi-blast+ (2.10.1-2) ... Setting up python3-mysqldb (1.4.4-2build1) ... Setting up python3-six (1.15.0-1) ... Setting up tex-common (6.15) ... update-language: texlive-base not installed and configured, doing nothing! Setting up python3-isodate (0.6.0-2) ... Setting up python3-decorator (4.4.2-0ubuntu1) ... Setting up libwind0-heimdal:arm64 (7.7.0+dfsg-2) ... Setting up libptexenc1:arm64 (2020.20200327.54578-4build1) ... Setting up python3-pyparsing (2.4.7-1) ... Setting up python3-linecache2 (1.0.0-4ubuntu1) ... Setting up libpython3.8:arm64 (3.8.6-1) ... Setting up python3-cycler (0.10.0-3) ... Setting up python3-reportlab-accel:arm64 (3.5.47-1) ... Setting up python3-kiwisolver (1.2.0-1) ... Setting up libcroco3:arm64 (0.6.13-1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.9.0-1) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-5) ... Setting up python3-rdflib (4.2.2-5) ... /usr/lib/python3/dist-packages/rdflib/plugins/memory.py:354: SyntaxWarning: "is" with a literal. Did you mean "=="? if triple is None or triple is (None,None,None): Setting up libx11-6:arm64 (2:1.6.10-3) ... Setting up python3-dateutil (2.8.1-4) ... Setting up libtiff5:arm64 (4.1.0+git191117-2build1) ... Setting up libfontconfig1:arm64 (2.13.1-2ubuntu3) ... Setting up libjs-jquery (3.5.1+dfsg-4) ... Setting up python3-lib2to3 (3.8.5-1) ... Setting up libsm6:arm64 (2:1.2.3-1) ... Setting up libavahi-client3:arm64 (0.8-3ubuntu1) ... Setting up liblbfgsb0:arm64 (3.0+dfsg.3-9) ... Setting up python3-pkg-resources (49.3.1-2) ... Setting up automake (1:1.16.2-4ubuntu1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up python3-distutils (3.8.5-1) ... Setting up dh-python (4.20200925) ... Setting up flex (2.6.4-8) ... Setting up gettext (0.19.8.1-10build1) ... Setting up python3-renderpm:arm64 (3.5.47-1) ... Setting up python3-setuptools (49.3.1-2) ... Setting up libxpm4:arm64 (1:3.5.12-1) ... Setting up libxrender1:arm64 (1:0.9.10-1) ... Setting up libhx509-5-heimdal:arm64 (7.7.0+dfsg-2) ... Setting up preview-latex-style (11.91-2ubuntu2) ... Setting up libxext6:arm64 (2:1.3.4-0ubuntu1) ... Setting up python3-traceback2 (1.4.0-6) ... Setting up python3-all (3.8.2-0ubuntu2) ... Setting up python3-networkx (2.4-4ubuntu1) ... /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_graphml.py:933: SyntaxWarning: "is" with a literal. Did you mean "=="? assert H.nodes['n1']['special'] is 0 /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_graphml.py:935: SyntaxWarning: "is" with a literal. Did you mean "=="? assert H.edges['n0','n1',1]['special'] is 0 Setting up man-db (2.9.3-2) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up libcairo2:arm64 (1.16.0-4ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up python3-pil:arm64 (7.2.0-1) ... Setting up python3-pygments (2.3.1+dfsg-4) ... Setting up libjs-jquery-ui (1.12.1+dfsg-6) ... Setting up libpython3.8-dev:arm64 (3.8.6-1) ... Setting up libgd3:arm64 (2.3.0-2) ... Setting up python3-unittest2 (1.1.0-7) ... update-alternatives: using /usr/bin/python3-unit2 to provide /usr/bin/unit2 (unit2) in auto mode Setting up netpbm (2:10.0-15.3build1) ... Setting up libxt6:arm64 (1:1.2.0-1) ... Setting up python3-numpy (1:1.18.4-1ubuntu1) ... Setting up python3.8-dev (3.8.6-1) ... Setting up python3-reportlab (3.5.47-1) ... Setting up libcups2:arm64 (2.3.3-3ubuntu1) ... Setting up libkrb5-26-heimdal:arm64 (7.7.0+dfsg-2) ... Setting up python3-matplotlib (3.3.0-3) ... Setting up libxmu6:arm64 (2:1.1.3-0ubuntu1) ... Setting up python3-scipy (1.5.2-2) ... Setting up libpython3-dev:arm64 (3.8.2-0ubuntu2) ... Setting up libgs9:arm64 (9.52~dfsg-1ubuntu2) ... Setting up libxi6:arm64 (2:1.7.10-1) ... Setting up po-debconf (1.0.21) ... Setting up libxaw7:arm64 (2:1.0.13-1) ... Setting up ghostscript (9.52~dfsg-1ubuntu2) ... Setting up libheimntlm0-heimdal:arm64 (7.7.0+dfsg-2) ... Setting up libgssapi3-heimdal:arm64 (7.7.0+dfsg-2) ... Setting up libpython3-all-dev:arm64 (3.8.2-0ubuntu2) ... Setting up python3-dev (3.8.2-0ubuntu2) ... Setting up texlive-binaries (2020.20200327.54578-4build1) ... 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 (2020.20200804-2) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/config/pdftexconfig.tex Setting up python3-all-dev (3.8.2-0ubuntu2) ... Setting up libldap-2.4-2:arm64 (2.4.53+dfsg-1ubuntu1) ... Setting up libcurl3-gnutls:arm64 (7.68.0-1ubuntu4) ... Setting up texlive-latex-base (2020.20200804-2) ... Setting up texlive-latex-recommended (2020.20200804-2) ... Setting up hevea (2.34-2build2) ... Setting up texlive-pictures (2020.20200804-2) ... Setting up texlive-fonts-recommended (2020.20200804-2) ... Setting up libhts3:arm64 (1.10.2-5) ... Setting up libpq5:arm64 (12.4-1) ... Setting up texlive-latex-extra (2020.20200804-3) ... Setting up samtools (1.10-4) ... Setting up python3-psycopg2 (2.8.5-1) ... Setting up emboss-lib (6.6.0+dfsg-7ubuntu2) ... Setting up emboss (6.6.0+dfsg-7ubuntu2) ... Setting up dh-autoreconf (19) ... Setting up debhelper (13.2.1ubuntu1) ... Setting up sbuild-build-depends-python-biopython-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.32-0ubuntu3) ... Processing triggers for systemd (246.6-1ubuntu1) ... Processing triggers for tex-common (6.15) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. 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libsynctex2_2020.20200327.54578-4build1 libsystemd0_246.6-1ubuntu1 libtasn1-6_4.16.0-2 libteckit0_2.5.8+ds2-5ubuntu2 libtexlua53_2020.20200327.54578-4build1 libtiff5_4.1.0+git191117-2build1 libtinfo6_6.2-1 libtirpc-common_1.2.6-1build1 libtirpc-dev_1.2.6-1build1 libtirpc3_1.2.6-1build1 libtool_2.4.6-14 libtsan0_10.2.0-11ubuntu1 libubsan1_10.2.0-11ubuntu1 libuchardet0_0.0.7-1 libudev1_246.6-1ubuntu1 libunistring2_0.9.10-4 libuuid1_2.36-3ubuntu1 libwebp6_0.6.1-2 libwebpdemux2_0.6.1-2 libwebpmux3_0.6.1-2 libwind0-heimdal_7.7.0+dfsg-2 libx11-6_2:1.6.10-3 libx11-data_2:1.6.10-3 libxau6_1:1.0.9-0ubuntu1 libxaw7_2:1.0.13-1 libxcb-render0_1.14-2 libxcb-shm0_1.14-2 libxcb1_1.14-2 libxdmcp6_1:1.1.3-0ubuntu1 libxext6_2:1.3.4-0ubuntu1 libxi6_2:1.7.10-1 libxml2_2.9.10+dfsg-5build1 libxmu6_2:1.1.3-0ubuntu1 libxpm4_1:3.5.12-1 libxrender1_1:0.9.10-1 libxt6_1:1.2.0-1 libzstd1_1.4.5+dfsg-4 libzzip-0-13_0.13.62-3.2ubuntu1 linux-libc-dev_5.8.0-20.21 lockfile-progs_0.1.18 login_1:4.8.1-1ubuntu6 logsave_1.45.6-1ubuntu1 lsb-base_11.1.0ubuntu2 m4_1.4.18-4 mafft_7.471-1 make_4.3-4ubuntu1 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mime-support_3.64ubuntu1 mount_2.36-3ubuntu1 muscle_1:3.8.1551-2build1 mysql-common_5.8+1.0.5ubuntu2 ncbi-blast+_2.10.1-2 ncbi-data_6.1.20170106+dfsg1-8 ncurses-base_6.2-1 ncurses-bin_6.2-1 netpbm_2:10.0-15.3build1 node-jquery_3.5.1+dfsg-4 openssl_1.1.1f-1ubuntu4 optipng_0.7.7-1 passwd_1:4.8.1-1ubuntu6 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.30_5.30.3-4 phylip_1:3.697+dfsg-2 pinentry-curses_1.1.0-4build1 pkgbinarymangler_146 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 poppler-data_0.4.9-2 prank_0.0.170427+dfsg-2build1 preview-latex-style_11.91-2ubuntu2 probcons_1.12-12build1 procps_2:3.3.16-5ubuntu1 python-matplotlib-data_3.3.0-3 python3_3.8.2-0ubuntu2 python3-all_3.8.2-0ubuntu2 python3-all-dev_3.8.2-0ubuntu2 python3-cycler_0.10.0-3 python3-dateutil_2.8.1-4 python3-decorator_4.4.2-0ubuntu1 python3-dev_3.8.2-0ubuntu2 python3-distutils_3.8.5-1 python3-isodate_0.6.0-2 python3-kiwisolver_1.2.0-1 python3-lib2to3_3.8.5-1 python3-linecache2_1.0.0-4ubuntu1 python3-matplotlib_3.3.0-3 python3-minimal_3.8.2-0ubuntu2 python3-mysqldb_1.4.4-2build1 python3-networkx_2.4-4ubuntu1 python3-numpy_1:1.18.4-1ubuntu1 python3-pil_7.2.0-1 python3-pkg-resources_49.3.1-2 python3-psycopg2_2.8.5-1 python3-pygments_2.3.1+dfsg-4 python3-pyparsing_2.4.7-1 python3-rdflib_4.2.2-5 python3-renderpm_3.5.47-1 python3-reportlab_3.5.47-1 python3-reportlab-accel_3.5.47-1 python3-scipy_1.5.2-2 python3-setuptools_49.3.1-2 python3-six_1.15.0-1 python3-traceback2_1.4.0-6 python3-unittest2_1.1.0-7 python3.8_3.8.6-1 python3.8-dev_3.8.6-1 python3.8-minimal_3.8.6-1 readline-common_8.0-4 rpcsvc-proto_1.4.2-0ubuntu3 samtools_1.10-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-python-biopython-dummy_0.invalid.0 sed_4.7-1build1 sensible-utils_0.0.13 systemd_246.6-1ubuntu1 systemd-sysv_246.6-1ubuntu1 systemd-timesyncd_246.6-1ubuntu1 sysvinit-utils_2.96-3ubuntu1 t-coffee_13.41.0.28bdc39+dfsg-4 t1utils_1.41-4 tar_1.30+dfsg-7 tex-common_6.15 texlive-base_2020.20200804-2 texlive-binaries_2020.20200327.54578-4build1 texlive-fonts-recommended_2020.20200804-2 texlive-latex-base_2020.20200804-2 texlive-latex-extra_2020.20200804-3 texlive-latex-recommended_2020.20200804-2 texlive-pictures_2020.20200804-2 ttf-bitstream-vera_1.10-8 tzdata_2020a-0ubuntu1 ubuntu-keyring_2020.06.17.1 ucf_3.0043 util-linux_2.36-3ubuntu1 wise_2.4.1-23 wise-data_2.4.1-23 x11-common_1:7.7+19ubuntu14 xdg-utils_1.1.3-2ubuntu1 xz-utils_5.2.4-1ubuntu1 zlib1g_1:1.2.11.dfsg-2ubuntu2 zlib1g-dev_1:1.2.11.dfsg-2ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Fri Dec 20 19:02:29 2019 UTC gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./python-biopython_1.76+dfsg-1.dsc dpkg-source: info: extracting python-biopython in /<>/python-biopython-1.76+dfsg dpkg-source: info: unpacking python-biopython_1.76+dfsg.orig.tar.xz dpkg-source: info: unpacking python-biopython_1.76+dfsg-1.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 exclude_docstring_tests.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym 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-20043692 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-20043692 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-20043692 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package python-biopython dpkg-buildpackage: info: source version 1.76+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/python-biopython-1.76+dfsg' dh_auto_clean pybuild --clean -i python{version} -p 3.8 I: pybuild base:217: python3.8 setup.py clean running clean removing '/<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build' (and everything under it) 'build/bdist.linux-arm64' does not exist -- can't clean it 'build/scripts-3.8' does not exist -- can't clean it rm -rf .pybuild/ find . -name \*.pyc -exec rm {} \; cd Doc && make distclean make[2]: Entering directory '/<>/python-biopython-1.76+dfsg/Doc' ( for f in ; do make clean -C $f ; done ) rm -f Tutorial.aux rm -f Tutorial.toc rm -f Tutorial.log rm -f Tutorial.out rm -f Tutorial.haux rm -f Tutorial.htoc rm -f biopdb_faq.aux rm -f biopdb_faq.log rm -f biopdb_faq.out rm -f Tutorial/*.aux ( for f in ; do make distclean -C $f ; done ) rm -f biopdb_faq.pdf rm -f Tutorial.pdf rm -f Tutorial.html rm -f Tutorial.txt rm -f *_motif.gif #output from hacha make[2]: Leaving directory '/<>/python-biopython-1.76+dfsg/Doc' rm -f Doc/install/Installation.pdf rm -f Doc/install/Installation.txt rm -f Doc/install/Installation.html rm -f Doc/Tutorial.pdf Doc/biopdb_faq.pdf rm -f Doc/Tutorial/*.aux rm -rf biopython.egg-info rm -rf .pybuild if [ -d Tests_avoid ] ; then \ mv Tests_avoid/* Tests ; \ rmdir Tests_avoid ; \ fi rm -rf debian/tmp_tests make[1]: Leaving directory '/<>/python-biopython-1.76+dfsg' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/python3-biopython.substvars debian/python-biopython-doc.substvars debian/python3-biopython-sql.substvars debian/files rm -fr -- debian/python3-biopython/ debian/tmp/ debian/python-biopython-doc/ debian/python3-biopython-sql/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules build-arch dh build-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 3.8 I: pybuild base:217: python3.8 setup.py config running config debian/rules override_dh_auto_build make[1]: Entering directory '/<>/python-biopython-1.76+dfsg' dh_auto_build pybuild --build -i python{version} -p 3.8 I: pybuild base:217: /usr/bin/python3 setup.py build running build running build_py creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/_utils.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/kNN.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/bgzf.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/pairwise2.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/SeqRecord.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/SeqFeature.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/Seq.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/File.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/LogisticRegression.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/Index.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/NaiveBayes.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/MarkovModel.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/MaxEntropy.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/triefind.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align copying Bio/Align/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align copying Bio/Align/AlignInfo.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/Applications copying Bio/Align/Applications/_ClustalOmega.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/Applications copying Bio/Align/Applications/_Clustalw.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/Applications copying Bio/Align/Applications/_Probcons.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/Applications copying Bio/Align/Applications/_Dialign.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/Applications copying Bio/Align/Applications/_Muscle.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/Applications copying Bio/Align/Applications/_Prank.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/Applications copying Bio/Align/Applications/_TCoffee.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/Applications copying Bio/Align/Applications/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/Applications copying Bio/Align/Applications/_Mafft.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/Applications copying Bio/Align/Applications/_MSAProbs.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/Applications creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/AlignIO copying Bio/AlignIO/PhylipIO.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/AlignIO copying Bio/AlignIO/EmbossIO.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/AlignIO copying Bio/AlignIO/MauveIO.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/AlignIO copying Bio/AlignIO/NexusIO.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/AlignIO copying Bio/AlignIO/StockholmIO.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/AlignIO copying Bio/AlignIO/MsfIO.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/AlignIO copying Bio/AlignIO/FastaIO.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/AlignIO copying Bio/AlignIO/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/AlignIO copying Bio/AlignIO/ClustalIO.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/AlignIO copying Bio/AlignIO/Interfaces.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/AlignIO copying Bio/AlignIO/MafIO.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/AlignIO creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Alphabet copying Bio/Alphabet/Reduced.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Alphabet copying Bio/Alphabet/IUPAC.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Alphabet copying Bio/Alphabet/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Alphabet creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Application copying Bio/Application/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Application creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Blast copying Bio/Blast/NCBIWWW.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Blast copying Bio/Blast/Applications.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Blast copying Bio/Blast/ParseBlastTable.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Blast copying Bio/Blast/Record.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Blast copying Bio/Blast/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Blast copying Bio/Blast/NCBIXML.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Blast creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/CAPS copying Bio/CAPS/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/CAPS creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/codonalign copying Bio/codonalign/codonseq.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/codonalign copying Bio/codonalign/chisq.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/codonalign copying Bio/codonalign/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/codonalign copying Bio/codonalign/codonalphabet.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/codonalign copying Bio/codonalign/codonalignment.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/codonalign creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Compass copying Bio/Compass/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Compass creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Crystal copying Bio/Crystal/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Crystal creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Data copying Bio/Data/SCOPData.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Data copying Bio/Data/CodonTable.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Data copying Bio/Data/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Data copying Bio/Data/IUPACData.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Data creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Emboss copying Bio/Emboss/Primer3.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Emboss copying Bio/Emboss/Applications.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Emboss copying Bio/Emboss/PrimerSearch.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Emboss copying Bio/Emboss/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Emboss creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez copying Bio/Entrez/Parser.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez copying Bio/Entrez/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/ExPASy copying Bio/ExPASy/Prosite.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/ExPASy copying Bio/ExPASy/cellosaurus.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/ExPASy copying Bio/ExPASy/ScanProsite.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/ExPASy copying Bio/ExPASy/Prodoc.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/ExPASy copying Bio/ExPASy/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/ExPASy copying Bio/ExPASy/Enzyme.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/ExPASy creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/FSSP copying Bio/FSSP/fssp_rec.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/FSSP copying Bio/FSSP/FSSPTools.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/FSSP copying Bio/FSSP/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/FSSP creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/GenBank copying Bio/GenBank/Record.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/GenBank copying Bio/GenBank/Scanner.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/GenBank copying Bio/GenBank/utils.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/GenBank copying Bio/GenBank/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/GenBank creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Geo copying Bio/Geo/Record.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Geo copying Bio/Geo/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Geo creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics copying Bio/Graphics/BasicChromosome.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics copying Bio/Graphics/Comparative.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics copying Bio/Graphics/ColorSpiral.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics copying Bio/Graphics/DisplayRepresentation.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics copying Bio/Graphics/KGML_vis.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics copying Bio/Graphics/Distribution.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics copying Bio/Graphics/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Track.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Graph.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Diagram.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Colors.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_GraphSet.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CrossLink.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Feature.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Graphics/GenomeDiagram creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/HMM copying Bio/HMM/DynamicProgramming.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/HMM copying Bio/HMM/Trainer.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/HMM copying Bio/HMM/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/HMM copying Bio/HMM/MarkovModel.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/HMM copying Bio/HMM/Utilities.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/HMM creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/KEGG copying Bio/KEGG/REST.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/KEGG copying Bio/KEGG/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/KEGG creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/KEGG/Compound copying Bio/KEGG/Compound/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/KEGG/Compound creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/KEGG/Enzyme copying Bio/KEGG/Enzyme/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/KEGG/Enzyme creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/KEGG/Gene copying Bio/KEGG/Gene/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/KEGG/Gene creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/KEGG/Map copying Bio/KEGG/Map/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/KEGG/Map creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB/mmtf copying Bio/PDB/mmtf/DefaultParser.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB/mmtf copying Bio/PDB/mmtf/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB/mmtf copying Bio/PDB/mmtf/mmtfio.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB/mmtf creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_pathway.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/KEGG/KGML copying Bio/KEGG/KGML/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_parser.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/KEGG/KGML creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Medline copying Bio/Medline/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Medline creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs copying Bio/motifs/xms.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs copying Bio/motifs/minimal.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs copying Bio/motifs/thresholds.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs copying Bio/motifs/pfm.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs copying Bio/motifs/alignace.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs copying Bio/motifs/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs copying Bio/motifs/meme.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs copying Bio/motifs/clusterbuster.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs copying Bio/motifs/transfac.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs copying Bio/motifs/mast.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs copying Bio/motifs/matrix.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs/applications copying Bio/motifs/applications/_xxmotif.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs/applications copying Bio/motifs/applications/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs/applications creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs/jaspar copying Bio/motifs/jaspar/db.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs/jaspar copying Bio/motifs/jaspar/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs/jaspar creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Nexus copying Bio/Nexus/StandardData.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Nexus copying Bio/Nexus/Nodes.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Nexus copying Bio/Nexus/Nexus.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Nexus copying Bio/Nexus/Trees.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Nexus copying Bio/Nexus/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Nexus creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/NMR copying Bio/NMR/NOEtools.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/NMR copying Bio/NMR/xpktools.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/NMR copying Bio/NMR/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/NMR creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Pathway copying Bio/Pathway/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Pathway creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Pathway/Rep copying Bio/Pathway/Rep/MultiGraph.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Pathway/Rep copying Bio/Pathway/Rep/Graph.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Pathway/Rep copying Bio/Pathway/Rep/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Pathway/Rep copying Bio/PDB/NACCESS.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/HSExposure.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/Chain.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/Structure.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/Residue.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/Superimposer.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/ResidueDepth.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/PDBParser.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/DSSP.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/StructureAlignment.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/Polypeptide.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/NeighborSearch.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/Model.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/parse_pdb_header.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/FragmentMapper.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/StructureBuilder.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/Dice.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/MMCIFParser.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/Atom.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/mmcifio.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/PDBIO.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/Entity.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/PDBList.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/vectors.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/MMCIF2Dict.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/PSEA.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/Selection.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/AbstractPropertyMap.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/PDBExceptions.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PopGen copying Bio/PopGen/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PopGen creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/Utils.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/FileParser.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/EasyController.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/Controller.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/LargeFileParser.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PopGen/GenePop creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Restriction copying Bio/Restriction/PrintFormat.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Restriction copying Bio/Restriction/Restriction_Dictionary.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Restriction copying Bio/Restriction/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Restriction copying Bio/Restriction/Restriction.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Restriction creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SCOP copying Bio/SCOP/Des.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SCOP copying Bio/SCOP/Dom.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SCOP copying Bio/SCOP/Residues.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SCOP copying Bio/SCOP/Raf.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SCOP copying Bio/SCOP/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SCOP copying Bio/SCOP/Cla.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SCOP copying Bio/SCOP/Hie.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SCOP creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO copying Bio/SearchIO/_utils.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO copying Bio/SearchIO/_index.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO copying Bio/SearchIO/BlatIO.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO copying Bio/SearchIO/FastaIO.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO copying Bio/SearchIO/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/_legacy copying Bio/SearchIO/_legacy/ParserSupport.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/_legacy copying Bio/SearchIO/_legacy/NCBIStandalone.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/_legacy copying Bio/SearchIO/_legacy/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/_legacy creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/hsp.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/query.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/_base.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/hit.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/_model creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_xml.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_tab.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_text.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/BlastIO creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/HHsuiteIO copying Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/HHsuiteIO copying Bio/SearchIO/HHsuiteIO/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/HHsuiteIO creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/_base.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_text.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_tab.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/HmmerIO creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/_base.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_text.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/ExonerateIO creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/interproscan_xml.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SearchIO/InterproscanIO creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/GckIO.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/TabIO.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/SeqXmlIO.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/_index.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/PhdIO.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/PirIO.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/_convert.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/InsdcIO.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/SnapGeneIO.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/FastaIO.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/XdnaIO.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/NibIO.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/AceIO.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/IgIO.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/Interfaces.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/PdbIO.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/QualityIO.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/UniprotIO.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/SffIO.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/SwissIO.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO copying Bio/SeqIO/AbiIO.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqIO creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqUtils copying Bio/SeqUtils/lcc.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqUtils copying Bio/SeqUtils/CodonUsageIndices.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqUtils copying Bio/SeqUtils/ProtParam.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqUtils copying Bio/SeqUtils/CheckSum.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqUtils copying Bio/SeqUtils/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqUtils copying Bio/SeqUtils/MeltingTemp.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqUtils copying Bio/SeqUtils/ProtParamData.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqUtils copying Bio/SeqUtils/CodonUsage.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqUtils copying Bio/SeqUtils/IsoelectricPoint.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SeqUtils creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Sequencing copying Bio/Sequencing/Ace.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Sequencing copying Bio/Sequencing/Phd.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Sequencing copying Bio/Sequencing/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Sequencing creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_samtools.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_bwa.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_Novoalign.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Sequencing/Applications creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Statistics copying Bio/Statistics/lowess.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Statistics copying Bio/Statistics/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Statistics creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SubsMat copying Bio/SubsMat/FreqTable.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SubsMat copying Bio/SubsMat/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SubsMat copying Bio/SubsMat/MatrixInfo.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SubsMat creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SVDSuperimposer copying Bio/SVDSuperimposer/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SVDSuperimposer creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB/QCPSuperimposer copying Bio/PDB/QCPSuperimposer/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB/QCPSuperimposer creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SwissProt copying Bio/SwissProt/KeyWList.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SwissProt copying Bio/SwissProt/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/SwissProt creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/TogoWS copying Bio/TogoWS/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/TogoWS creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo copying Bio/Phylo/_utils.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo copying Bio/Phylo/Newick.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo copying Bio/Phylo/TreeConstruction.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo copying Bio/Phylo/NeXML.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo copying Bio/Phylo/PhyloXMLIO.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo copying Bio/Phylo/_cdao_owl.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo copying Bio/Phylo/Consensus.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo copying Bio/Phylo/NeXMLIO.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo copying Bio/Phylo/PhyloXML.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo copying Bio/Phylo/NexusIO.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo copying Bio/Phylo/BaseTree.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo copying Bio/Phylo/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo copying Bio/Phylo/CDAO.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo copying Bio/Phylo/NewickIO.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo copying Bio/Phylo/CDAOIO.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo copying Bio/Phylo/_io.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Fasttree.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Phyml.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Raxml.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo/Applications creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/chi2.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_paml.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_baseml.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/yn00.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_yn00.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/codeml.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_codeml.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/baseml.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Phylo/PAML creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/UniGene copying Bio/UniGene/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/UniGene creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/UniProt copying Bio/UniProt/GOA.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/UniProt copying Bio/UniProt/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/UniProt creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Wise copying Bio/Wise/psw.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Wise copying Bio/Wise/dnal.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Wise copying Bio/Wise/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Wise creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/_py3k copying Bio/_py3k/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/_py3k creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/BioSQL copying BioSQL/BioSeqDatabase.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/BioSQL copying BioSQL/BioSeq.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/BioSQL copying BioSQL/Loader.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/BioSQL copying BioSQL/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/BioSQL copying BioSQL/DBUtils.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/BioSQL creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Affy copying Bio/Affy/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Affy copying Bio/Affy/CelFile.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Affy creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/substitution_matrices copying Bio/Align/substitution_matrices/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/substitution_matrices creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Cluster copying Bio/Cluster/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Cluster creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/KDTree copying Bio/KDTree/KDTree.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/KDTree copying Bio/KDTree/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/KDTree creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/phenotype copying Bio/phenotype/__init__.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/phenotype copying Bio/phenotype/pm_fitting.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/phenotype copying Bio/phenotype/phen_micro.py -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/phenotype 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 writing manifest file 'biopython.egg-info/SOURCES.txt' copying Bio/cpairwise2module.c -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/trie.c -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/trie.h -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/triemodule.c -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio copying Bio/Align/_aligners.c -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Gene.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_General.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_General.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medlars.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medline.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mim.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mime.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Organism.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Project.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Protein.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Pub.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PubMed.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_RNA.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Remap.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Rsite.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqres.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqset.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Sequence.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Submit.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Systems.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TSeq.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TxInit.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Variation.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_all.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NSE.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NSE.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/OMSSA.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/OMSSA.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PDB_General.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PDB_General.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PIR_General.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PIR_General.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PRF_General.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PRF_General.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/SP_General.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/SP_General.mod.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/XHTMLtablesetup.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivearticle.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-classes.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-mixes.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-models.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-modules.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/articlemeta.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/backmatter.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_100301.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_110101.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_120101.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_130101.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_140101.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_150101.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/chars.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/common.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/default-classes.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/default-mixes.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/display.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eInfo_020511.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eLink_090910.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eLink_101123.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/ePost_020511.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSearch_020511.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSpell.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSummary_041029.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/egquery.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/einfo.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/elink_020122.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esearch.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esummary-v1.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/format.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/htmltable.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsa.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsb.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsc.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsn.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamso.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsr.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isobox.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isocyr1.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isocyr2.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isodia.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk1.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk2.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk3.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk4.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isolat1.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isolat2.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomfrk.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomopf.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomscr.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isonum.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isopub.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isotech.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/journalmeta.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/link.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/list.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/math.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml-in-pubmed.mod -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml2.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml3-qname1.mod -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml3.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathmlsetup.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mmlalias.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mmlextra.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/modules.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_011101.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_080101.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_090101.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_011101.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_080101.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_090101.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_080101.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_100101.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/notat.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/para.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/phrase.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pmc-1.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_020114.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_080101.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_090101.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100101.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100301.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_110101.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_120101.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130101.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130501.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_140101.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_150101.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180101.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180601.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_190101.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/references.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/section.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/taxon.dtd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xmlspecchars.ent -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/DTDs creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/XSDs copying Bio/Entrez/XSDs/IPGReportSet.xsd -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Entrez/XSDs copying Bio/motifs/_pwm.c -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs copying Bio/Nexus/cnexus.c -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Nexus copying Bio/PDB/kdtrees.c -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB copying Bio/PDB/QCPSuperimposer/qcprotmodule.c -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB/QCPSuperimposer creating /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER22 -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER6 -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER74 -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM45 -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM50 -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM62 -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM80 -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM90 -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/DAYHOFF -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/FENG -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/GENETIC -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/GONNET1992 -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/JOHNSON -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/JONES -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/LEVIN -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MCLACHLAN -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MDM78 -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/NUC.4.4 -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM250 -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM30 -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM70 -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/RAO -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/RISLER -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/SCHNEIDER -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/STR -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/substitution_matrices/data copying Bio/Cluster/cluster.c -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Cluster copying Bio/Cluster/cluster.h -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Cluster copying Bio/Cluster/clustermodule.c -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Cluster copying Bio/KDTree/KDTree.c -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/KDTree copying Bio/KDTree/KDTree.h -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/KDTree copying Bio/KDTree/KDTreemodule.c -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/KDTree copying Bio/KDTree/Neighbor.h -> /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/KDTree running build_ext building 'Bio.Align._aligners' extension creating build creating build/temp.linux-arm64-3.8 creating build/temp.linux-arm64-3.8/Bio creating build/temp.linux-arm64-3.8/Bio/Align aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.76+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.8 -c Bio/Align/_aligners.c -o build/temp.linux-arm64-3.8/Bio/Align/_aligners.o aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.76+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.8/Bio/Align/_aligners.o -o /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Align/_aligners.cpython-38-aarch64-linux-gnu.so building 'Bio.cpairwise2' extension aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.76+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.8 -c Bio/cpairwise2module.c -o build/temp.linux-arm64-3.8/Bio/cpairwise2module.o aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.76+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.8/Bio/cpairwise2module.o -o /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/cpairwise2.cpython-38-aarch64-linux-gnu.so building 'Bio.Nexus.cnexus' extension creating build/temp.linux-arm64-3.8/Bio/Nexus aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.76+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.8 -c Bio/Nexus/cnexus.c -o build/temp.linux-arm64-3.8/Bio/Nexus/cnexus.o aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.76+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.8/Bio/Nexus/cnexus.o -o /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Nexus/cnexus.cpython-38-aarch64-linux-gnu.so building 'Bio.PDB.QCPSuperimposer.qcprotmodule' extension creating build/temp.linux-arm64-3.8/Bio/PDB creating build/temp.linux-arm64-3.8/Bio/PDB/QCPSuperimposer aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.76+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.8 -c Bio/PDB/QCPSuperimposer/qcprotmodule.c -o build/temp.linux-arm64-3.8/Bio/PDB/QCPSuperimposer/qcprotmodule.o aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.76+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.8/Bio/PDB/QCPSuperimposer/qcprotmodule.o -o /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-38-aarch64-linux-gnu.so building 'Bio.motifs._pwm' extension creating build/temp.linux-arm64-3.8/Bio/motifs aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.76+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.8 -c Bio/motifs/_pwm.c -o build/temp.linux-arm64-3.8/Bio/motifs/_pwm.o aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.76+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.8/Bio/motifs/_pwm.o -o /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/motifs/_pwm.cpython-38-aarch64-linux-gnu.so building 'Bio.Cluster._cluster' extension creating build/temp.linux-arm64-3.8/Bio/Cluster aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.76+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.8 -c Bio/Cluster/cluster.c -o build/temp.linux-arm64-3.8/Bio/Cluster/cluster.o aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.76+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.8 -c Bio/Cluster/clustermodule.c -o build/temp.linux-arm64-3.8/Bio/Cluster/clustermodule.o aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.76+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.8/Bio/Cluster/cluster.o build/temp.linux-arm64-3.8/Bio/Cluster/clustermodule.o -o /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Cluster/_cluster.cpython-38-aarch64-linux-gnu.so building 'Bio.PDB.kdtrees' extension aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.76+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.8 -c Bio/PDB/kdtrees.c -o build/temp.linux-arm64-3.8/Bio/PDB/kdtrees.o aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.76+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.8/Bio/PDB/kdtrees.o -o /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB/kdtrees.cpython-38-aarch64-linux-gnu.so building 'Bio.KDTree._CKDTree' extension creating build/temp.linux-arm64-3.8/Bio/KDTree aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.76+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.8 -c Bio/KDTree/KDTree.c -o build/temp.linux-arm64-3.8/Bio/KDTree/KDTree.o aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.76+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.8 -c Bio/KDTree/KDTreemodule.c -o build/temp.linux-arm64-3.8/Bio/KDTree/KDTreemodule.o aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.76+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.8/Bio/KDTree/KDTree.o build/temp.linux-arm64-3.8/Bio/KDTree/KDTreemodule.o -o /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/KDTree/_CKDTree.cpython-38-aarch64-linux-gnu.so building 'Bio.trie' extension aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.76+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -IBio -I/usr/include/python3.8 -c Bio/triemodule.c -o build/temp.linux-arm64-3.8/Bio/triemodule.o aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.76+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -IBio -I/usr/include/python3.8 -c Bio/trie.c -o build/temp.linux-arm64-3.8/Bio/trie.o In file included from /usr/include/string.h:519, from Bio/trie.c:17: In function ‘strncat’, inlined from ‘_with_prefix_helper.constprop’ at Bio/trie.c:595:6: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:137:10: warning: ‘__builtin___strncat_chk’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 137 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Bio/trie.c: In function ‘_with_prefix_helper.constprop’: Bio/trie.c:561:14: note: length computed here 561 | suffixlen = strlen(suffix); | ^~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.76+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.8/Bio/triemodule.o build/temp.linux-arm64-3.8/Bio/trie.o -o /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/trie.cpython-38-aarch64-linux-gnu.so cd Doc && make make[2]: Entering directory '/<>/python-biopython-1.76+dfsg/Doc' hevea -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:218: Warning: Undefined label: 'sec:seq-comparison' ./Tutorial/chapter_introduction.tex:228: 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:35: Warning: Undefined label: 'chapter:seq_objects' ./Tutorial/chapter_quick_start.tex:49: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_quick_start.tex:69: Warning: Undefined label: 'sec:sequence-parsing' ./Tutorial/chapter_quick_start.tex:69: Warning: Undefined label: 'chapter:entrez' ./Tutorial/chapter_quick_start.tex:69: Warning: Undefined label: 'chapter:uniprot' ./Tutorial/chapter_quick_start.tex:69: Warning: Undefined label: 'sec:align_clustal' ./Tutorial/chapter_quick_start.tex:76: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_quick_start.tex:83: Warning: Undefined label: 'sec:connecting-with-biological-databases' ./Tutorial/chapter_quick_start.tex:151: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_quick_start.tex:151: Warning: Undefined label: 'chapter:align' ./Tutorial/chapter_quick_start.tex:156: Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_quick_start.tex:164: Warning: Undefined label: 'chapter:entrez' ./Tutorial/chapter_quick_start.tex:165: Warning: Undefined label: 'chapter:uniprot' ./Tutorial/chapter_quick_start.tex:175: 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:137: Warning: Undefined label: 'sec:mutable-seq' ./Tutorial/chapter_seq_objects.tex:210: Warning: Undefined label: 'sec:SeqRecord-format' ./Tutorial/chapter_seq_objects.tex:212: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_objects.tex:379: Warning: Undefined label: 'sec:SeqIO-reverse-complement' ./Tutorial/chapter_seq_objects.tex:456: Warning: Undefined label: 'sec:seq-module-functions' ./Tutorial/chapter_seq_objects.tex:576: Warning: Undefined label: 'sec:SeqIO-translate' ./Tutorial/chapter_seq_objects.tex:582: Warning: Undefined label: 'sec:seq-module-functions' ./Tutorial/chapter_seq_objects.tex:734: Warning: Undefined label: 'sec:seq-to-string' ./Tutorial/chapter_seq_objects.tex:827: Warning: Undefined label: 'sec:seq-to-string' ./Tutorial/chapter_seq_objects.tex:888: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_annot.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined label: 'chapter:seq_objects' ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_annot.tex:21: Warning: Undefined label: 'chapter:seq_objects' ./Tutorial/chapter_seq_annot.tex:21: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_annot.tex:34: Warning: Undefined label: 'sec:FASTQ-filtering-example' ./Tutorial/chapter_seq_annot.tex:38: Warning: Undefined label: 'sec:seq_features' ./Tutorial/chapter_seq_annot.tex:48: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_annot.tex:131: Warning: Undefined label: 'chapter:quick_start' ./Tutorial/chapter_seq_annot.tex:133: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_annot.tex:158: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_annot.tex:217: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_annot.tex:230: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_annot.tex:280: Warning: Undefined label: 'sec:seq_features' ./Tutorial/chapter_seq_annot.tex:283: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_annot.tex:289: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:297: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:529: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:633: Warning: Undefined label: 'sec:seq-comparison' ./Tutorial/chapter_seq_annot.tex:641: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:682: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_annot.tex:685: Warning: Undefined label: 'sec:Bio.SeqIO-and-StringIO' ./Tutorial/chapter_seq_annot.tex:841: Warning: Undefined label: 'sec:SeqRecord-format' ./Tutorial/chapter_seq_annot.tex:849: Warning: Undefined label: 'sec:FASTQ-slicing-off-primer' ./Tutorial/chapter_seq_annot.tex:850: 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citation: 'dehoon2004' ./Tutorial/chapter_cluster.tex:30: Warning: Undefined citation: 'lecuyer1988' ./Tutorial/chapter_cluster.tex:30: Warning: Undefined citation: 'kachitvichyanukul1988' ./Tutorial/chapter_cluster.tex:154: Warning: Undefined citation: 'snedecor1989' ./Tutorial/chapter_cluster.tex:183: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:277: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:345: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:555: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:599: Warning: Undefined citation: 'kohonen1997' ./Tutorial/chapter_cluster.tex:599: Warning: Undefined citation: 'tamayo1999' ./Tutorial/chapter_cluster.tex:646: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:659: Warning: Undefined citation: 'yeung2001' ./Tutorial/chapter_cluster.tex:667: Warning: Undefined citation: 'golub1971' ./Tutorial/chapter_cluster.tex:806: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:809: Warning: Undefined label: 'sec:distancematrix' ./Tutorial/chapter_cluster.tex:827: Warning: Undefined label: 'sec:clustercentroids' ./Tutorial/chapter_cluster.tex:850: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:875: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:904: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:926: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:958: Warning: Undefined citation: 'hihara2001' ./Tutorial/chapter_learning.tex:40: Warning: Undefined label: 'eq:OP' ./Tutorial/chapter_learning.tex:40: Warning: Undefined label: 'eq:NOP' ./Tutorial/chapter_learning.tex:75: Warning: Undefined label: 'table:training' ./Tutorial/chapter_learning.tex:211: Warning: Undefined label: 'eq:OP' 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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' 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./Tutorial/chapter_graphics.tex:752: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:752: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:759: Warning: Undefined citation: 'proux2002' ./Tutorial/chapter_graphics.tex:1012: Warning: Undefined citation: 'jupe2012' ./Tutorial/chapter_phenotype.tex:229: Warning: Optional argument to \item in itemize environment ./Tutorial/chapter_phenotype.tex:231: Warning: Optional argument to \item in itemize environment ./Tutorial/chapter_phenotype.tex:233: Warning: Optional argument to \item in itemize environment ./Tutorial/chapter_cookbook.tex:22: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_cookbook.tex:58: Warning: Undefined label: 'sec:low-level-fasta-fastq' ./Tutorial/chapter_cookbook.tex:146: Warning: Undefined label: 'sec:Bio.SeqIO-and-StringIO' ./Tutorial/chapter_cookbook.tex:200: Warning: Undefined label: 'sec:translation' ./Tutorial/chapter_cookbook.tex:205: Warning: Undefined 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Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_contributing.tex:38: Warning: '_' occurring outside math mode ./Tutorial/chapter_contributing.tex:85: Warning: Undefined label: 'chapter:testing' ./Tutorial/chapter_contributing.tex:101: Warning: Undefined label: 'chapter:testing' ./Tutorial/chapter_appendix.tex:91: Warning: Undefined label: 'sec:SeqIO_compressed' HeVeA Warning: Label(s) may have changed. Rerun me to get cross-references right. Run, run, again... Exclude comment 'comment' ./Tutorial/chapter_quick_start.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_objects.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_annot.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_annot.tex:283: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:332: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:415: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:427: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:427: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:521: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:521: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:521: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:575: Warning: '_' occurring outside math mode ./Tutorial/chapter_align.tex:907: Warning: '_' occurring 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outside math mode ./Tutorial/chapter_graphics.tex:591: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:591: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:752: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:752: Warning: '_' occurring outside math mode ./Tutorial/chapter_phenotype.tex:229: Warning: Optional argument to \item in itemize environment ./Tutorial/chapter_phenotype.tex:231: Warning: Optional argument to \item in itemize environment ./Tutorial/chapter_phenotype.tex:233: Warning: Optional argument to \item in itemize environment ./Tutorial/chapter_cookbook.tex:1418: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1541: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1541: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1636: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1645: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1645: Warning: '_' occurring outside math mode ./Tutorial/chapter_advanced.tex:223: Warning: '_' occurring outside math mode ./Tutorial/chapter_contributing.tex:38: Warning: '_' occurring outside math mode Fixpoint reached in 2 step(s) hevea -fix -text Tutorial.tex Exclude comment 'comment' ./Tutorial.tex:73: Warning: tt_mode is an empty style ./Tutorial.tex:100: Warning: Application of '\'' on 'n' failed ./Tutorial.htoc:355: Warning: Application of '\"' on 'i' failed ./Tutorial/chapter_quick_start.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:78: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:78: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:88: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:124: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_objects.tex:1: Warning: line too long 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outside math mode ./Tutorial/chapter_cookbook.tex:1645: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1782: Warning: '_' occurring outside math mode ./Tutorial/chapter_testing.tex:1: Warning: line too long ./Tutorial/chapter_testing.tex:1: Warning: line too long ./Tutorial/chapter_testing.tex:1: Warning: line too long ./Tutorial/chapter_testing.tex:1: Warning: line too long ./Tutorial/chapter_testing.tex:1: Warning: line too long ./Tutorial/chapter_testing.tex:1: Warning: line too long ./Tutorial/chapter_testing.tex:1: Warning: line too long ./Tutorial/chapter_testing.tex:222: Warning: line too long ./Tutorial/chapter_testing.tex:275: Warning: line too long ./Tutorial/chapter_advanced.tex:223: Warning: '_' occurring outside math mode ./Tutorial/chapter_contributing.tex:11: Warning: '_' occurring outside math mode ./Tutorial/chapter_contributing.tex:38: Warning: '_' occurring outside math mode ./Tutorial/chapter_contributing.tex:80: Warning: '_' occurring outside math mode ./Tutorial.tex:127: Warning: line too long ./Tutorial.tex:138: Warning: Application of '\'' on 'e' failed ./Tutorial.tex:138: Warning: Application of '\'' on 'o' failed ./Tutorial.tex:142: Warning: Application of '\"' on 'u' failed ./Tutorial.tex:213: Warning: Application of '\"' on 'o' failed ./Tutorial.tex:213: 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:539: 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: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:218: Warning: Undefined label: 'sec:seq-comparison' ./Tutorial/chapter_introduction.tex:228: 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:35: Warning: Undefined label: 'chapter:seq_objects' ./Tutorial/chapter_quick_start.tex:49: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_quick_start.tex:69: Warning: Undefined label: 'sec:sequence-parsing' ./Tutorial/chapter_quick_start.tex:69: Warning: Undefined label: 'chapter:entrez' ./Tutorial/chapter_quick_start.tex:69: Warning: Undefined label: 'chapter:uniprot' ./Tutorial/chapter_quick_start.tex:69: Warning: Undefined label: 'sec:align_clustal' ./Tutorial/chapter_quick_start.tex:76: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_quick_start.tex:78: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:78: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:83: Warning: Undefined label: 'sec:connecting-with-biological-databases' ./Tutorial/chapter_quick_start.tex:88: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:124: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:151: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_quick_start.tex:151: Warning: Undefined label: 'chapter:align' ./Tutorial/chapter_quick_start.tex:156: Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_quick_start.tex:164: Warning: Undefined label: 'chapter:entrez' ./Tutorial/chapter_quick_start.tex:165: Warning: Undefined label: 'chapter:uniprot' ./Tutorial/chapter_quick_start.tex:175: 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:5: Warning: Undefined label: 'chapter:seq_annot' ./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_objects.tex:137: Warning: Undefined label: 'sec:mutable-seq' ./Tutorial/chapter_seq_objects.tex:210: Warning: Undefined label: 'sec:SeqRecord-format' ./Tutorial/chapter_seq_objects.tex:212: Warning: Undefined label: 'chapter:seqio' ./Tutorial/chapter_seq_objects.tex:379: Warning: Undefined label: 'sec:SeqIO-reverse-complement' ./Tutorial/chapter_seq_objects.tex:397: Warning: Command not found: \downarrow ./Tutorial/chapter_seq_objects.tex:456: Warning: Undefined label: 'sec:seq-module-functions' ./Tutorial/chapter_seq_objects.tex:576: 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'altschul1990' ./Tutorial/chapter_align.tex:1895: Warning: Undefined label: 'table:align-meta-attributes' ./Tutorial/chapter_align.tex:1941: Warning: overfull line in array : array too wide ./Tutorial/chapter_align.tex:1941: Warning: line too long ./Tutorial/chapter_align.tex:1941: Warning: line too long ./Tutorial/chapter_align.tex:1941: Warning: line too long ./Tutorial/chapter_align.tex:1985: Warning: Undefined label: 'sec:pairwise-examples' ./Tutorial/chapter_align.tex:2120: Warning: Undefined citation: 'kent2002' ./Tutorial/chapter_align.tex:2125: Warning: line too long ./Tutorial/chapter_align.tex:2233: Warning: line too long ./Tutorial/chapter_align.tex:2234: Warning: line too long ./Tutorial/chapter_align.tex:2235: Warning: line too long ./Tutorial/chapter_align.tex:2265: Warning: line too long ./Tutorial/chapter_align.tex:2266: Warning: line too long ./Tutorial/chapter_align.tex:2267: Warning: line too long ./Tutorial/chapter_align.tex:2301: Warning: Undefined citation: 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There-fore the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write() LaTeX Warning: Reference `sec:SeqIO-conversion' on page 73 undefined on input l ine 455. Overfull \hbox (39.68698pt too wide) in paragraph at lines 453--458 [][]\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/F67EB3EFC88C7F65142EC6767FF0AFE814FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/BB07BFEAEC0855950DABA0EE61AB192B14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/F94237F1B0C3E6DC309DEB6BB87A63E014FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/8FD10ACD641F4427B35E96F33B44479F0C640781732628151051B15D85C 9070A.pygtex [73]) (./_minted-Tutorial/8F45D3C2413A4CA1D91A89D61294165814FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/7E530BB128C8AE6BCF7BCE91DD4AF1890C640781732628151051B15D85C 9070A.pygtex) (./_minted-Tutorial/526DE630895A1CFB3DEA37685B34B1BA14FA033DCB1376922271CBD58A8 A4A36.pygtex) [74] (./_minted-Tutorial/C02EB78C9555A4FEE4954D77162ACF990C640781732628151051B15D85C 9070A.pygtex) (./_minted-Tutorial/F825D7C594903CE498C70B50088C497114FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/CB14E2060AF38515C129AB5808537F1614FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/E78F5A80C222A5B2777910FED4F43F560C640781732628151051B15D85C 9070A.pygtex [75]) (./_minted-Tutorial/9997F06B70C62809223AE6CDAE409E2F14FA033DCB1376922271CBD58A8 A4A36.pygtex) LaTeX Warning: Reference `sec:SeqRecord-format' on page 76 undefined on input l ine 639. Overfull \hbox (16.49278pt too wide) in paragraph at lines 641--644 []\OT1/cmr/m/n/10 Internally the [][]\OT1/cmtt/m/n/10 format() []\OT1/cmr/m/n/1 0 method is us-ing the [][]\OT1/cmtt/m/n/10 StringIO []\OT1/cmr/m/n/10 string b ased han-dle and call-ing [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write()[]\OT1/cmr/m/ n/10 . 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(./_minted-Tutorial/B0688D31DEF0A3478F9AB4B7F5FE9D4F67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/544A0904C171F7ACED98D10D90A2BBA267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) Overfull \hbox (8.40039pt too wide) in paragraph at lines 1080--1084 []\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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Overfull \hbox (0.78606pt too wide) in paragraph at lines 1631--1634 \OT1/cmr/m/n/10 The new [][]\OT1/cmtt/m/n/10 Bio.Align.PairwiseAligner []\OT1/c mr/m/n/10 im-ple-ments the Needleman-Wunsch, Smith-Waterman, Go-toh (three- (./_minted-Tutorial/554024580088332FAF0EA9296BACE82E67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) LaTeX Warning: Reference `sec:pairwise-aligner' on page 90 undefined on input l ine 1646. (./_minted-Tutorial/0ED9274F8C36E3C47BA70FD5BADC364467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/A6265A24C74E31AABCC4CBCDC431287F67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/71831DAF6DA69540332844566CA78C5D67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [90]) LaTeX Warning: Citation `waterman1987' on page 91 undefined on input line 1704. (./_minted-Tutorial/827F8E23B39B02EEFF7FF938570EE26E67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) LaTeX Warning: Reference `sec:pairwise-substitution-scores' on page 91 undefine d on input line 1733. 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[118] [119 <./images/BlastRecord.png>] [120 <./i mages/PSIBlastRecord.png>] (./Tutorial/chapter_searchio.tex Chapter 8. (./_minted-Tutorial/6D0EADF658E662CBA394834EFAC7346E0C640781732628151051B15D85C 9070A.pygtex) [121] 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 738--740 []\OT1/cmr/m/n/10 It should not sur-prise you now that the [][]\OT1/cmtt/m/n/10 HSP []\OT1/cmr/m/n/10 ob-ject has an [][]\OT1/cmtt/m/n/10 alignment []\OT1/cmr /m/n/10 prop-erty which is a [][]\OT1/cmtt/m/n/10 MultipleSeqAlignment (./_minted-Tutorial/3126C0E9DA3CE19C3C28004A18A3B48867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/64A5027CB01EBC16D0BBBCFA493BDAE167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/31F43A46088F6D2E63B39857A353690967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/B35C581DC0102E618595FCC0BE2AFE9867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [131]) (./_minted-Tutorial/23A338D38E31EFFAE0C56C5A5AAB567A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/F1953B67CE735DCB6EDDECF134C333B967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/69130C6EA441D4D1DEB35E75101C9AB967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [132]) (./_minted-Tutorial/688EDDC69F177DE7868A4B0C32B1499267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/E295C926B8D61E45F6C5FA1C0767BFD467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [133] (./_minted-Tutorial/4CFB05EC7DD8FA77EFE275E81B5A1B9767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/5CF3105B98EAD5BFC67DAB51751378F867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [134] (./_minted-Tutorial/7A63CB5E786CCE052981F7DD10653DA967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) Overfull \hbox (14.20721pt too wide) in paragraph at lines 1050--1054 \OT1/cmr/m/n/10 func-tion re-turns a gen-er-a-tor ob-ject that yields a [][]\OT 1/cmtt/m/n/10 QueryResult []\OT1/cmr/m/n/10 ob-ject in each it-er-a-tion. Like [][]\OT1/cmtt/m/n/10 Bio.SearchIO.read[]\OT1/cmr/m/n/10 , (./_minted-Tutorial/B5F76D201899B345CB64AACD67C7346067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) LaTeX Warning: Reference `sec:SeqIO-index' on page 135 undefined on input line 1082. Overfull \hbox (20.13245pt too wide) in paragraph at lines 1080--1085 []\OT1/cmr/m/n/10 In this case, the ideal choice would be to in-dex the file us -ing [][]\OT1/cmtt/m/n/10 Bio.SearchIO.index []\OT1/cmr/m/n/10 or [][]\OT1/cmtt /m/n/10 Bio.SearchIO.index_db[]\OT1/cmr/m/n/10 . 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[203] Overfull \hbox (19.85507pt too wide) in paragraph at lines 438--445 \OT1/cmr/m/n/10 For ex-am-ple, in a tree with clade names Foo1, Foo2 and Foo3, [][]\OT1/cmtt/m/n/10 tree.find_clades({"name": "Foo1"}) [204 <./images/phylo-draw-example.png>] Overfull \hbox (13.48741pt too wide) in paragraph at lines 493--496 []\OT1/cmr/m/n/10 Find each clade con-tain-ing a match-ing el-e-ment. 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(./_minted-Tutorial/A2465D4E8908256A31684D5DDE7DA11114FA033DCB1376922271CBD58A8 A4A36.pygtex [285 <./images/three_track_simple.png>]) (./_minted-Tutorial/347EB36A3001532221DDF6C29AA04AFB14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/F46F39DD7A8EC7B20CD42ACF6EFD184014FA033DCB1376922271CBD58A8 A4A36.pygtex [286]) (./_minted-Tutorial/2CF2D2FC7E96B3F426F22452724A4C2814FA033DCB1376922271CBD58A8 A4A36.pygtex) Overfull \hbox (2.65141pt too wide) in paragraph at lines 873--879 []\OT1/cmr/m/n/10 There are sev-eral im-por-tant pieces to this code. First the [][]\OT1/cmtt/m/n/10 GenomeDiagram []\OT1/cmr/m/n/10 ob-ject has a [][]\OT1/cm tt/m/n/10 cross_track_links Excluding 'htmlonly' comment. LaTeX Warning: Reference `fig:three_track_cl' on page 287 undefined on input li ne 894. LaTeX Warning: Reference `sec:gd_cross_links' on page 287 undefined on input li ne 901. LaTeX Warning: Reference `sec:gd_cross_links' on page 287 undefined on input li ne 901. Excluding 'htmlonly' comment. 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How-ever, for large FASTQ files it woul d be faster the low-level [][]\OT1/cmtt/m/n/10 FastqGeneralIterator (./_minted-Tutorial/AB16E58608A2F17CC79E69295572088714FA033DCB1376922271CBD58A8 A4A36.pygtex) Overfull \hbox (4.57849pt too wide) in paragraph at lines 474--476 \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 309 undefined on input line 479. 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$210$, there are $38$ files mak-ing u p the vi-ral se-quences, \OT1/cmtt/m/n/10 gbvrl1.seq\OT1/cmr/m/n/10 , ..., \OT1 /cmtt/m/n/10 gbvrl38.seq\OT1/cmr/m/n/10 , (./_minted-Tutorial/D41A88D88AB398F0C3B719A5C7D017C16EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/B4D970E8C81930851D8639D77EC3E4106EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex [63]) (./_minted-Tutorial/7C4E0944FB13EC4E75DD6FC64900395A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/C68CC3C9B3A505FB972706356D7F336F67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/61AD507889ED86CFCEFC880BAF2A277767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/DC5117490176932EFB8A7F0E0DA450F667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [64]) (./_minted-Tutorial/657D43328835FC01F9133F8BC964475D6EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/82CBCD9B9F23373D67D9D0D7D2CA363F67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) 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(./_minted-Tutorial/AA1E8DC650125C8460BF37E380CAC1AB67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/1435F1CEA90A4D217A423340747F87F067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/CA5B97CA60402CA0078F215AFF31799567B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/C5CCC8DD50EFD0D9A75909DCB5134E3114FA033DCB1376922271CBD58A8 A4A36.pygtex [69]) (./_minted-Tutorial/EDF3737891061C33EDE0FBFD16CCC63B14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/D1EAD55A1F8AD3DEAB82383A4F020F5314FA033DCB1376922271CBD58A8 A4A36.pygtex) Overfull \hbox (19.46596pt too wide) in paragraph at lines 1337--1339 \OT1/cmr/m/n/10 Making a sin-gle call to [][]\OT1/cmtt/m/n/10 SeqIO.write(...) []\OT1/cmr/m/n/10 is also much quicker than mul-ti-ple calls to the [][]\OT1/cm tt/m/n/10 SeqRecord.format(...) (./_minted-Tutorial/2F337ECD1F936D416FF9C5C6F41A02D767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [70] (./_minted-Tutorial/3337CD054623BAC21B6021E996EE0DFD14FA033DCB1376922271CBD58A8 A4A36.pygtex) Overfull \hbox (21.32593pt too wide) in paragraph at lines 1381--1385 []\OT1/cmr/m/n/10 Likewise, when pars-ing FASTQ files, in-ter-nally [][]\OT1/cm tt/m/n/10 Bio.SeqIO.parse() []\OT1/cmr/m/n/10 calls the low-level [][]\OT1/cmtt /m/n/10 FastqGeneralIterator (./_minted-Tutorial/D3AF6542680CA390CDA8C8DF87C693D367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/D749A84299CF58E876E9A899069830DB14FA033DCB1376922271CBD58A8 A4A36.pygtex)) [71] (./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 453--458 [][]\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/F67EB3EFC88C7F65142EC6767FF0AFE814FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/BB07BFEAEC0855950DABA0EE61AB192B14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/F94237F1B0C3E6DC309DEB6BB87A63E014FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/8FD10ACD641F4427B35E96F33B44479F0C640781732628151051B15D85C 9070A.pygtex [80]) (./_minted-Tutorial/8F45D3C2413A4CA1D91A89D61294165814FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/7E530BB128C8AE6BCF7BCE91DD4AF1890C640781732628151051B15D85C 9070A.pygtex) (./_minted-Tutorial/526DE630895A1CFB3DEA37685B34B1BA14FA033DCB1376922271CBD58A8 A4A36.pygtex) [81] (./_minted-Tutorial/C02EB78C9555A4FEE4954D77162ACF990C640781732628151051B15D85C 9070A.pygtex) (./_minted-Tutorial/F825D7C594903CE498C70B50088C497114FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/CB14E2060AF38515C129AB5808537F1614FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/E78F5A80C222A5B2777910FED4F43F560C640781732628151051B15D85C 9070A.pygtex [82]) (./_minted-Tutorial/9997F06B70C62809223AE6CDAE409E2F14FA033DCB1376922271CBD58A8 A4A36.pygtex) Overfull \hbox (16.49278pt too wide) in paragraph at lines 641--644 []\OT1/cmr/m/n/10 Internally the [][]\OT1/cmtt/m/n/10 format() []\OT1/cmr/m/n/1 0 method is us-ing the [][]\OT1/cmtt/m/n/10 StringIO []\OT1/cmr/m/n/10 string b ased han-dle and call-ing [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write()[]\OT1/cmr/m/ n/10 . 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The [][]\OT1/cmtt/m/n/10 Bio.AlignIO (./_minted-Tutorial/008DB28D2F01F3F29F1F82EB0591003367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/AE24E0D965703AA4106AE5CF699F0A9A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [89] (./_minted-Tutorial/801A8AB951B5DA791C92C02EB6139DB567B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/E5C61524B99B9EB0B1188FA913DB74CC67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/A4A4165B3B710F3328DE27D13D1FDD0D67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [90] (./_minted-Tutorial/E2B86D066966C8BA13EEEF614D3E745467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/C4AEB9BD8A76F10ACD8C01403E911E8C67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/512DFE88FFA610D4550AF5A23966733167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/F551ABCEBB0043257A807C76B9D81B5C67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/E6EC8CA7208E2B4D0E1C09607D4D544367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [91] (./_minted-Tutorial/CAE38F81A1D019D5521A277248175B7067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/DDF45D576AE1ADD55C0A0943C2F2162467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/5D3CCD84BC2EC46BF5FD98E7A3FC72660C640781732628151051B15D85C 9070A.pygtex) (./_minted-Tutorial/D9565472E525C9F2B734FC37A70D258E0C640781732628151051B15D85C 9070A.pygtex) [92] (./_minted-Tutorial/798933B773DD1AAF5C2DC54E06491DCF67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/44B6EBA222E5AE2CF0E223148840D8AE67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/8EEB60D5ACC558D826F87E267ADD6ACF67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/4988824A3CF97A3309EED328C1CB00D167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/DF151703751D72BD556402B910190A8767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [93] (./_minted-Tutorial/A1C3A08FE82B17F3E1148CA705106BDB67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (/usr/share/texlive/texmf-dist/tex/latex/base/omlcmr.fd) (./_minted-Tutorial/A7706714F4982C826867A73C2B665ED067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [94] (./_minted-Tutorial/22A95DFD34F9A46AA0FD0D1BA057DEE567B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/33F41ECEE9298ED97DBC0E4EF724A92367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/CBF601313030C01230C4BB8FFA8A990C67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/DE0EA110F0D219D588B9C0B7DEC746B867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/6784884C27E4405A02EE59C0B5C842E767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/169CB53D6C778B2D796C0965E6502A6D67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [95]) (./_minted-Tutorial/8D1D8D68DB8CCFDB1DCEA6F3405B292567B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/8B72D4D00CC6F9AA4DA3A84A74E2CC5E67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/1D1D98CF394058EA9EB8F6FA3B0DB75A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [96] Overfull \hbox (0.78606pt too wide) in paragraph at lines 1631--1634 \OT1/cmr/m/n/10 The new [][]\OT1/cmtt/m/n/10 Bio.Align.PairwiseAligner []\OT1/c mr/m/n/10 im-ple-ments the Needleman-Wunsch, Smith-Waterman, Go-toh (three- (./_minted-Tutorial/554024580088332FAF0EA9296BACE82E67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/0ED9274F8C36E3C47BA70FD5BADC364467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/A6265A24C74E31AABCC4CBCDC431287F67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/71831DAF6DA69540332844566CA78C5D67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [97]) (./_minted-Tutorial/827F8E23B39B02EEFF7FF938570EE26E67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/52B42D5819C8EC5D57A21AE60D28F6CE67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/5F566D907B2F88621EC4175F1F17AE0467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [98]) (./_minted-Tutorial/0EDAB1611DCCA854E910FF7DD9D639FA67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/1759F78B85C00128FE82428859F9AAB267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/143B28DCB7501FFE4BC59788E9B56D4267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [99]) (./_minted-Tutorial/17CE58BCB76575958EE7A76C89836E6967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) Overfull \hbox (76.42714pt too wide) in paragraph at lines 1830--1834 []\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 1830--1834 []\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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lines 2209--2210 \OT1/cmr/m/n/10 In this ex-am-ple, the to-tal num-ber of op-ti-mal align-ments is huge (more than $4 \OMS/cmsy/m/n/10 ^^B \OT1/cmr/m/n/10 10[]$), and call-ing [][]\OT1/cmtt/m/n/10 len(alignments) (./_minted-Tutorial/F89522EF58FB067C6521C367C713471667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/76A8D90A1791A7B42DD5E6329FCCBE2067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/71A68A4BDF8B5654D3E2E0470AE163B467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [106]) (./_minted-Tutorial/CE4E999FF33F9D09A2BB895447AA462967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/3E4691AEB06522E457CDE497E3092DE867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [107]) (./_minted-Tutorial/2E1DF2678D7C68CA2C465BCE6BBBBD6367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/C149B172A838F697839B85AE70CC6CDB67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/467CA50C36874E405E988587FEC0768667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) 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Excluding 'htmlonly' comment.) [125] [126 <./images/BlastRecord.png>] [127 <./i mages/PSIBlastRecord.png>] (./Tutorial/chapter_searchio.tex Chapter 8. (./_minted-Tutorial/6D0EADF658E662CBA394834EFAC7346E0C640781732628151051B15D85C 9070A.pygtex) [128] Overfull \hbox (2.9019pt too wide) in paragraph at lines 85--93 [][][]\OT1/cmtt/m/n/10 HSPFragment[]\OT1/cmr/m/n/10 , to rep-re-sent a sin-gle con-tigu-ous align-ment be-tween query and hit se-quences. [][]\OT1/cmtt/m/n/10 HSPFragment Overfull \hbox (8.43927pt too wide) in paragraph at lines 105--107 [][][]\OT1/cmtt/m/n/10 parse []\OT1/cmr/m/n/10 is used for search out-put files with mul-ti-ple queries and re-turns a gen-er-a-tor that yields [][]\OT1/cmtt/ m/n/10 QueryResult (./_minted-Tutorial/0EF47CD31A1F702FF10BD5C95E6D18FC67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [129]) (./_minted-Tutorial/BCDD1F95C8585B3C70DE9C1280B5195567B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [130]) (./_minted-Tutorial/5218313E7181C19A936D3F4347E1930A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/7BE69614D007F3BE3249A547A9661D0767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/40227DD719AAD22E8DC2923BF43CE32767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [131]) (./_minted-Tutorial/DC6D0E585B2AACAC1C88A760863B4E4E67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/130BC5013C07805E69A888444A0B34DB67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/CA24D00985B075C56E7C71A246E439FF67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/DE8A481953AA0F7BD7A99C0E281AD1A067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/E7AA701BE1D007CE77D402E8CBFC777A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/906546E8B6F7831A0E7C5FC93AA56A0367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [132] (./_minted-Tutorial/0E8B9F4E4323CB258CA049D41E4AB7F767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/DAA6FD197F3F78FDFB781210387FEC2667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [133]) (./_minted-Tutorial/67A62206561049F4B7E307FD79F028C967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/5E1CC554EC31697163DDD9D33E32A45667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [134]) (./_minted-Tutorial/0A806FC81D8F7F64321B4A6911027F0C67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [135] (./_minted-Tutorial/DC76D831C6E940E11ED2C9452F770E0C67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/A2EA3A12F7596A64ECEE374A9C53499A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/3A61EC24A4603554A3865574A6B7378067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [136] (./_minted-Tutorial/4D85AB21D9819B066A1C948098FDB54B67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/DAAFD2AAF126ED8D7284764B561B5E2B67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/4B4824DE2ED3215F02082987EE57357767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/4D9A79F8BB08FCA20BAEA3DFAAA08BA467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/62792AA2C0390B83FD6A91F3B267312A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [137]) (./_minted-Tutorial/CE618F26D70602D511E57E53CD88044467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/69CA04D2F1A8BE0FD871F68441214DFA67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) Overfull \hbox (27.24287pt too wide) in paragraph at lines 738--740 []\OT1/cmr/m/n/10 It should not sur-prise you now that the [][]\OT1/cmtt/m/n/10 HSP []\OT1/cmr/m/n/10 ob-ject has an [][]\OT1/cmtt/m/n/10 alignment []\OT1/cmr /m/n/10 prop-erty which is a [][]\OT1/cmtt/m/n/10 MultipleSeqAlignment (./_minted-Tutorial/3126C0E9DA3CE19C3C28004A18A3B48867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/64A5027CB01EBC16D0BBBCFA493BDAE167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/31F43A46088F6D2E63B39857A353690967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/B35C581DC0102E618595FCC0BE2AFE9867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [138]) (./_minted-Tutorial/23A338D38E31EFFAE0C56C5A5AAB567A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/F1953B67CE735DCB6EDDECF134C333B967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/69130C6EA441D4D1DEB35E75101C9AB967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [139]) (./_minted-Tutorial/688EDDC69F177DE7868A4B0C32B1499267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/E295C926B8D61E45F6C5FA1C0767BFD467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [140] (./_minted-Tutorial/4CFB05EC7DD8FA77EFE275E81B5A1B9767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/5CF3105B98EAD5BFC67DAB51751378F867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [141] (./_minted-Tutorial/7A63CB5E786CCE052981F7DD10653DA967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) Overfull \hbox (14.20721pt too wide) in paragraph at lines 1050--1054 \OT1/cmr/m/n/10 func-tion re-turns a gen-er-a-tor ob-ject that yields a [][]\OT 1/cmtt/m/n/10 QueryResult []\OT1/cmr/m/n/10 ob-ject in each it-er-a-tion. Like [][]\OT1/cmtt/m/n/10 Bio.SearchIO.read[]\OT1/cmr/m/n/10 , (./_minted-Tutorial/B5F76D201899B345CB64AACD67C7346067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) Overfull \hbox (20.13245pt too wide) in paragraph at lines 1080--1085 []\OT1/cmr/m/n/10 In this case, the ideal choice would be to in-dex the file us -ing [][]\OT1/cmtt/m/n/10 Bio.SearchIO.index []\OT1/cmr/m/n/10 or [][]\OT1/cmtt /m/n/10 Bio.SearchIO.index_db[]\OT1/cmr/m/n/10 . (./_minted-Tutorial/0AB25750C7D89E832295045C60D6B8C467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [142]) (./_minted-Tutorial/DFACFE04880AE0CA2E8E32ABDC9E986867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/E4B312798560C8CE4ABF272A364D9E2F67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/35C0940CA4025285AAECA54EF82C993367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) Overfull \hbox (11.82602pt too wide) in paragraph at lines 1160--1163 []\OT1/cmr/m/n/10 Finally, [][]\OT1/cmtt/m/n/10 Bio.SearchIO []\OT1/cmr/m/n/10 also pro-vides a [][]\OT1/cmtt/m/n/10 convert []\OT1/cmr/m/n/10 func-tion, whic h is sim-ply a short-cut for [][]\OT1/cmtt/m/n/10 Bio.SearchIO.parse (./_minted-Tutorial/BDE985FA3ADA6B0D37013C3D5F37C17667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex)) [143] [144] (./Tutorial/chapter_entrez.tex Chapter 9. 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(./_minted-Tutorial/6C5156DAD460519324A5B7657B301B5D67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/1836031BC83AA94C8906762F613E6CBA67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [206] (./_minted-Tutorial/D0A75FB8C1C791E4AA80420B93F216A867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/FEC6C2CB5FA0AFCFE00D995BD3642FF267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/2B435DC3041611A5D6A663B437ADB1AD67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) Overfull \hbox (25.13162pt too wide) in paragraph at lines 175--178 []\OT1/cmr/m/n/10 Let's tar-get the most re-cent com-mon an-ces-tor (MRCA) of t he nodes named ``E'' and ``F''. The [][]\OT1/cmtt/m/n/10 common_ancestor (./_minted-Tutorial/29624A9666C9430AABADF395148BBF2767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/D0F05D42BA0A9BC594EEDB16319A972D67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/87517FEF82BFE1AB8D89A83F4DC5E8B967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [207 <./images/phylo-simple-draw.png>]) Excluding 'htmlonly' comment. 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[210] Overfull \hbox (19.85507pt too wide) in paragraph at lines 438--445 \OT1/cmr/m/n/10 For ex-am-ple, in a tree with clade names Foo1, Foo2 and Foo3, [][]\OT1/cmtt/m/n/10 tree.find_clades({"name": "Foo1"}) [211 <./images/phylo-draw-example.png>] Overfull \hbox (13.48741pt too wide) in paragraph at lines 493--496 []\OT1/cmr/m/n/10 Find each clade con-tain-ing a match-ing el-e-ment. That is, find each el-e-ment as with [][]\OT1/cmtt/m/n/10 find_elements[]\OT1/cmr/m/n/10 , [212] (./_minted-Tutorial/6AAB725DBD2E5B7C5FD79A9A16536BF614FA033DCB1376922271CBD58A8 A4A36.pygtex) [213] (./_minted-Tutorial/5B477DBF8C94B1E6FDC020E6A741C0DC67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/A317CBB9F004B52870B25AB07ACF279167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) Overfull \hbox (4.04672pt too wide) in paragraph at lines 704--707 []\OT1/cmr/m/n/10 A sim-i-lar wrap-per for RAxML ([][]$\OT1/cmtt/m/n/10 https : / / sco . h-[]its . org / exelixis / software . html$[][]\OT1/cmr/m/n/10 ) was added in Biopy- [214] (./_minted-Tutorial/4A4A0B08C37495B73842BFCD67A687D367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/C395044A3DB827E8D2E36BA5259475D267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [215]) [216] (./Tutorial/chapter_motifs.tex Chapter 14. 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[244] [245] [246] [247] (./_minted-Tutorial/C7B59059E3AE6CDE790EFE6EB0ED414067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/2CEA2595B9B8CEAD10513E8D15566D0167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/425EDAA643B5AA9589F3EEE60173582767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/50B5971EFCF22FCC4E1302DB2D0A250014FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/293084E63EA5C0E01F325A4DD59469C067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [248]) Overfull \hbox (78.60634pt too wide) in paragraph at lines 244--245 \OT1/cmr/m/n/10 men-sions of these ar-rays are $[]$ if [][]\OT1/cmtt/m/n/10 tra nspose []\OT1/cmr/m/n/10 is [][]\OT1/cmtt/m/n/10 0[]\OT1/cmr/m/n/10 , or $[]$ (./_minted-Tutorial/05DC01C08B8EDF71F86E3C3A9C28EB3467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [249] [250] (./_minted-Tutorial/A4A28B5A443208DEAB3B4D76AA3B762E67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [251] (./_minted-Tutorial/C286E2777B917B774560CBDC7CF9262667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/D04E097D8E8C4C039FEC20FA103CED1814FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/36EF8931044EF448BC70F722AFADB43D14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/805B33438269C932AC54C0DAB5A3D7AC14FA033DCB1376922271CBD58A8 A4A36.pygtex) [252] [253] Overfull \hbox (16.73593pt too wide) in paragraph at lines 422--423 [][]\OT1/cmtt/m/n/10 distance []\OT1/cmr/m/n/10 is the dis-tance be-tween them. The items be-ing clus-tered are num-bered from 0 to $[]$, (./_minted-Tutorial/015798D317E9D8732518AFD186C997CA67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/A27E6BF4EEB8E8B1C23904926786173967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [254] (./_minted-Tutorial/81E4060E427D22B8F0C63B69EEC10A2A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/B8D2A546EC4941692F427A363193FBDE67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/A54EF6455421EFDFA1F63EB361CD74F667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/8975A4CCBC4C6138C302117E04F203AD67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/636486BB1CF700F6391685224211BE2267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [255] (./_minted-Tutorial/6EFE1AC811BF16FF597EBE3E25BD2F7267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/F8E41E59FD44DADEB3740B0C0ED17D4167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/1B924FC8FA13A8B73C1C9E6EF889505567B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/77B32E49165B4345FFCA9FACF597BEEB67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [256]) (./_minted-Tutorial/D04E097D8E8C4C039FEC20FA103CED1814FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/36EF8931044EF448BC70F722AFADB43D14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/805B33438269C932AC54C0DAB5A3D7AC14FA033DCB1376922271CBD58A8 A4A36.pygtex) [257] (./_minted-Tutorial/E542C07D0131DF56A89D92F80416C17567B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [258] Overfull \hbox (106.77225pt too wide) in paragraph at lines 653--655 \OT1/cmr/m/n/10 An ar-ray with di-men-sions $[]$ if rows are be-ing clus-tered, or $[]$ (./_minted-Tutorial/7476A2D5F9D3A46EE00108837901FAEA67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [259] (./_minted-Tutorial/0420D397BA03971C0079F52E55FEABAB67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/6A7DB1B14B8C3B59B03D102D4BEECDD167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/485FBF40932E9746A77212F14D1BC1C767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/9F9B1D1BD004D8BA7669CE44CA695E5267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [260] Overfull \hbox (25.39864pt too wide) in paragraph at lines 743--754 [] [261] (./_minted-Tutorial/EFB8602799AD543446B386107A8147F767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/43B30B527C3A2D8148F25CA143719CAF67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/C77F1ABB31C6A53C1626E0E0B34BB0FC67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [262] (./_minted-Tutorial/1F3E2EFB988F2639C701A920B547241D67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [263] (./_minted-Tutorial/3CAD921471DA4CA4441D02558CD1F2E067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/1A863BDE3A5754AA2C865F2A82DA850467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [264] Overfull \hbox (106.77225pt too wide) in paragraph at lines 933--935 \OT1/cmr/m/n/10 An ar-ray with di-men-sions $[]$ if rows are be-ing clus-tered, or $[]$ (./_minted-Tutorial/A39469F362670EDC6C7E8FD9FDF412C467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [265] (./_minted-Tutorial/12B5F20EFF78F0E8FE505D45A9786D7067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/E6C8D570402CFDDB43A6AE5A198BCF5867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex)) Overfull \hbox (26.21434pt too wide) in paragraph at lines 990--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 . 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[288 <./images/plasmid_linear_nice.png (PNG copy) >] [289 <./images/plasmid_circular_nice.png>] (./_minted-Tutorial/7CAF22FEDE98A6B9B7990010CA8709DC14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/FA676816242752C9FE9F5EB12D4DAA8914FA033DCB1376922271CBD58A8 A4A36.pygtex [290]) (./_minted-Tutorial/7926619D7609A591C404A01B2A99177A14FA033DCB1376922271CBD58A8 A4A36.pygtex [291]) Excluding 'htmlonly' comment. [292 <./images/three_track_si mple.png>] (./_minted-Tutorial/A2465D4E8908256A31684D5DDE7DA11114FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/347EB36A3001532221DDF6C29AA04AFB14FA033DCB1376922271CBD58A8 A4A36.pygtex [293]) (./_minted-Tutorial/F46F39DD7A8EC7B20CD42ACF6EFD184014FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/2CF2D2FC7E96B3F426F22452724A4C2814FA033DCB1376922271CBD58A8 A4A36.pygtex) Overfull \hbox (2.65141pt too wide) in paragraph at lines 873--879 []\OT1/cmr/m/n/10 There are sev-eral im-por-tant pieces to this code. First the [][]\OT1/cmtt/m/n/10 GenomeDiagram []\OT1/cmr/m/n/10 ob-ject has a [][]\OT1/cm tt/m/n/10 cross_track_links Excluding 'htmlonly' comment. [294] Excluding 'htmlonly' comment. [295 <./image s/three_track_cl.png>] [296 <./images/three_track_cl2a.png>] (./_minted-Tutorial/F9FFB9659EC22BC166AEB6F72841497714FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/A9695DE54C455E13B400269BF9F424FE14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/F545B5C3D394029AA34E76D27DC2DBAF14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/3BACFFDF9009929D690C44BF09EFB67F14FA033DCB1376922271CBD58A8 A4A36.pygtex) [297] (./_minted-Tutorial/0AC11BF466D4AA0B0536F05378BEC9CC14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/F5380F7F462C2A51219D9EF8994C192C14FA033DCB1376922271CBD58A8 A4A36.pygtex [298] [299 <./images/simple_chrom.pdf> <./images/tRNA_chrom.pdf>]) Excluding 'htmlonly' comment. 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How-ever, for large FASTQ files it woul d be faster the low-level [][]\OT1/cmtt/m/n/10 FastqGeneralIterator (./_minted-Tutorial/AB16E58608A2F17CC79E69295572088714FA033DCB1376922271CBD58A8 A4A36.pygtex) Overfull \hbox (4.57849pt too wide) in paragraph at lines 474--476 \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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[325] Overfull \hbox (4.00363pt too wide) in paragraph at lines 1115--1118 []\OT1/cmr/m/it/10 Tip: \OT1/cmr/m/n/10 Rather than us-ing [][]\OT1/cmtt/m/n/10 pylab.show() []\OT1/cmr/m/n/10 to show the plot in a win-dow, you can also use [][]\OT1/cmtt/m/n/10 pylab.savefig(...) (./_minted-Tutorial/7C23BDB073E316E7093E4D3A77BD752E14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/CB78AD94DFE82ADBAF348C0EC1D261CD14FA033DCB1376922271CBD58A8 A4A36.pygtex [326 <./images/hist_plot.png>]) Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. (./_minted-Tutorial/6E0DA723E11A7B9CA8E2353A984B5DF714FA033DCB1376922271CBD58A8 A4A36.pygtex) [327 <./images/gc_plot.png>] (./_minted-Tutorial/219B67DCB31F2334EDD0B85471FABDEA14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/9574E55C4A182E2A0201DF18689F52F414FA033DCB1376922271CBD58A8 A4A36.pygtex [328 <./images/dot_plot.png>]) Excluding 'htmlonly' comment. 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(./_minted-Tutorial/415024C641C8DA7A09117B3DFE240C7867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [61]) (./_minted-Tutorial/487DCC9F44A2539C9B32C0122AEF406567B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/E83C4A508EFF6905997163871410F4F267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/EEEF4ABAD66CE989F67C9E27EEDE95CC67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/6209F8400B12665DC9E51BC20774DF7014FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/C4099CB0613585FCCD5EA7D8198704CE67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [62] Overfull \hbox (9.93459pt too wide) in paragraph at lines 843--848 \OT1/cmr/m/n/10 FTP site ([][]$\OT1/cmtt/m/n/10 ftp : / / ftp . uniprot . org / pub / databases / uniprot / current _ release / knowledgebase / complete / (./_minted-Tutorial/D52DA4EEEEE2BF0FBE89EE253714929D67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) Overfull \hbox (4.48064pt too wide) in paragraph at lines 886--889 []\OT1/cmr/m/n/10 As of Gen-Bank re-lease $210$, there are $38$ files mak-ing u p the vi-ral se-quences, \OT1/cmtt/m/n/10 gbvrl1.seq\OT1/cmr/m/n/10 , ..., \OT1 /cmtt/m/n/10 gbvrl38.seq\OT1/cmr/m/n/10 , (./_minted-Tutorial/D41A88D88AB398F0C3B719A5C7D017C16EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/B4D970E8C81930851D8639D77EC3E4106EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex [63]) (./_minted-Tutorial/7C4E0944FB13EC4E75DD6FC64900395A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/C68CC3C9B3A505FB972706356D7F336F67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/61AD507889ED86CFCEFC880BAF2A277767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/DC5117490176932EFB8A7F0E0DA450F667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [64]) (./_minted-Tutorial/657D43328835FC01F9133F8BC964475D6EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/82CBCD9B9F23373D67D9D0D7D2CA363F67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) 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(./_minted-Tutorial/AA1E8DC650125C8460BF37E380CAC1AB67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/1435F1CEA90A4D217A423340747F87F067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/CA5B97CA60402CA0078F215AFF31799567B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/C5CCC8DD50EFD0D9A75909DCB5134E3114FA033DCB1376922271CBD58A8 A4A36.pygtex [69]) (./_minted-Tutorial/EDF3737891061C33EDE0FBFD16CCC63B14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/D1EAD55A1F8AD3DEAB82383A4F020F5314FA033DCB1376922271CBD58A8 A4A36.pygtex) Overfull \hbox (19.46596pt too wide) in paragraph at lines 1337--1339 \OT1/cmr/m/n/10 Making a sin-gle call to [][]\OT1/cmtt/m/n/10 SeqIO.write(...) []\OT1/cmr/m/n/10 is also much quicker than mul-ti-ple calls to the [][]\OT1/cm tt/m/n/10 SeqRecord.format(...) (./_minted-Tutorial/2F337ECD1F936D416FF9C5C6F41A02D767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [70] (./_minted-Tutorial/3337CD054623BAC21B6021E996EE0DFD14FA033DCB1376922271CBD58A8 A4A36.pygtex) Overfull \hbox (21.32593pt too wide) in paragraph at lines 1381--1385 []\OT1/cmr/m/n/10 Likewise, when pars-ing FASTQ files, in-ter-nally [][]\OT1/cm tt/m/n/10 Bio.SeqIO.parse() []\OT1/cmr/m/n/10 calls the low-level [][]\OT1/cmtt /m/n/10 FastqGeneralIterator (./_minted-Tutorial/D3AF6542680CA390CDA8C8DF87C693D367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/D749A84299CF58E876E9A899069830DB14FA033DCB1376922271CBD58A8 A4A36.pygtex)) [71] (./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 453--458 [][]\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/F67EB3EFC88C7F65142EC6767FF0AFE814FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/BB07BFEAEC0855950DABA0EE61AB192B14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/F94237F1B0C3E6DC309DEB6BB87A63E014FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/8FD10ACD641F4427B35E96F33B44479F0C640781732628151051B15D85C 9070A.pygtex [80]) (./_minted-Tutorial/8F45D3C2413A4CA1D91A89D61294165814FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/7E530BB128C8AE6BCF7BCE91DD4AF1890C640781732628151051B15D85C 9070A.pygtex) (./_minted-Tutorial/526DE630895A1CFB3DEA37685B34B1BA14FA033DCB1376922271CBD58A8 A4A36.pygtex) [81] (./_minted-Tutorial/C02EB78C9555A4FEE4954D77162ACF990C640781732628151051B15D85C 9070A.pygtex) (./_minted-Tutorial/F825D7C594903CE498C70B50088C497114FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/CB14E2060AF38515C129AB5808537F1614FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/E78F5A80C222A5B2777910FED4F43F560C640781732628151051B15D85C 9070A.pygtex [82]) (./_minted-Tutorial/9997F06B70C62809223AE6CDAE409E2F14FA033DCB1376922271CBD58A8 A4A36.pygtex) Overfull \hbox (16.49278pt too wide) in paragraph at lines 641--644 []\OT1/cmr/m/n/10 Internally the [][]\OT1/cmtt/m/n/10 format() []\OT1/cmr/m/n/1 0 method is us-ing the [][]\OT1/cmtt/m/n/10 StringIO []\OT1/cmr/m/n/10 string b ased han-dle and call-ing [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write()[]\OT1/cmr/m/ n/10 . 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The [][]\OT1/cmtt/m/n/10 Bio.AlignIO (./_minted-Tutorial/008DB28D2F01F3F29F1F82EB0591003367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/AE24E0D965703AA4106AE5CF699F0A9A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [89] (./_minted-Tutorial/801A8AB951B5DA791C92C02EB6139DB567B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/E5C61524B99B9EB0B1188FA913DB74CC67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/A4A4165B3B710F3328DE27D13D1FDD0D67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [90] (./_minted-Tutorial/E2B86D066966C8BA13EEEF614D3E745467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/C4AEB9BD8A76F10ACD8C01403E911E8C67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/512DFE88FFA610D4550AF5A23966733167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/F551ABCEBB0043257A807C76B9D81B5C67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/E6EC8CA7208E2B4D0E1C09607D4D544367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [91] (./_minted-Tutorial/CAE38F81A1D019D5521A277248175B7067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/DDF45D576AE1ADD55C0A0943C2F2162467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/5D3CCD84BC2EC46BF5FD98E7A3FC72660C640781732628151051B15D85C 9070A.pygtex) (./_minted-Tutorial/D9565472E525C9F2B734FC37A70D258E0C640781732628151051B15D85C 9070A.pygtex) [92] (./_minted-Tutorial/798933B773DD1AAF5C2DC54E06491DCF67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/44B6EBA222E5AE2CF0E223148840D8AE67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/8EEB60D5ACC558D826F87E267ADD6ACF67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/4988824A3CF97A3309EED328C1CB00D167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/DF151703751D72BD556402B910190A8767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [93] (./_minted-Tutorial/A1C3A08FE82B17F3E1148CA705106BDB67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (/usr/share/texlive/texmf-dist/tex/latex/base/omlcmr.fd) (./_minted-Tutorial/A7706714F4982C826867A73C2B665ED067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [94] (./_minted-Tutorial/22A95DFD34F9A46AA0FD0D1BA057DEE567B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/33F41ECEE9298ED97DBC0E4EF724A92367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/CBF601313030C01230C4BB8FFA8A990C67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/DE0EA110F0D219D588B9C0B7DEC746B867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/6784884C27E4405A02EE59C0B5C842E767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/169CB53D6C778B2D796C0965E6502A6D67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [95]) (./_minted-Tutorial/8D1D8D68DB8CCFDB1DCEA6F3405B292567B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/8B72D4D00CC6F9AA4DA3A84A74E2CC5E67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/1D1D98CF394058EA9EB8F6FA3B0DB75A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [96] Overfull \hbox (0.78606pt too wide) in paragraph at lines 1631--1634 \OT1/cmr/m/n/10 The new [][]\OT1/cmtt/m/n/10 Bio.Align.PairwiseAligner []\OT1/c mr/m/n/10 im-ple-ments the Needleman-Wunsch, Smith-Waterman, Go-toh (three- (./_minted-Tutorial/554024580088332FAF0EA9296BACE82E67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/0ED9274F8C36E3C47BA70FD5BADC364467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/A6265A24C74E31AABCC4CBCDC431287F67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/71831DAF6DA69540332844566CA78C5D67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [97]) (./_minted-Tutorial/827F8E23B39B02EEFF7FF938570EE26E67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/52B42D5819C8EC5D57A21AE60D28F6CE67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/5F566D907B2F88621EC4175F1F17AE0467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [98]) (./_minted-Tutorial/0EDAB1611DCCA854E910FF7DD9D639FA67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/1759F78B85C00128FE82428859F9AAB267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/143B28DCB7501FFE4BC59788E9B56D4267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [99]) (./_minted-Tutorial/17CE58BCB76575958EE7A76C89836E6967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) Overfull \hbox (76.42714pt too wide) in paragraph at lines 1830--1834 []\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 1830--1834 []\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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lines 2209--2210 \OT1/cmr/m/n/10 In this ex-am-ple, the to-tal num-ber of op-ti-mal align-ments is huge (more than $4 \OMS/cmsy/m/n/10 ^^B \OT1/cmr/m/n/10 10[]$), and call-ing [][]\OT1/cmtt/m/n/10 len(alignments) (./_minted-Tutorial/F89522EF58FB067C6521C367C713471667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/76A8D90A1791A7B42DD5E6329FCCBE2067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/71A68A4BDF8B5654D3E2E0470AE163B467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [106]) (./_minted-Tutorial/CE4E999FF33F9D09A2BB895447AA462967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/3E4691AEB06522E457CDE497E3092DE867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [107]) (./_minted-Tutorial/2E1DF2678D7C68CA2C465BCE6BBBBD6367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/C149B172A838F697839B85AE70CC6CDB67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/467CA50C36874E405E988587FEC0768667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) 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Excluding 'htmlonly' comment.) [125] [126 <./images/BlastRecord.png>] [127 <./i mages/PSIBlastRecord.png>] (./Tutorial/chapter_searchio.tex Chapter 8. (./_minted-Tutorial/6D0EADF658E662CBA394834EFAC7346E0C640781732628151051B15D85C 9070A.pygtex) [128] Overfull \hbox (2.9019pt too wide) in paragraph at lines 85--93 [][][]\OT1/cmtt/m/n/10 HSPFragment[]\OT1/cmr/m/n/10 , to rep-re-sent a sin-gle con-tigu-ous align-ment be-tween query and hit se-quences. [][]\OT1/cmtt/m/n/10 HSPFragment Overfull \hbox (8.43927pt too wide) in paragraph at lines 105--107 [][][]\OT1/cmtt/m/n/10 parse []\OT1/cmr/m/n/10 is used for search out-put files with mul-ti-ple queries and re-turns a gen-er-a-tor that yields [][]\OT1/cmtt/ m/n/10 QueryResult (./_minted-Tutorial/0EF47CD31A1F702FF10BD5C95E6D18FC67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [129]) (./_minted-Tutorial/BCDD1F95C8585B3C70DE9C1280B5195567B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [130]) (./_minted-Tutorial/5218313E7181C19A936D3F4347E1930A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/7BE69614D007F3BE3249A547A9661D0767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/40227DD719AAD22E8DC2923BF43CE32767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [131]) (./_minted-Tutorial/DC6D0E585B2AACAC1C88A760863B4E4E67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/130BC5013C07805E69A888444A0B34DB67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/CA24D00985B075C56E7C71A246E439FF67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/DE8A481953AA0F7BD7A99C0E281AD1A067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/E7AA701BE1D007CE77D402E8CBFC777A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/906546E8B6F7831A0E7C5FC93AA56A0367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [132] (./_minted-Tutorial/0E8B9F4E4323CB258CA049D41E4AB7F767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/DAA6FD197F3F78FDFB781210387FEC2667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [133]) (./_minted-Tutorial/67A62206561049F4B7E307FD79F028C967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/5E1CC554EC31697163DDD9D33E32A45667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [134]) (./_minted-Tutorial/0A806FC81D8F7F64321B4A6911027F0C67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [135] (./_minted-Tutorial/DC76D831C6E940E11ED2C9452F770E0C67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/A2EA3A12F7596A64ECEE374A9C53499A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/3A61EC24A4603554A3865574A6B7378067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [136] (./_minted-Tutorial/4D85AB21D9819B066A1C948098FDB54B67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/DAAFD2AAF126ED8D7284764B561B5E2B67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/4B4824DE2ED3215F02082987EE57357767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/4D9A79F8BB08FCA20BAEA3DFAAA08BA467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/62792AA2C0390B83FD6A91F3B267312A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [137]) (./_minted-Tutorial/CE618F26D70602D511E57E53CD88044467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/69CA04D2F1A8BE0FD871F68441214DFA67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) Overfull \hbox (27.24287pt too wide) in paragraph at lines 738--740 []\OT1/cmr/m/n/10 It should not sur-prise you now that the [][]\OT1/cmtt/m/n/10 HSP []\OT1/cmr/m/n/10 ob-ject has an [][]\OT1/cmtt/m/n/10 alignment []\OT1/cmr /m/n/10 prop-erty which is a [][]\OT1/cmtt/m/n/10 MultipleSeqAlignment (./_minted-Tutorial/3126C0E9DA3CE19C3C28004A18A3B48867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/64A5027CB01EBC16D0BBBCFA493BDAE167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/31F43A46088F6D2E63B39857A353690967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/B35C581DC0102E618595FCC0BE2AFE9867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [138]) (./_minted-Tutorial/23A338D38E31EFFAE0C56C5A5AAB567A67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/F1953B67CE735DCB6EDDECF134C333B967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/69130C6EA441D4D1DEB35E75101C9AB967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [139]) (./_minted-Tutorial/688EDDC69F177DE7868A4B0C32B1499267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/E295C926B8D61E45F6C5FA1C0767BFD467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [140] (./_minted-Tutorial/4CFB05EC7DD8FA77EFE275E81B5A1B9767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/5CF3105B98EAD5BFC67DAB51751378F867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [141] (./_minted-Tutorial/7A63CB5E786CCE052981F7DD10653DA967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) Overfull \hbox (14.20721pt too wide) in paragraph at lines 1050--1054 \OT1/cmr/m/n/10 func-tion re-turns a gen-er-a-tor ob-ject that yields a [][]\OT 1/cmtt/m/n/10 QueryResult []\OT1/cmr/m/n/10 ob-ject in each it-er-a-tion. Like [][]\OT1/cmtt/m/n/10 Bio.SearchIO.read[]\OT1/cmr/m/n/10 , (./_minted-Tutorial/B5F76D201899B345CB64AACD67C7346067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) Overfull \hbox (20.13245pt too wide) in paragraph at lines 1080--1085 []\OT1/cmr/m/n/10 In this case, the ideal choice would be to in-dex the file us -ing [][]\OT1/cmtt/m/n/10 Bio.SearchIO.index []\OT1/cmr/m/n/10 or [][]\OT1/cmtt /m/n/10 Bio.SearchIO.index_db[]\OT1/cmr/m/n/10 . (./_minted-Tutorial/0AB25750C7D89E832295045C60D6B8C467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [142]) (./_minted-Tutorial/DFACFE04880AE0CA2E8E32ABDC9E986867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/E4B312798560C8CE4ABF272A364D9E2F67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/35C0940CA4025285AAECA54EF82C993367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) Overfull \hbox (11.82602pt too wide) in paragraph at lines 1160--1163 []\OT1/cmr/m/n/10 Finally, [][]\OT1/cmtt/m/n/10 Bio.SearchIO []\OT1/cmr/m/n/10 also pro-vides a [][]\OT1/cmtt/m/n/10 convert []\OT1/cmr/m/n/10 func-tion, whic h is sim-ply a short-cut for [][]\OT1/cmtt/m/n/10 Bio.SearchIO.parse (./_minted-Tutorial/BDE985FA3ADA6B0D37013C3D5F37C17667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex)) [143] [144] (./Tutorial/chapter_entrez.tex Chapter 9. [145] (./_minted-Tutorial/95F72AA1E59C898262005610BC25A6BA67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/320E9A38F759168BA03B078BD9CC013B67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/DAEC2235DDE454C09ECEB0DF4CD26FB567B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/7692669934D8ED6DEE1B8B668474542167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [146]) (./_minted-Tutorial/4E8E7490F3E1B9120A0B1B53C024FA3667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [147]) (./_minted-Tutorial/C21F612C84412948C9890ED976F536B067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/B40E136307D84542C2292F35A77DC45E67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/846A93AAA063B5CBA3EDEF3D5FC8C00867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/03DD15474BC34E37527B593FC22220FC67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/7B7AA3167A6472C6C33ACA91F8E88FAC67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) 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(./_minted-Tutorial/E5F1866C3CBB485B8C06B62764ACFBB214FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/B115204AFF525DDD4F3CF69B79C0739114FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/6CD64A1F591B16F512F7EB6B68E5B3FC14FA033DCB1376922271CBD58A8 A4A36.pygtex [203])) [204] (./Tutorial/chapter_phylo.tex Chapter 13. (./_minted-Tutorial/8F8EFC1C83277AE6C5B5A259FAAC56710C640781732628151051B15D85C 9070A.pygtex) (./_minted-Tutorial/4914B4679D1C933D9AD76E95F18CE1586EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/3D758844BE2A5D4414B741470EDE8C2467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/719B0C758B666CDEEB2B250C2143A4AD67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [205]) (./_minted-Tutorial/8698B66B622D8A91E7706D889D5F35DD67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/3E6F23F473B4E07E8F7181EEE5B0B4A567B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) Excluding 'htmlonly' comment. (./_minted-Tutorial/6C5156DAD460519324A5B7657B301B5D67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/1836031BC83AA94C8906762F613E6CBA67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [206] (./_minted-Tutorial/D0A75FB8C1C791E4AA80420B93F216A867B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/FEC6C2CB5FA0AFCFE00D995BD3642FF267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/2B435DC3041611A5D6A663B437ADB1AD67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) Overfull \hbox (25.13162pt too wide) in paragraph at lines 175--178 []\OT1/cmr/m/n/10 Let's tar-get the most re-cent com-mon an-ces-tor (MRCA) of t he nodes named ``E'' and ``F''. The [][]\OT1/cmtt/m/n/10 common_ancestor (./_minted-Tutorial/29624A9666C9430AABADF395148BBF2767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/D0F05D42BA0A9BC594EEDB16319A972D67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/87517FEF82BFE1AB8D89A83F4DC5E8B967B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [207 <./images/phylo-simple-draw.png>]) Excluding 'htmlonly' comment. 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[210] Overfull \hbox (19.85507pt too wide) in paragraph at lines 438--445 \OT1/cmr/m/n/10 For ex-am-ple, in a tree with clade names Foo1, Foo2 and Foo3, [][]\OT1/cmtt/m/n/10 tree.find_clades({"name": "Foo1"}) [211 <./images/phylo-draw-example.png>] Overfull \hbox (13.48741pt too wide) in paragraph at lines 493--496 []\OT1/cmr/m/n/10 Find each clade con-tain-ing a match-ing el-e-ment. That is, find each el-e-ment as with [][]\OT1/cmtt/m/n/10 find_elements[]\OT1/cmr/m/n/10 , [212] (./_minted-Tutorial/6AAB725DBD2E5B7C5FD79A9A16536BF614FA033DCB1376922271CBD58A8 A4A36.pygtex) [213] (./_minted-Tutorial/5B477DBF8C94B1E6FDC020E6A741C0DC67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/A317CBB9F004B52870B25AB07ACF279167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) Overfull \hbox (4.04672pt too wide) in paragraph at lines 704--707 []\OT1/cmr/m/n/10 A sim-i-lar wrap-per for RAxML ([][]$\OT1/cmtt/m/n/10 https : / / sco . h-[]its . org / exelixis / software . html$[][]\OT1/cmr/m/n/10 ) was added in Biopy- [214] (./_minted-Tutorial/4A4A0B08C37495B73842BFCD67A687D367B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/C395044A3DB827E8D2E36BA5259475D267B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [215]) [216] (./Tutorial/chapter_motifs.tex Chapter 14. 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[244] [245] [246] [247] (./_minted-Tutorial/C7B59059E3AE6CDE790EFE6EB0ED414067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/2CEA2595B9B8CEAD10513E8D15566D0167B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/425EDAA643B5AA9589F3EEE60173582767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/50B5971EFCF22FCC4E1302DB2D0A250014FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/293084E63EA5C0E01F325A4DD59469C067B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex [248]) Overfull \hbox (78.60634pt too wide) in paragraph at lines 244--245 \OT1/cmr/m/n/10 men-sions of these ar-rays are $[]$ if [][]\OT1/cmtt/m/n/10 tra nspose []\OT1/cmr/m/n/10 is [][]\OT1/cmtt/m/n/10 0[]\OT1/cmr/m/n/10 , or $[]$ (./_minted-Tutorial/05DC01C08B8EDF71F86E3C3A9C28EB3467B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [249] [250] (./_minted-Tutorial/A4A28B5A443208DEAB3B4D76AA3B762E67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) [251] (./_minted-Tutorial/C286E2777B917B774560CBDC7CF9262667B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/D04E097D8E8C4C039FEC20FA103CED1814FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/36EF8931044EF448BC70F722AFADB43D14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/805B33438269C932AC54C0DAB5A3D7AC14FA033DCB1376922271CBD58A8 A4A36.pygtex) [252] [253] Overfull \hbox (16.73593pt too wide) in paragraph at lines 422--423 [][]\OT1/cmtt/m/n/10 distance []\OT1/cmr/m/n/10 is the dis-tance be-tween them. 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[288 <./images/plasmid_linear_nice.png (PNG copy) >] [289 <./images/plasmid_circular_nice.png>] (./_minted-Tutorial/7CAF22FEDE98A6B9B7990010CA8709DC14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/FA676816242752C9FE9F5EB12D4DAA8914FA033DCB1376922271CBD58A8 A4A36.pygtex [290]) (./_minted-Tutorial/7926619D7609A591C404A01B2A99177A14FA033DCB1376922271CBD58A8 A4A36.pygtex [291]) Excluding 'htmlonly' comment. [292 <./images/three_track_si mple.png>] (./_minted-Tutorial/A2465D4E8908256A31684D5DDE7DA11114FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/347EB36A3001532221DDF6C29AA04AFB14FA033DCB1376922271CBD58A8 A4A36.pygtex [293]) (./_minted-Tutorial/F46F39DD7A8EC7B20CD42ACF6EFD184014FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/2CF2D2FC7E96B3F426F22452724A4C2814FA033DCB1376922271CBD58A8 A4A36.pygtex) Overfull \hbox (2.65141pt too wide) in paragraph at lines 873--879 []\OT1/cmr/m/n/10 There are sev-eral im-por-tant pieces to this code. First the [][]\OT1/cmtt/m/n/10 GenomeDiagram []\OT1/cmr/m/n/10 ob-ject has a [][]\OT1/cm tt/m/n/10 cross_track_links Excluding 'htmlonly' comment. [294] Excluding 'htmlonly' comment. [295 <./image s/three_track_cl.png>] [296 <./images/three_track_cl2a.png>] (./_minted-Tutorial/F9FFB9659EC22BC166AEB6F72841497714FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/A9695DE54C455E13B400269BF9F424FE14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/F545B5C3D394029AA34E76D27DC2DBAF14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/3BACFFDF9009929D690C44BF09EFB67F14FA033DCB1376922271CBD58A8 A4A36.pygtex) [297] (./_minted-Tutorial/0AC11BF466D4AA0B0536F05378BEC9CC14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/F5380F7F462C2A51219D9EF8994C192C14FA033DCB1376922271CBD58A8 A4A36.pygtex [298] [299 <./images/simple_chrom.pdf> <./images/tRNA_chrom.pdf>]) Excluding 'htmlonly' comment. 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How-ever, for large FASTQ files it woul d be faster the low-level [][]\OT1/cmtt/m/n/10 FastqGeneralIterator (./_minted-Tutorial/AB16E58608A2F17CC79E69295572088714FA033DCB1376922271CBD58A8 A4A36.pygtex) Overfull \hbox (4.57849pt too wide) in paragraph at lines 474--476 \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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[325] Overfull \hbox (4.00363pt too wide) in paragraph at lines 1115--1118 []\OT1/cmr/m/it/10 Tip: \OT1/cmr/m/n/10 Rather than us-ing [][]\OT1/cmtt/m/n/10 pylab.show() []\OT1/cmr/m/n/10 to show the plot in a win-dow, you can also use [][]\OT1/cmtt/m/n/10 pylab.savefig(...) (./_minted-Tutorial/7C23BDB073E316E7093E4D3A77BD752E14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/CB78AD94DFE82ADBAF348C0EC1D261CD14FA033DCB1376922271CBD58A8 A4A36.pygtex [326 <./images/hist_plot.png>]) Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. (./_minted-Tutorial/6E0DA723E11A7B9CA8E2353A984B5DF714FA033DCB1376922271CBD58A8 A4A36.pygtex) [327 <./images/gc_plot.png>] (./_minted-Tutorial/219B67DCB31F2334EDD0B85471FABDEA14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/9574E55C4A182E2A0201DF18689F52F414FA033DCB1376922271CBD58A8 A4A36.pygtex [328 <./images/dot_plot.png>]) Excluding 'htmlonly' comment. 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[331 <./images/SRR001666.png>] (./_minted-Tutorial/9D2779E6D02C00C016A7A73A452EBC7314FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/06CAA397021B5D0CD904B7CF0209DCA314FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/6E116EF74541395FE187AA3D3E41BEE90C640781732628151051B15D85C 9070A.pygtex) (./_minted-Tutorial/16711B0A63F93BBACAF3C86CFFB7BEFA0C640781732628151051B15D85C 9070A.pygtex [332]) (./_minted-Tutorial/96EC77291C119EF69670ACDB1C35CE210C640781732628151051B15D85C 9070A.pygtex) (./_minted-Tutorial/6C14F4F0692168BA7165351C706B643D14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/E686FC2D122CF1560FAF4512CD53777F14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/E09A8EBF1B7CB9F831FC2D9DA481453514FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/E598995EF885D7803642E8685DCB8F900C640781732628151051B15D85C 9070A.pygtex) Overfull \hbox (49.0755pt too wide) in paragraph at lines 1531--1532 []\OT1/cmr/m/n/10 You can ac-cess any el-e-ment of the PSSM by sub-script-ing l ike [][]\OT1/cmtt/m/n/10 your_pssm[sequence_number][residue_count_name][]\OT1/c mr/m/n/10 . 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(./_minted-Tutorial/867AD481B37AFD4F1A17FC0F2F42FCAE6EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/E8078015A2C53794A733DDC875BD06216EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/754EBE4BCCE307413E74F18728530D046EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/E40D6903CCE8EA230C75C80B7C2D90736EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/7A0DBB9735CDAA1699A6FA164701062F6EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/BC243371043473AEE20C23FF0FABFF0D6EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) Overfull \hbox (39.35472pt too wide) in paragraph at lines 73--77 []\OT1/cmr/m/n/10 Tests based on Python's stan-dard [][]\OT1/cmtt/m/n/10 unitte st []\OT1/cmr/m/n/10 frame-work will [][]\OT1/cmtt/m/n/10 import unittest []\OT 1/cmr/m/n/10 and then de-fine [][]\OT1/cmtt/m/n/10 unittest.TestCase [338] (./_minted-Tutorial/1D61711C528533FBB5B198E42FABC51C0C640781732628151051B15D85C 9070A.pygtex) (./_minted-Tutorial/2A1F0B8D037B993D748BF652420448ED6EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex [339]) (./_minted-Tutorial/61465735FDB5BC7ADF12D7A4628FC9A714FA033DCB1376922271CBD58A8 A4A36.pygtex) [340] (./_minted-Tutorial/826F7B9143F73D7CFCAB00906377DAB914FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/B1E279D3993E4775FBE4555B6DD342AD6EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/313C740A73E814DA220EB71149FE706E14FA033DCB1376922271CBD58A8 A4A36.pygtex [341]) (./_minted-Tutorial/99DA0A53F2BD41D9D1BCE2B0332444F46EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/4916E014295B56C6CDDB3C287542DA2914FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/11CE164E202C147B18E9ADEA155A760214FA033DCB1376922271CBD58A8 A4A36.pygtex [342]) (./_minted-Tutorial/7A0DBB9735CDAA1699A6FA164701062F6EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) [343] (./_minted-Tutorial/3E57444149EF1ACC12DA2995F5B034566EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/DD3A1A642CB850F292FC934F9336EC436EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex)) [344] (./Tutorial/chapter_advanced.tex Chapter 22. Overfull \hbox (61.48412pt too wide) in paragraph at lines 40--42 []\OT1/cmr/m/n/10 The [][]\OT1/cmtt/m/n/10 SeqMat []\OT1/cmr/m/n/10 class de-ri ves from a dic-tio-nary. The dic-tio-nary is of the form [][]\OT1/cmtt/m/n/10 { (i1,j1):n1, (i1,j2):n2,...,(ik,jk):nk} (./_minted-Tutorial/B9AA829C45C3718734961EED663138A314FA033DCB1376922271CBD58A8 A4A36.pygtex) [345] (./_minted-Tutorial/C91962005319864FA8A80F7CE461D6C614FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/949D631F5CFAE16DADE8A9B46DC246FE14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/D57E65C15B8337B55081A0ABDE216E8B14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/30813B956DA3EC8A9CBD746D69F32D000C640781732628151051B15D85C 9070A.pygtex) (./_minted-Tutorial/758DB025D865DFC37AEBF0F3FB3EAF8D0C640781732628151051B15D85C 9070A.pygtex) (./_minted-Tutorial/0C3F6A07854D0D0ACBB80A71C6F047250C640781732628151051B15D85C 9070A.pygtex) [346] (./_minted-Tutorial/01598304B617194419D3D22E288DDBB414FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/2EE2B4E009A2AA257D683D54D33A379814FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/092222FC5487DB13D5744BF56515DC5767B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex) (./_minted-Tutorial/3FBCEA7E512BCF1A100675C665984F1E14FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/F90C13646B17B56314C7FA6500465F7F14FA033DCB1376922271CBD58A8 A4A36.pygtex) Overfull \hbox (30.74179pt too wide) in paragraph at lines 197--198 [][][]\OT1/cmtt/m/n/10 factor[]\OT1/cmr/m/n/10 : fac-tor used to mul-ti-ply the log-odds val-ues. Each en-try is gen-er-ated by log(LOM[key])*factor (./_minted-Tutorial/4C4AB8D87E6E7015C3AF4CC8FB7D06D214FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/F0DBB62056D7DE5645E8992BD297EBAE14FA033DCB1376922271CBD58A8 A4A36.pygtex [347]) (./_minted-Tutorial/3C40FC62A59A2301A420D8E25D52D8FB0C640781732628151051B15D85C 9070A.pygtex) (./_minted-Tutorial/9AD3043016CF73EB0A57C6DFA985DB280C640781732628151051B15D85C 9070A.pygtex) (./_minted-Tutorial/D009E3834E447E34C2A0FF5922F938B814FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/4E08040CCAE3D812784651E566C1B38314FA033DCB1376922271CBD58A8 A4A36.pygtex) (./_minted-Tutorial/ACABC0B74314C452E389E9078BF83C3D67B6D4EEEA70E83368C1BFCE3E2 2EA7D.pygtex)) [348] (./Tutorial/chapter_contributing.tex Chapter 23. [349] (./_minted-Tutorial/7713FA97EA16E9508BA3E6B9449449256EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) (./_minted-Tutorial/61D19A91BF1A1F95030292E40EF87A366EA57A5CF4D3F0EFF6188E720E8 9664B.pygtex) [350]) [351] (./Tutorial/chapter_appendix.tex Chapter 24. 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Transcript written on Tutorial.log. pdflatex biopdb_faq.tex This is pdfTeX, Version 3.14159265-2.6-1.40.21 (TeX Live 2020/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./biopdb_faq.tex LaTeX2e <2020-02-02> patch level 5 L3 programming layer <2020-07-17> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2019/12/20 v1.4l Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/bookman.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pbk.fd)) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def)) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/generic/iftex/ifvtex.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty)) (/usr/share/texlive/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty) (/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/generic/atbegshi/atbegshi.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/atveryend/atveryend.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 56. (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def)) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf)) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def) No file biopdb_faq.aux. *geometry* driver: auto-detecting *geometry* detected driver: pdftex *geometry* verbose mode - [ preamble ] result: * driver: pdftex * paper: a4paper * layout: * layoutoffset:(h,v)=(0.0pt,0.0pt) * modes: * h-part:(L,W,R)=(89.62709pt, 418.25368pt, 89.6271pt) * v-part:(T,H,B)=(56.9055pt, 731.23584pt, 56.9055pt) * \paperwidth=597.50787pt * \paperheight=845.04684pt * \textwidth=418.25368pt * \textheight=731.23584pt * \oddsidemargin=17.3571pt * \evensidemargin=17.3571pt * \topmargin=-52.36449pt * \headheight=12.0pt * \headsep=25.0pt * \topskip=10.0pt * \footskip=30.0pt * \marginparwidth=65.0pt * \marginparsep=11.0pt * \columnsep=10.0pt * \skip\footins=9.0pt plus 4.0pt minus 2.0pt * \hoffset=0.0pt * \voffset=0.0pt * \mag=1000 * \@twocolumnfalse * \@twosidefalse * \@mparswitchfalse * \@reversemarginfalse * (1in=72.27pt=25.4mm, 1cm=28.453pt) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) Overfull \hbox (40.90678pt too wide) in paragraph at lines 112--119 []\T1/pbk/l/n/10 However, the [][]\T1/pcr/m/n/10 Bio.PDB.mmCIF.MMCIFlex []\T1/p bk/l/n/10 mod-ule (used in-ter-nally by [][]\T1/pcr/m/n/10 Bio.PDB.MMCIFParser [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pbk.fd) [2] Overfull \hbox (21.75009pt too wide) in paragraph at lines 257--262 \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 298--304 \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 298--304 \T1/pcr/m/n/10 method, resolution, structure_-reference \T1/pbk/l/n/10 (maps to a list of ref-er-ences), \T1/pcr/m/n/10 journal_- LaTeX Warning: Reference `sub:The-Structure-object' on page 4 undefined on inpu t line 321. [4] [5] LaTeX Warning: Reference `cap:SMCRA' on page 6 undefined on input line 528. [6] [7 <./images/smcra.png (PNG copy)>] [8] LaTeX Warning: Reference `cap:SMCRA' on page 9 undefined on input line 730. LaTeX Warning: Reference `cap:SMCRA' on page 9 undefined on input line 759. LaTeX Warning: Reference `sub:Analysis' on page 9 undefined on input line 801. [9] LaTeX Warning: Reference `sub:Analysis' on page 10 undefined on input line 806. [10] Overfull \hbox (45.08351pt too wide) in paragraph at lines 961--965 \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 969--974 \T1/pbk/l/n/10 try). The se-quence of each polypep-tide can then eas-ily be ob- tained from the \T1/pcr/m/n/10 Polypeptide LaTeX Warning: Reference `cap:DSSP-codes' on page 11 undefined on input line 99 1. [11] Overfull \hbox (87.74638pt too wide) in paragraph at lines 1098--1099 []\T1/pcr/m/n/10 # Calculate classical coordination number exp_fs=hse.calc_fs_e xposure(model) [12] Overfull \hbox (20.6135pt too wide) in paragraph at lines 1119--1124 \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 1281--1289 []\T1/pbk/l/n/10 THE CON-TRIB-U-TORS AND COPY-RIGHT HOLD-ERS OF THIS SOFT-WARE DIS-CLAIM [15] (./biopdb_faq.aux) Package rerunfilecheck Warning: File `biopdb_faq.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on biopdb_faq.pdf (15 pages, 155666 bytes). Transcript written on biopdb_faq.log. pdflatex biopdb_faq.tex This is pdfTeX, Version 3.14159265-2.6-1.40.21 (TeX Live 2020/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./biopdb_faq.tex LaTeX2e <2020-02-02> patch level 5 L3 programming layer <2020-07-17> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2019/12/20 v1.4l Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/bookman.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pbk.fd)) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def)) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/generic/iftex/ifvtex.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty)) (/usr/share/texlive/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty) (/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/generic/atbegshi/atbegshi.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/atveryend/atveryend.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 56. (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def)) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf)) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def) (./biopdb_faq.aux) *geometry* driver: auto-detecting *geometry* detected driver: pdftex *geometry* verbose mode - [ preamble ] result: * driver: pdftex * paper: a4paper * layout: * layoutoffset:(h,v)=(0.0pt,0.0pt) * modes: * h-part:(L,W,R)=(89.62709pt, 418.25368pt, 89.6271pt) * v-part:(T,H,B)=(56.9055pt, 731.23584pt, 56.9055pt) * \paperwidth=597.50787pt * \paperheight=845.04684pt * \textwidth=418.25368pt * \textheight=731.23584pt * \oddsidemargin=17.3571pt * \evensidemargin=17.3571pt * \topmargin=-52.36449pt * \headheight=12.0pt * \headsep=25.0pt * \topskip=10.0pt * \footskip=30.0pt * \marginparwidth=65.0pt * \marginparsep=11.0pt * \columnsep=10.0pt * \skip\footins=9.0pt plus 4.0pt minus 2.0pt * \hoffset=0.0pt * \voffset=0.0pt * \mag=1000 * \@twocolumnfalse * \@twosidefalse * \@mparswitchfalse * \@reversemarginfalse * (1in=72.27pt=25.4mm, 1cm=28.453pt) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty)) (./biopdb_faq.out) (./biopdb_faq.out) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) Overfull \hbox (40.90678pt too wide) in paragraph at lines 112--119 []\T1/pbk/l/n/10 However, the [][]\T1/pcr/m/n/10 Bio.PDB.mmCIF.MMCIFlex []\T1/p bk/l/n/10 mod-ule (used in-ter-nally by [][]\T1/pcr/m/n/10 Bio.PDB.MMCIFParser [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pbk.fd) [2] Overfull \hbox (21.75009pt too wide) in paragraph at lines 257--262 \T1/pbk/l/n/10 file to their val-ues. 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The se-quence of each polypep-tide can then eas-ily be ob- tained from the \T1/pcr/m/n/10 Polypeptide [11] Overfull \hbox (87.74638pt too wide) in paragraph at lines 1098--1099 []\T1/pcr/m/n/10 # Calculate classical coordination number exp_fs=hse.calc_fs_e xposure(model) [12] Overfull \hbox (20.6135pt too wide) in paragraph at lines 1119--1124 \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 1281--1289 []\T1/pbk/l/n/10 THE CON-TRIB-U-TORS AND COPY-RIGHT HOLD-ERS OF THIS SOFT-WARE DIS-CLAIM [15] (./biopdb_faq.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on biopdb_faq.pdf (15 pages, 157183 bytes). Transcript written on biopdb_faq.log. pdflatex biopdb_faq.tex This is pdfTeX, Version 3.14159265-2.6-1.40.21 (TeX Live 2020/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./biopdb_faq.tex LaTeX2e <2020-02-02> patch level 5 L3 programming layer <2020-07-17> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2019/12/20 v1.4l Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/bookman.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pbk.fd)) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def)) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/generic/iftex/ifvtex.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty)) (/usr/share/texlive/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty) (/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/generic/atbegshi/atbegshi.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/atveryend/atveryend.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 56. (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def)) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf)) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def) (./biopdb_faq.aux) *geometry* driver: auto-detecting *geometry* detected driver: pdftex *geometry* verbose mode - [ preamble ] result: * driver: pdftex * paper: a4paper * layout: * layoutoffset:(h,v)=(0.0pt,0.0pt) * modes: * h-part:(L,W,R)=(89.62709pt, 418.25368pt, 89.6271pt) * v-part:(T,H,B)=(56.9055pt, 731.23584pt, 56.9055pt) * \paperwidth=597.50787pt * \paperheight=845.04684pt * \textwidth=418.25368pt * \textheight=731.23584pt * \oddsidemargin=17.3571pt * \evensidemargin=17.3571pt * \topmargin=-52.36449pt * \headheight=12.0pt * \headsep=25.0pt * \topskip=10.0pt * \footskip=30.0pt * \marginparwidth=65.0pt * \marginparsep=11.0pt * \columnsep=10.0pt * \skip\footins=9.0pt plus 4.0pt minus 2.0pt * \hoffset=0.0pt * \voffset=0.0pt * \mag=1000 * \@twocolumnfalse * \@twosidefalse * \@mparswitchfalse * \@reversemarginfalse * (1in=72.27pt=25.4mm, 1cm=28.453pt) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty)) (./biopdb_faq.out) (./biopdb_faq.out) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) Overfull \hbox (40.90678pt too wide) in paragraph at lines 112--119 []\T1/pbk/l/n/10 However, the [][]\T1/pcr/m/n/10 Bio.PDB.mmCIF.MMCIFlex []\T1/p bk/l/n/10 mod-ule (used in-ter-nally by [][]\T1/pcr/m/n/10 Bio.PDB.MMCIFParser [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pbk.fd) [2] Overfull \hbox (21.75009pt too wide) in paragraph at lines 257--262 \T1/pbk/l/n/10 file to their val-ues. 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The se-quence of each polypep-tide can then eas-ily be ob- tained from the \T1/pcr/m/n/10 Polypeptide [11] Overfull \hbox (87.74638pt too wide) in paragraph at lines 1098--1099 []\T1/pcr/m/n/10 # Calculate classical coordination number exp_fs=hse.calc_fs_e xposure(model) [12] Overfull \hbox (20.6135pt too wide) in paragraph at lines 1119--1124 \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 1281--1289 []\T1/pbk/l/n/10 THE CON-TRIB-U-TORS AND COPY-RIGHT HOLD-ERS OF THIS SOFT-WARE DIS-CLAIM [15] (./biopdb_faq.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on biopdb_faq.pdf (15 pages, 157183 bytes). Transcript written on biopdb_faq.log. make[2]: Leaving directory '/<>/python-biopython-1.76+dfsg/Doc' make[1]: Leaving directory '/<>/python-biopython-1.76+dfsg' rm -f debian/python3-biopython.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/<>/python-biopython-1.76+dfsg' mkdir -p Tests_avoid for avoid in PAML_tools EmbossPhylipNew MSAProbs_tool NACCESS_tool PopGen_GenePop PopGen_GenePop_EasyController XXmotif_tool PDB_ResidueDepth mmtf mmtf_online raxml_tool BioSQL_MySQLdb BioSQL_psycopg2 \ ; do \ mv Tests/test_${avoid}.py Tests_avoid ; \ done # 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 3.8 --test --system=custom "--test-args=set -e; \\\ mkdir -p {build_dir}/home; \\\ mkdir -p {build_dir}/Doc/examples; \\\ cp -a Doc/Tutorial.tex {build_dir}/Doc; \\\ cp -a Doc/Tutorial {build_dir}/Doc; \\\ cp -a Doc/examples {build_dir}/Doc; \\\ cp -a Tests {build_dir}; \\\ cd {build_dir}/Tests; \\\ env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME={build_dir}/home {interpreter} run_tests.py --offline" I: pybuild base:217: set -e; \ mkdir -p /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/home; \ mkdir -p /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Doc/examples; \ cp -a Doc/Tutorial.tex /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Doc; \ cp -a Doc/Tutorial /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Doc; \ cp -a Doc/examples /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Doc; \ cp -a Tests /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build; \ cd /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Tests; \ env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=/<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/home python3.8 run_tests.py --offline test_Ace ... ok test_Affy ... ok test_AlignIO ... ok test_AlignIO_ClustalIO ... ok test_AlignIO_EmbossIO ... ok test_AlignIO_FastaIO ... ok test_AlignIO_MauveIO ... ok test_AlignIO_PhylipIO ... ok test_AlignIO_convert ... ok test_AlignInfo ... ok test_Application ... ok test_BWA_tool ... ok test_BioSQL_MySQLdb_online ... skipping. internet not available test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) test_BioSQL_mysql_connector_online ... skipping. internet not available test_BioSQL_psycopg2_online ... skipping. internet not available test_BioSQL_sqlite3 ... ok test_BioSQL_sqlite3_online ... skipping. internet not available test_Blast_Record ... ok test_CAPS ... ok test_CelFile ... ok test_Chi2 ... ok test_ClustalOmega_tool ... ok test_Clustalw_tool ... ok test_Cluster ... ok test_CodonTable ... ok test_ColorSpiral ... ok test_Compass ... ok test_Consensus ... ok test_Crystal ... ok test_DSSP_tool ... ok test_Dialign_tool ... ok test_EMBL_unittest ... ok test_Emboss ... ok test_EmbossPrimer ... ok test_Entrez ... ok test_Entrez_online ... skipping. internet not available test_Entrez_parser ... ok test_Enzyme ... ok test_ExPASy ... skipping. internet not available test_FSSP ... ok test_Fasttree_tool ... ok test_File ... ok test_GenBank ... ok test_GenomeDiagram ... Warn: Can't find .pfb for face 'Times-Roman' ok test_GraphicsBitmaps ... skipping. Check the fonts needed by ReportLab if you want bitmaps from Bio.Graphics Can't setFont(Times-Roman) missing the T1 files? Originally : makeT1Font() argument 2 must be str, not None test_GraphicsChromosome ... ok test_GraphicsDistribution ... ok test_GraphicsGeneral ... ok test_HMMCasino ... ok test_HMMGeneral ... ok test_KDTree ... ok test_KEGG ... ok test_KEGG_online ... skipping. internet not available test_KGML_graphics ... ok test_KGML_graphics_online ... skipping. internet not available test_KGML_nographics ... ok test_KeyWList ... ok test_LogisticRegression ... ok test_MafIO_index ... ok test_Mafft_tool ... ok test_MarkovModel ... ok test_Medline ... ok test_Muscle_tool ... ok test_NCBITextParser ... ok test_NCBIXML ... ok test_NCBI_BLAST_tools ... /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:398: UserWarning: NCBI BLAST+ blastn and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids) warnings.warn("NCBI BLAST+ %s and Biopython out sync. Please " /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:398: UserWarning: NCBI BLAST+ blastp and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -ipglist,-negative_ipglist,-negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids) warnings.warn("NCBI BLAST+ %s and Biopython out sync. Please " /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:398: UserWarning: NCBI BLAST+ blastx and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -ipglist,-negative_ipglist,-negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids) warnings.warn("NCBI BLAST+ %s and Biopython out sync. Please " /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:398: UserWarning: NCBI BLAST+ deltablast and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids) warnings.warn("NCBI BLAST+ %s and Biopython out sync. Please " /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:398: UserWarning: NCBI BLAST+ makeblastdb and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -blastdb_version) warnings.warn("NCBI BLAST+ %s and Biopython out sync. Please " /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:398: UserWarning: NCBI BLAST+ psiblast and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -ipglist,-negative_ipglist,-negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids) warnings.warn("NCBI BLAST+ %s and Biopython out sync. Please " /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:398: UserWarning: NCBI BLAST+ rpsblast and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -sorthits,-sorthsps,-subject_besthit) warnings.warn("NCBI BLAST+ %s and Biopython out sync. Please " /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:398: UserWarning: NCBI BLAST+ rpstblastn and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -sorthits,-sorthsps) warnings.warn("NCBI BLAST+ %s and Biopython out sync. Please " /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:398: UserWarning: NCBI BLAST+ tblastn and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids) warnings.warn("NCBI BLAST+ %s and Biopython out sync. Please " /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:398: UserWarning: NCBI BLAST+ tblastx and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids) warnings.warn("NCBI BLAST+ %s and Biopython out sync. Please " FAIL test_NCBI_qblast ... skipping. internet not available test_NMR ... ok test_NaiveBayes ... ok test_Nexus ... ok test_PAML_baseml ... ok test_PAML_codeml ... ok test_PAML_yn00 ... ok test_PDB ... ok test_PDBList ... skipping. internet not available test_PDB_Dice ... ok test_PDB_FragmentMapper ... ok test_PDB_KDTree ... ok test_PDB_MMCIF2Dict ... ok test_PDB_MMCIFParser ... ok test_PDB_Polypetide ... ok test_PDB_StructureAlignment ... /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB/StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain A is discontinuous at line 13298. warnings.warn( /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB/StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain B is discontinuous at line 13344. warnings.warn( ok test_PDB_Superimposer ... ok test_PDB_parse_pdb_header ... ok test_PDB_vectors ... ok test_Pathway ... ok test_Phd ... ok test_Phylo ... ok test_PhyloXML ... ok test_Phylo_CDAO ... ok test_Phylo_NeXML ... ok test_Phylo_matplotlib ... ok test_Phylo_networkx ... ok test_PopGen_GenePop_nodepend ... ok test_Prank_tool ... ok test_Probcons_tool ... ok test_ProtParam ... ok test_QCPSuperimposer ... ok test_RCSBFormats ... ok test_Restriction ... ok test_SCOP_Astral ... ok test_SCOP_Cla ... ok test_SCOP_Des ... ok test_SCOP_Dom ... ok test_SCOP_Hie ... ok test_SCOP_Raf ... ok test_SCOP_Residues ... ok test_SCOP_Scop ... ok test_SCOP_online ... skipping. internet not available test_SVDSuperimposer ... ok test_SearchIO_blast_tab ... ok test_SearchIO_blast_tab_index ... ok test_SearchIO_blast_text ... ok test_SearchIO_blast_xml ... ok test_SearchIO_blast_xml_index ... ok test_SearchIO_blat_psl ... ok test_SearchIO_blat_psl_index ... ok test_SearchIO_exonerate ... ok test_SearchIO_exonerate_text_index ... ok test_SearchIO_exonerate_vulgar_index ... ok test_SearchIO_fasta_m10 ... ok test_SearchIO_fasta_m10_index ... ok test_SearchIO_hhsuite2_text ... ok test_SearchIO_hmmer2_text ... ok test_SearchIO_hmmer2_text_index ... ok test_SearchIO_hmmer3_domtab ... ok test_SearchIO_hmmer3_domtab_index ... ok test_SearchIO_hmmer3_tab ... ok test_SearchIO_hmmer3_tab_index ... ok test_SearchIO_hmmer3_text ... ok test_SearchIO_hmmer3_text_index ... ok test_SearchIO_interproscan_xml ... ok test_SearchIO_legacy ... ok test_SearchIO_model ... ok test_SearchIO_write ... ok test_SeqFeature ... ok test_SeqIO ... ok test_SeqIO_AbiIO ... ok test_SeqIO_FastaIO ... ok test_SeqIO_Gck ... ok test_SeqIO_Insdc ... /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/GenBank/Scanner.py:303: BiopythonParserWarning: Non-standard feature line wrapping (didn't break on comma)? warnings.warn( ok test_SeqIO_NibIO ... ok test_SeqIO_PdbIO ... ok test_SeqIO_QualityIO ... ok test_SeqIO_SeqXML ... ok test_SeqIO_SnapGene ... ok test_SeqIO_Xdna ... ok test_SeqIO_convert ... ok test_SeqIO_features ... ok test_SeqIO_index ... ok test_SeqIO_online ... skipping. internet not available test_SeqIO_write ... ok test_SeqRecord ... ok test_SeqUtils ... ok test_Seq_objs ... ok test_SffIO ... ok test_SubsMat ... ok test_SwissProt ... ok test_TCoffee_tool ... ok test_TogoWS ... skipping. internet not available test_TreeConstruction ... ok test_Tutorial ... ok test_UniGene ... ok test_UniProt_GOA ... ok test_Uniprot ... ok test_Wise ... ok test_align ... ok test_align_substitution_matrices ... ok test_bgzf ... ok test_cellosaurus ... ok test_codonalign ... /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Seq.py:2828: 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( /usr/lib/python3/dist-packages/scipy/optimize/_numdiff.py:519: RuntimeWarning: invalid value encountered in true_divide J_transposed[i] = df / dx FAIL test_geo ... ok test_kNN ... ok test_lowess ... /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Bio/Statistics/__init__.py:14: BiopythonDeprecationWarning: Bio.Statistics has been deprecated, and we intend to remove it in a future release of Biopython. warnings.warn("Bio.Statistics has been deprecated, and we intend to remove it " ok test_motifs ... ok test_motifs_online ... skipping. internet not available test_pairwise2 ... ok test_pairwise2_no_C ... ok test_pairwise_aligner ... ok test_phenotype ... ok test_phenotype_fit ... ok test_phyml_tool ... skipping. Install PhyML 3.0 or later if you want to use the Bio.Phylo.Applications wrapper. test_prodoc ... ok test_prosite1 ... ok test_prosite2 ... ok test_psw ... ok test_samtools_tool ... ok test_seq ... ok test_translate ... ok test_trie ... ok Bio docstring test ... ok Bio.Affy docstring test ... ok Bio.Affy.CelFile docstring test ... ok Bio.Align docstring test ... ok Bio.Align.AlignInfo docstring test ... ok Bio.Align.Applications docstring test ... ok Bio.Align.Applications._ClustalOmega docstring test ... ok Bio.Align.Applications._Clustalw docstring test ... ok Bio.Align.Applications._Dialign docstring test ... ok Bio.Align.Applications._MSAProbs docstring test ... ok Bio.Align.Applications._Mafft docstring test ... ok Bio.Align.Applications._Muscle docstring test ... ok Bio.Align.Applications._Prank docstring test ... ok Bio.Align.Applications._Probcons docstring test ... ok Bio.Align.Applications._TCoffee docstring test ... ok Bio.Align._aligners docstring test ... ok Bio.Align.substitution_matrices docstring test ... ok Bio.AlignIO docstring test ... ok Bio.AlignIO.ClustalIO docstring test ... ok Bio.AlignIO.EmbossIO docstring test ... ok Bio.AlignIO.FastaIO docstring test ... ok Bio.AlignIO.Interfaces docstring test ... ok Bio.AlignIO.MafIO docstring test ... ok Bio.AlignIO.MauveIO docstring test ... ok Bio.AlignIO.MsfIO docstring test ... ok Bio.AlignIO.NexusIO docstring test ... ok Bio.AlignIO.PhylipIO docstring test ... ok Bio.AlignIO.StockholmIO docstring test ... ok Bio.Alphabet docstring test ... ok Bio.Alphabet.IUPAC docstring test ... ok Bio.Alphabet.Reduced docstring test ... ok Bio.Application docstring test ... ok Bio.Blast docstring test ... ok Bio.Blast.Applications docstring test ... ok Bio.Blast.NCBIWWW docstring test ... ok Bio.Blast.NCBIXML docstring test ... ok Bio.Blast.ParseBlastTable docstring test ... ok Bio.Blast.Record docstring test ... ok Bio.CAPS docstring test ... ok Bio.Cluster docstring test ... ok Bio.Cluster._cluster docstring test ... ok Bio.Compass docstring test ... ok Bio.Crystal docstring test ... ok Bio.Data docstring test ... ok Bio.Data.CodonTable docstring test ... ok Bio.Data.IUPACData docstring test ... ok Bio.Data.SCOPData docstring test ... ok Bio.Emboss docstring test ... ok Bio.Emboss.Applications docstring test ... ok Bio.Emboss.Primer3 docstring test ... ok Bio.Emboss.PrimerSearch docstring test ... ok Bio.Entrez.Parser docstring test ... ok Bio.ExPASy.Enzyme docstring test ... ok Bio.ExPASy.Prodoc docstring test ... ok Bio.ExPASy.Prosite docstring test ... ok Bio.ExPASy.ScanProsite docstring test ... ok Bio.ExPASy.cellosaurus docstring test ... ok Bio.FSSP docstring test ... ok Bio.FSSP.FSSPTools docstring test ... ok Bio.FSSP.fssp_rec docstring test ... ok Bio.File docstring test ... ok Bio.GenBank docstring test ... ok Bio.GenBank.Record docstring test ... ok Bio.GenBank.Scanner docstring test ... ok Bio.GenBank.utils docstring test ... ok Bio.Geo docstring test ... ok Bio.Geo.Record docstring test ... ok Bio.Graphics docstring test ... ok Bio.Graphics.BasicChromosome docstring test ... ok Bio.Graphics.ColorSpiral docstring test ... ok Bio.Graphics.Comparative docstring test ... ok Bio.Graphics.DisplayRepresentation docstring test ... ok Bio.Graphics.Distribution docstring test ... ok Bio.Graphics.GenomeDiagram docstring test ... ok Bio.Graphics.GenomeDiagram._AbstractDrawer docstring test ... ok Bio.Graphics.GenomeDiagram._CircularDrawer docstring test ... ok Bio.Graphics.GenomeDiagram._Colors docstring test ... ok Bio.Graphics.GenomeDiagram._CrossLink docstring test ... ok Bio.Graphics.GenomeDiagram._Diagram docstring test ... ok Bio.Graphics.GenomeDiagram._Feature docstring test ... ok Bio.Graphics.GenomeDiagram._FeatureSet docstring test ... ok Bio.Graphics.GenomeDiagram._Graph docstring test ... ok Bio.Graphics.GenomeDiagram._GraphSet docstring test ... ok Bio.Graphics.GenomeDiagram._LinearDrawer docstring test ... ok Bio.Graphics.GenomeDiagram._Track docstring test ... ok Bio.Graphics.KGML_vis docstring test ... ok Bio.HMM docstring test ... ok Bio.HMM.DynamicProgramming docstring test ... ok Bio.HMM.MarkovModel docstring test ... ok Bio.HMM.Trainer docstring test ... ok Bio.HMM.Utilities docstring test ... ok Bio.Index docstring test ... ok Bio.KDTree docstring test ... ok Bio.KDTree.KDTree docstring test ... ok Bio.KDTree._CKDTree 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.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.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.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.kdtrees docstring test ... ok Bio.PDB.mmcifio docstring test ... ok Bio.PDB.mmtf docstring test ... skipped, missing Python dependency Bio.PDB.mmtf.DefaultParser docstring test ... skipped, missing Python dependency Bio.PDB.mmtf.mmtfio docstring test ... skipped, missing Python dependency Bio.PDB.parse_pdb_header docstring test ... ok Bio.PDB.vectors docstring test ... ok Bio.Pathway docstring test ... ok Bio.Pathway.Rep docstring test ... ok Bio.Pathway.Rep.Graph docstring test ... ok Bio.Pathway.Rep.MultiGraph docstring test ... ok Bio.Phylo docstring test ... ok Bio.Phylo.Applications docstring test ... ok Bio.Phylo.Applications._Fasttree docstring test ... ok Bio.Phylo.Applications._Phyml docstring test ... ok Bio.Phylo.Applications._Raxml docstring test ... ok Bio.Phylo.BaseTree docstring test ... ok Bio.Phylo.CDAO docstring test ... ok Bio.Phylo.CDAOIO docstring test ... ok Bio.Phylo.Consensus docstring test ... ok Bio.Phylo.NeXML docstring test ... ok Bio.Phylo.NeXMLIO docstring test ... ok Bio.Phylo.Newick docstring test ... ok Bio.Phylo.NewickIO docstring test ... ok Bio.Phylo.NexusIO docstring test ... ok Bio.Phylo.PAML docstring test ... ok Bio.Phylo.PAML._paml docstring test ... ok Bio.Phylo.PAML._parse_baseml docstring test ... ok Bio.Phylo.PAML._parse_codeml docstring test ... ok Bio.Phylo.PAML._parse_yn00 docstring test ... ok Bio.Phylo.PAML.baseml docstring test ... ok Bio.Phylo.PAML.chi2 docstring test ... ok Bio.Phylo.PAML.codeml docstring test ... ok Bio.Phylo.PAML.yn00 docstring test ... ok Bio.Phylo.PhyloXML docstring test ... ok Bio.Phylo.PhyloXMLIO docstring test ... ok Bio.Phylo.TreeConstruction docstring test ... ok Bio.Phylo._cdao_owl docstring test ... ok Bio.Phylo._io docstring test ... ok Bio.Phylo._utils docstring test ... ok Bio.PopGen docstring test ... ok Bio.PopGen.GenePop docstring test ... ok Bio.PopGen.GenePop.Controller docstring test ... ok Bio.PopGen.GenePop.EasyController docstring test ... ok Bio.PopGen.GenePop.FileParser docstring test ... ok Bio.PopGen.GenePop.LargeFileParser docstring test ... ok Bio.PopGen.GenePop.Utils docstring test ... ok Bio.Restriction docstring test ... ok Bio.Restriction.PrintFormat docstring test ... ok Bio.Restriction.Restriction docstring test ... ok Bio.Restriction.Restriction_Dictionary docstring test ... ok Bio.SCOP docstring test ... ok Bio.SCOP.Cla docstring test ... ok Bio.SCOP.Des docstring test ... ok Bio.SCOP.Dom docstring test ... ok Bio.SCOP.Hie docstring test ... ok Bio.SCOP.Raf docstring test ... ok Bio.SCOP.Residues docstring test ... ok Bio.SVDSuperimposer docstring test ... ok Bio.SearchIO docstring test ... ok Bio.SearchIO.BlastIO docstring test ... ok Bio.SearchIO.BlastIO.blast_tab docstring test ... ok Bio.SearchIO.BlastIO.blast_text docstring test ... ok Bio.SearchIO.BlastIO.blast_xml docstring test ... ok Bio.SearchIO.BlatIO docstring test ... ok Bio.SearchIO.ExonerateIO docstring test ... ok Bio.SearchIO.ExonerateIO._base docstring test ... ok Bio.SearchIO.ExonerateIO.exonerate_cigar docstring test ... ok Bio.SearchIO.ExonerateIO.exonerate_text docstring test ... ok Bio.SearchIO.ExonerateIO.exonerate_vulgar docstring test ... ok Bio.SearchIO.FastaIO docstring test ... ok Bio.SearchIO.HHsuiteIO docstring test ... ok Bio.SearchIO.HHsuiteIO.hhsuite2_text docstring test ... ok Bio.SearchIO.HmmerIO docstring test ... ok Bio.SearchIO.HmmerIO._base docstring test ... ok Bio.SearchIO.HmmerIO.hmmer2_text docstring test ... ok Bio.SearchIO.HmmerIO.hmmer3_domtab docstring test ... ok Bio.SearchIO.HmmerIO.hmmer3_tab docstring test ... ok Bio.SearchIO.HmmerIO.hmmer3_text docstring test ... ok Bio.SearchIO.InterproscanIO docstring test ... ok Bio.SearchIO.InterproscanIO.interproscan_xml docstring test ... ok Bio.SearchIO._index docstring test ... ok Bio.SearchIO._legacy docstring test ... ok Bio.SearchIO._legacy.NCBIStandalone docstring test ... ok Bio.SearchIO._legacy.ParserSupport docstring test ... ok Bio.SearchIO._model docstring test ... ok Bio.SearchIO._model._base docstring test ... ok Bio.SearchIO._model.hit docstring test ... ok Bio.SearchIO._model.hsp docstring test ... ok Bio.SearchIO._model.query docstring test ... ok Bio.SearchIO._utils docstring test ... ok Bio.Seq docstring test ... ok Bio.SeqFeature docstring test ... ok Bio.SeqIO docstring test ... ok Bio.SeqIO.AbiIO docstring test ... ok Bio.SeqIO.AceIO docstring test ... ok Bio.SeqIO.FastaIO docstring test ... ok Bio.SeqIO.GckIO docstring test ... ok Bio.SeqIO.IgIO docstring test ... ok Bio.SeqIO.InsdcIO docstring test ... ok Bio.SeqIO.Interfaces docstring test ... ok Bio.SeqIO.NibIO docstring test ... ok Bio.SeqIO.PdbIO docstring test ... ok Bio.SeqIO.PhdIO docstring test ... ok Bio.SeqIO.PirIO docstring test ... ok Bio.SeqIO.QualityIO docstring test ... ok Bio.SeqIO.SeqXmlIO docstring test ... ok Bio.SeqIO.SffIO docstring test ... ok Bio.SeqIO.SnapGeneIO docstring test ... ok Bio.SeqIO.SwissIO docstring test ... ok Bio.SeqIO.TabIO docstring test ... ok Bio.SeqIO.UniprotIO docstring test ... ok Bio.SeqIO.XdnaIO docstring test ... ok Bio.SeqIO._convert docstring test ... ok Bio.SeqIO._index docstring test ... ok Bio.SeqRecord docstring test ... ok Bio.SeqUtils docstring test ... ok Bio.SeqUtils.CheckSum docstring test ... ok Bio.SeqUtils.CodonUsage docstring test ... ok Bio.SeqUtils.CodonUsageIndices docstring test ... ok Bio.SeqUtils.IsoelectricPoint docstring test ... ok Bio.SeqUtils.MeltingTemp docstring test ... ok Bio.SeqUtils.ProtParam docstring test ... ok Bio.SeqUtils.ProtParamData docstring test ... ok Bio.SeqUtils.lcc docstring test ... ok Bio.Sequencing docstring test ... ok Bio.Sequencing.Ace docstring test ... ok Bio.Sequencing.Applications docstring test ... ok Bio.Sequencing.Applications._Novoalign docstring test ... ok Bio.Sequencing.Applications._bwa docstring test ... ok Bio.Sequencing.Applications._samtools docstring test ... ok Bio.Sequencing.Phd docstring test ... ok Bio.Statistics docstring test ... ok Bio.Statistics.lowess docstring test ... ok Bio.SubsMat docstring test ... ok Bio.SubsMat.FreqTable docstring test ... ok Bio.SubsMat.MatrixInfo docstring test ... ok Bio.SwissProt docstring test ... ok Bio.SwissProt.KeyWList docstring test ... ok Bio.UniGene docstring test ... ok Bio.UniProt docstring test ... ok Bio.UniProt.GOA docstring test ... ok Bio.Wise docstring test ... ok Bio.Wise.dnal docstring test ... ok Bio.Wise.psw docstring test ... ok Bio._py3k docstring test ... ok Bio._utils docstring test ... ok Bio.bgzf docstring test ... ok Bio.codonalign docstring test ... ok Bio.codonalign.chisq docstring test ... ok Bio.codonalign.codonalignment docstring test ... ok Bio.codonalign.codonalphabet 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 Bio.trie docstring test ... ok Bio.triefind 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 ====================================================================== FAIL: test_fasta_db_nucl (test_NCBI_BLAST_tools.BlastDB) Test makeblastdb wrapper with nucleotide database. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py", line 248, in test_fasta_db_nucl self.assertTrue(os.path.isfile("GenBank/NC_005816.fna.nsd")) AssertionError: False is not true ====================================================================== FAIL: test_fasta_db_prot (test_NCBI_BLAST_tools.BlastDB) Test makeblastdb wrapper with protein database. ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py", line 213, in test_fasta_db_prot self.assertTrue(os.path.isfile("GenBank/NC_005816.faa.psd")) AssertionError: False is not true ====================================================================== FAIL: test_dn_ds (test_codonalign.Test_dn_ds) ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Tests/test_codonalign.py", line 250, in test_dn_ds self.assertAlmostEqual(dN, 0.0194, places=4) AssertionError: 0.018550963446549371 != 0.0194 within 4 places (0.00084903655345063 difference) ---------------------------------------------------------------------- Ran 518 tests in 948.419 seconds FAILED (failures = 2) Skipping any tests requiring internet access Python version: 3.8.6 (default, Sep 25 2020, 09:36:53) [GCC 10.2.0] Operating system: posix linux E: pybuild pybuild:352: test: plugin custom failed with: exit code=1: set -e; \ mkdir -p /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/home; \ mkdir -p /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Doc/examples; \ cp -a Doc/Tutorial.tex /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Doc; \ cp -a Doc/Tutorial /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Doc; \ cp -a Doc/examples /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Doc; \ cp -a Tests /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build; \ cd /<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/Tests; \ env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=/<>/python-biopython-1.76+dfsg/.pybuild/cpython3_3.8/build/home python3.8 run_tests.py --offline dh_auto_test: error: pybuild --test -i python{version} -p 3.8 --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:83: override_dh_auto_test] Error 25 make[1]: Leaving directory '/<>/python-biopython-1.76+dfsg' make: *** [debian/rules:42: build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2020-10-01T03:49:54Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build Type: any Build-Space: n/a Build-Time: 1263 Distribution: groovy Fail-Stage: build Host Architecture: arm64 Install-Time: 168 Job: python-biopython_1.76+dfsg-1.dsc Machine Architecture: arm64 Package: python-biopython Package-Time: 1436 Source-Version: 1.76+dfsg-1 Space: n/a Status: attempted Version: 1.76+dfsg-1 -------------------------------------------------------------------------------- Finished at 2020-10-01T03:49:54Z Build needed 00:23:56, no disk space E: Build failure (dpkg-buildpackage died) RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=groovy --arch=arm64 PACKAGEBUILD-20043692 Scanning for processes to kill in build PACKAGEBUILD-20043692