https://launchpad.net/ubuntu/+source/python-cogent/2021.10.12a1+dfsg-1/+build/22372247 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-066 5.4.0-107-generic #121-Ubuntu SMP Thu Mar 24 16:07:22 UTC 2022 aarch64 Buildd toolchain package versions: launchpad-buildd_211~547~ubuntu20.04.1 python3-lpbuildd_211~547~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.2 dpkg-dev_1.19.7ubuntu3 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 9 Apr 09:08:17 ntpdate[1753]: adjust time server 10.211.37.1 offset -0.000124 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=jammy --arch=armhf PACKAGEBUILD-22372247 --image-type chroot /home/buildd/filecache-default/c698bf6badd89264039f6cdfcd7c983f87611a3e Creating target for build PACKAGEBUILD-22372247 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=jammy --arch=armhf PACKAGEBUILD-22372247 Starting target for build PACKAGEBUILD-22372247 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=jammy --arch=armhf PACKAGEBUILD-22372247 'deb http://ftpmaster.internal/ubuntu jammy main universe' 'deb http://ftpmaster.internal/ubuntu jammy-security main universe' 'deb http://ftpmaster.internal/ubuntu jammy-updates main universe' 'deb http://ftpmaster.internal/ubuntu jammy-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-22372247 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=jammy --arch=armhf PACKAGEBUILD-22372247 Updating target for build PACKAGEBUILD-22372247 Get:1 http://ftpmaster.internal/ubuntu jammy InRelease [270 kB] Get:2 http://ftpmaster.internal/ubuntu jammy-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu jammy-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu jammy-proposed InRelease [121 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main armhf Packages [1325 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main Translation-en [512 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/universe armhf Packages [13.5 MB] Get:8 http://ftpmaster.internal/ubuntu jammy/universe Translation-en [5651 kB] Get:9 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf Packages [19.7 kB] Get:10 http://ftpmaster.internal/ubuntu jammy-proposed/main Translation-en [9808 B] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/universe armhf Packages [151 kB] Get:12 http://ftpmaster.internal/ubuntu jammy-proposed/universe Translation-en [64.9 kB] Fetched 21.8 MB in 5s (4701 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: libperl5.32 perl-modules-5.32 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libsemanage1* The following NEW packages will be installed: gcc-12-base libperl5.34 libsemanage2 libsepol2 libssl3 perl-modules-5.34 The following packages will be upgraded: advancecomp apt base-files base-passwd bash binutils binutils-arm-linux-gnueabihf binutils-common bsdutils build-essential bzip2 ca-certificates coreutils cpp-11 dash debconf debianutils diffutils dpkg dpkg-dev e2fsprogs fakeroot findutils g++-11 gcc-11 gcc-11-base gpg gpg-agent gpgconf gpgv grep gzip hostname init init-system-helpers libacl1 libapparmor1 libapt-pkg6.0 libargon2-1 libasan6 libassuan0 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdb5.3 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libext2fs2 libfakeroot libffi8 libgcc-11-dev libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgmp10 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libhogweed6 libidn2-0 libip4tc2 libisl23 libjson-c5 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblockfile-bin liblockfile1 liblz4-1 liblzma5 libmount1 libmpc3 libmpfr6 libncurses6 libncursesw6 libnettle8 libnpth0 libnsl-dev libnsl2 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libpcre3 libpng16-16 libprocps8 libreadline8 libseccomp2 libselinux1 libsemanage-common libsmartcols1 libsqlite3-0 libss2 libstdc++-11-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libtirpc-common libtirpc-dev libtirpc3 libubsan1 libudev1 libunistring2 libuuid1 libxxhash0 libzstd1 linux-libc-dev lockfile-progs login logsave lsb-base lto-disabled-list make mawk mount ncurses-base ncurses-bin openssl optipng passwd patch perl perl-base pinentry-curses pkgbinarymangler procps readline-common rpcsvc-proto sed sensible-utils systemd systemd-sysv systemd-timesyncd sysvinit-utils tar tzdata usrmerge util-linux xz-utils zlib1g 165 upgraded, 6 newly installed, 1 to remove and 0 not upgraded. Need to get 89.9 MB of archives. After this operation, 298 MB disk space will be freed. Get:1 http://ftpmaster.internal/ubuntu jammy/main armhf rpcsvc-proto armhf 1.4.2-0ubuntu6 [63.7 kB] Get:2 http://ftpmaster.internal/ubuntu jammy/main armhf libnsl-dev armhf 1.3.0-2build2 [66.1 kB] Get:3 http://ftpmaster.internal/ubuntu jammy/main armhf libcrypt-dev armhf 1:4.4.27-1 [122 kB] Get:4 http://ftpmaster.internal/ubuntu jammy/main armhf libc6-dev armhf 2.35-0ubuntu3 [1331 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main armhf libc-dev-bin armhf 2.35-0ubuntu3 [19.0 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main armhf libtirpc-common all 1.3.2-2build1 [7616 B] Get:7 http://ftpmaster.internal/ubuntu jammy/main armhf libtirpc-dev armhf 1.3.2-2build1 [184 kB] Get:8 http://ftpmaster.internal/ubuntu jammy/main armhf libssl3 armhf 3.0.2-0ubuntu1 [1578 kB] Get:9 http://ftpmaster.internal/ubuntu jammy/main armhf libk5crypto3 armhf 1.19.2-2 [83.6 kB] Get:10 http://ftpmaster.internal/ubuntu jammy/main armhf libkrb5support0 armhf 1.19.2-2 [30.4 kB] Get:11 http://ftpmaster.internal/ubuntu jammy/main armhf libkrb5-3 armhf 1.19.2-2 [330 kB] Get:12 http://ftpmaster.internal/ubuntu jammy/main armhf libgssapi-krb5-2 armhf 1.19.2-2 [120 kB] Get:13 http://ftpmaster.internal/ubuntu jammy/main armhf libc6 armhf 2.35-0ubuntu3 [2517 kB] Get:14 http://ftpmaster.internal/ubuntu jammy/main armhf libc-bin armhf 2.35-0ubuntu3 [546 kB] Get:15 http://ftpmaster.internal/ubuntu jammy/main armhf perl-modules-5.34 all 5.34.0-3ubuntu1 [2975 kB] Get:16 http://ftpmaster.internal/ubuntu jammy/main armhf libperl5.34 armhf 5.34.0-3ubuntu1 [4039 kB] Get:17 http://ftpmaster.internal/ubuntu jammy/main armhf perl armhf 5.34.0-3ubuntu1 [232 kB] Get:18 http://ftpmaster.internal/ubuntu jammy/main armhf perl-base armhf 5.34.0-3ubuntu1 [1613 kB] Get:19 http://ftpmaster.internal/ubuntu jammy/main armhf bzip2 armhf 1.0.8-5build1 [34.2 kB] Get:20 http://ftpmaster.internal/ubuntu jammy/main armhf libbz2-1.0 armhf 1.0.8-5build1 [31.7 kB] Get:21 http://ftpmaster.internal/ubuntu jammy/main armhf libaudit-common all 1:3.0.7-1build1 [4726 B] Get:22 http://ftpmaster.internal/ubuntu jammy/main armhf libcap-ng0 armhf 0.7.9-2.2build3 [10.1 kB] Get:23 http://ftpmaster.internal/ubuntu jammy/main armhf libaudit1 armhf 1:3.0.7-1build1 [43.6 kB] Get:24 http://ftpmaster.internal/ubuntu jammy/main armhf libpam0g armhf 1.4.0-11ubuntu2 [55.4 kB] Get:25 http://ftpmaster.internal/ubuntu jammy/main armhf libcrypt1 armhf 1:4.4.27-1 [94.0 kB] Get:26 http://ftpmaster.internal/ubuntu jammy/main armhf libdb5.3 armhf 5.3.28+dfsg1-0.8ubuntu3 [648 kB] Get:27 http://ftpmaster.internal/ubuntu jammy/main armhf libgdbm6 armhf 1.23-1 [30.0 kB] Get:28 http://ftpmaster.internal/ubuntu jammy/main armhf libgdbm-compat4 armhf 1.23-1 [6070 B] Get:29 http://ftpmaster.internal/ubuntu jammy/main armhf zlib1g armhf 1:1.2.11.dfsg-2ubuntu9 [51.5 kB] Get:30 http://ftpmaster.internal/ubuntu jammy/main armhf debconf all 1.5.79ubuntu1 [126 kB] Get:31 http://ftpmaster.internal/ubuntu jammy/main armhf libcom-err2 armhf 1.46.5-2ubuntu1 [9002 B] Get:32 http://ftpmaster.internal/ubuntu jammy/main armhf libkeyutils1 armhf 1.6.1-2ubuntu3 [8966 B] Get:33 http://ftpmaster.internal/ubuntu jammy/main armhf libtirpc3 armhf 1.3.2-2build1 [72.2 kB] Get:34 http://ftpmaster.internal/ubuntu jammy/main armhf libnsl2 armhf 1.3.0-2build2 [36.6 kB] Get:35 http://ftpmaster.internal/ubuntu jammy/main armhf linux-libc-dev armhf 5.15.0-25.25 [1268 kB] Get:36 http://ftpmaster.internal/ubuntu jammy/main armhf gcc-12-base armhf 12-20220319-1ubuntu1 [18.9 kB] Get:37 http://ftpmaster.internal/ubuntu jammy/main armhf libgcc-s1 armhf 12-20220319-1ubuntu1 [42.7 kB] Get:38 http://ftpmaster.internal/ubuntu jammy/main armhf base-files armhf 12ubuntu3 [63.0 kB] Get:39 http://ftpmaster.internal/ubuntu jammy/main armhf debianutils armhf 5.5-1ubuntu2 [106 kB] Get:40 http://ftpmaster.internal/ubuntu jammy/main armhf bash armhf 5.1-6ubuntu1 [655 kB] Get:41 http://ftpmaster.internal/ubuntu jammy/main armhf bsdutils armhf 1:2.37.2-4ubuntu3 [87.0 kB] Get:42 http://ftpmaster.internal/ubuntu jammy/main armhf coreutils armhf 8.32-4.1ubuntu1 [1301 kB] Get:43 http://ftpmaster.internal/ubuntu jammy/main armhf libgpg-error0 armhf 1.43-3 [61.9 kB] Get:44 http://ftpmaster.internal/ubuntu jammy/main armhf libgcrypt20 armhf 1.9.4-3ubuntu3 [439 kB] Get:45 http://ftpmaster.internal/ubuntu jammy/main armhf liblz4-1 armhf 1.9.3-2build2 [54.8 kB] Get:46 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf liblzma5 armhf 5.2.5-2ubuntu1 [87.0 kB] Get:47 http://ftpmaster.internal/ubuntu jammy/main armhf libstdc++6 armhf 12-20220319-1ubuntu1 [616 kB] Get:48 http://ftpmaster.internal/ubuntu jammy/main armhf libargon2-1 armhf 0~20171227-0.3 [21.0 kB] Get:49 http://ftpmaster.internal/ubuntu jammy/main armhf libblkid1 armhf 2.37.2-4ubuntu3 [136 kB] Get:50 http://ftpmaster.internal/ubuntu jammy/main armhf libpcre2-8-0 armhf 10.39-3build1 [190 kB] Get:51 http://ftpmaster.internal/ubuntu jammy/main armhf libselinux1 armhf 3.3-1build2 [66.8 kB] Get:52 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libudev1 armhf 249.11-0ubuntu3 [69.5 kB] Get:53 http://ftpmaster.internal/ubuntu jammy/main armhf libdevmapper1.02.1 armhf 2:1.02.175-2.1ubuntu4 [134 kB] Get:54 http://ftpmaster.internal/ubuntu jammy/main armhf libjson-c5 armhf 0.15-2build4 [28.9 kB] Get:55 http://ftpmaster.internal/ubuntu jammy/main armhf libuuid1 armhf 2.37.2-4ubuntu3 [23.6 kB] Get:56 http://ftpmaster.internal/ubuntu jammy/main armhf libcryptsetup12 armhf 2:2.4.3-1ubuntu1 [189 kB] Get:57 http://ftpmaster.internal/ubuntu jammy/main armhf libgmp10 armhf 2:6.2.1+dfsg-3ubuntu1 [205 kB] Get:58 http://ftpmaster.internal/ubuntu jammy/main armhf libnettle8 armhf 3.7.3-1build2 [174 kB] Get:59 http://ftpmaster.internal/ubuntu jammy/main armhf libhogweed6 armhf 3.7.3-1build2 [187 kB] Get:60 http://ftpmaster.internal/ubuntu jammy/main armhf libunistring2 armhf 1.0-1 [533 kB] Get:61 http://ftpmaster.internal/ubuntu jammy/main armhf libidn2-0 armhf 2.3.2-2build1 [67.6 kB] Get:62 http://ftpmaster.internal/ubuntu jammy/main armhf libffi8 armhf 3.4.2-4 [19.0 kB] Get:63 http://ftpmaster.internal/ubuntu jammy/main armhf libp11-kit0 armhf 0.24.0-6build1 [219 kB] Get:64 http://ftpmaster.internal/ubuntu jammy/main armhf libtasn1-6 armhf 4.18.0-4build1 [36.3 kB] Get:65 http://ftpmaster.internal/ubuntu jammy/main armhf libgnutls30 armhf 3.7.3-4ubuntu1 [934 kB] Get:66 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf systemd-sysv armhf 249.11-0ubuntu3 [10.5 kB] Get:67 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf systemd-timesyncd armhf 249.11-0ubuntu3 [31.0 kB] Get:68 http://ftpmaster.internal/ubuntu jammy/main armhf libacl1 armhf 2.3.1-1 [14.9 kB] Get:69 http://ftpmaster.internal/ubuntu jammy/main armhf libapparmor1 armhf 3.0.4-2ubuntu2 [33.0 kB] Get:70 http://ftpmaster.internal/ubuntu jammy/main armhf libip4tc2 armhf 1.8.7-1ubuntu5 [17.7 kB] Get:71 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libzstd1 armhf 1.4.8+dfsg-3build1 [285 kB] Get:72 http://ftpmaster.internal/ubuntu jammy/main armhf libkmod2 armhf 29-1ubuntu1 [40.9 kB] Get:73 http://ftpmaster.internal/ubuntu jammy/main armhf libmount1 armhf 2.37.2-4ubuntu3 [152 kB] Get:74 http://ftpmaster.internal/ubuntu jammy/main armhf libseccomp2 armhf 2.5.3-2ubuntu2 [46.8 kB] Get:75 http://ftpmaster.internal/ubuntu jammy/main armhf login armhf 1:4.8.1-2ubuntu2 [186 kB] Get:76 http://ftpmaster.internal/ubuntu jammy/main armhf util-linux armhf 2.37.2-4ubuntu3 [1130 kB] Get:77 http://ftpmaster.internal/ubuntu jammy/main armhf mount armhf 2.37.2-4ubuntu3 [125 kB] Get:78 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf systemd armhf 249.11-0ubuntu3 [4455 kB] Get:79 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libsystemd0 armhf 249.11-0ubuntu3 [295 kB] Get:80 http://ftpmaster.internal/ubuntu jammy/main armhf libxxhash0 armhf 0.8.1-1 [26.3 kB] Get:81 http://ftpmaster.internal/ubuntu jammy/main armhf libapt-pkg6.0 armhf 2.4.3 [899 kB] Get:82 http://ftpmaster.internal/ubuntu jammy/main armhf tar armhf 1.34+dfsg-1build3 [272 kB] Get:83 http://ftpmaster.internal/ubuntu jammy/main armhf dpkg armhf 1.21.1ubuntu2 [1190 kB] Get:84 http://ftpmaster.internal/ubuntu jammy/main armhf dash armhf 0.5.11+git20210903+057cd650a4ed-3build1 [83.8 kB] Get:85 http://ftpmaster.internal/ubuntu jammy/main armhf diffutils armhf 1:3.8-0ubuntu2 [164 kB] Get:86 http://ftpmaster.internal/ubuntu jammy/main armhf findutils armhf 4.8.0-1ubuntu3 [323 kB] Get:87 http://ftpmaster.internal/ubuntu jammy/main armhf grep armhf 3.7-1build1 [150 kB] Get:88 http://ftpmaster.internal/ubuntu jammy/main armhf gzip armhf 1.10-4ubuntu4 [95.3 kB] Get:89 http://ftpmaster.internal/ubuntu jammy/main armhf hostname armhf 3.23ubuntu2 [10.7 kB] Get:90 http://ftpmaster.internal/ubuntu jammy/main armhf libncurses6 armhf 6.3-2 [87.5 kB] Get:91 http://ftpmaster.internal/ubuntu jammy/main armhf libncursesw6 armhf 6.3-2 [117 kB] Get:92 http://ftpmaster.internal/ubuntu jammy/main armhf libtinfo6 armhf 6.3-2 [87.9 kB] Get:93 http://ftpmaster.internal/ubuntu jammy/main armhf ncurses-bin armhf 6.3-2 [175 kB] Get:94 http://ftpmaster.internal/ubuntu jammy/main armhf sed armhf 4.8-1ubuntu2 [186 kB] Get:95 http://ftpmaster.internal/ubuntu jammy/main armhf libdebconfclient0 armhf 0.261ubuntu1 [6552 B] Get:96 http://ftpmaster.internal/ubuntu jammy/main armhf base-passwd armhf 3.5.52build1 [49.2 kB] Get:97 http://ftpmaster.internal/ubuntu jammy/main armhf init-system-helpers all 1.62 [38.5 kB] Get:98 http://ftpmaster.internal/ubuntu jammy/main armhf ncurses-base all 6.3-2 [20.1 kB] Get:99 http://ftpmaster.internal/ubuntu jammy/main armhf lsb-base all 11.1.0ubuntu4 [12.3 kB] Get:100 http://ftpmaster.internal/ubuntu jammy/main armhf sysvinit-utils armhf 3.01-1ubuntu1 [20.5 kB] Get:101 http://ftpmaster.internal/ubuntu jammy/main armhf gpgv armhf 2.2.27-3ubuntu2 [186 kB] Get:102 http://ftpmaster.internal/ubuntu jammy/main armhf apt armhf 2.4.3 [1369 kB] Get:103 http://ftpmaster.internal/ubuntu jammy/main armhf libsepol2 armhf 3.3-1build1 [259 kB] Get:104 http://ftpmaster.internal/ubuntu jammy/main armhf libsemanage-common all 3.3-1build2 [9874 B] Get:105 http://ftpmaster.internal/ubuntu jammy/main armhf libsemanage2 armhf 3.3-1build2 [83.9 kB] Get:106 http://ftpmaster.internal/ubuntu jammy/main armhf passwd armhf 1:4.8.1-2ubuntu2 [740 kB] Get:107 http://ftpmaster.internal/ubuntu jammy/main armhf libpam-modules-bin armhf 1.4.0-11ubuntu2 [35.6 kB] Get:108 http://ftpmaster.internal/ubuntu jammy/main armhf libpam-modules armhf 1.4.0-11ubuntu2 [263 kB] Get:109 http://ftpmaster.internal/ubuntu jammy/main armhf logsave armhf 1.46.5-2ubuntu1 [10.1 kB] Get:110 http://ftpmaster.internal/ubuntu jammy/main armhf libext2fs2 armhf 1.46.5-2ubuntu1 [191 kB] Get:111 http://ftpmaster.internal/ubuntu jammy/main armhf e2fsprogs armhf 1.46.5-2ubuntu1 [566 kB] Get:112 http://ftpmaster.internal/ubuntu jammy/main armhf init armhf 1.62 [5412 B] Get:113 http://ftpmaster.internal/ubuntu jammy/main armhf libattr1 armhf 1:2.5.1-1build1 [12.1 kB] Get:114 http://ftpmaster.internal/ubuntu jammy/main armhf libcap2 armhf 1:2.44-1build3 [15.3 kB] Get:115 http://ftpmaster.internal/ubuntu jammy/main armhf libpam-runtime all 1.4.0-11ubuntu2 [40.3 kB] Get:116 http://ftpmaster.internal/ubuntu jammy/main armhf libpcre3 armhf 2:8.39-13build5 [225 kB] Get:117 http://ftpmaster.internal/ubuntu jammy/main armhf libsmartcols1 armhf 2.37.2-4ubuntu3 [93.9 kB] Get:118 http://ftpmaster.internal/ubuntu jammy/main armhf libprocps8 armhf 2:3.3.17-6ubuntu2 [32.7 kB] Get:119 http://ftpmaster.internal/ubuntu jammy/main armhf libss2 armhf 1.46.5-2ubuntu1 [10.1 kB] Get:120 http://ftpmaster.internal/ubuntu jammy/main armhf mawk armhf 1.3.4.20200120-3 [91.5 kB] Get:121 http://ftpmaster.internal/ubuntu jammy/main armhf procps armhf 2:3.3.17-6ubuntu2 [372 kB] Get:122 http://ftpmaster.internal/ubuntu jammy/main armhf sensible-utils all 0.0.17 [20.1 kB] Get:123 http://ftpmaster.internal/ubuntu jammy/main armhf usrmerge all 25ubuntu2 [54.7 kB] Get:124 http://ftpmaster.internal/ubuntu jammy/main armhf openssl armhf 3.0.2-0ubuntu1 [1153 kB] Get:125 http://ftpmaster.internal/ubuntu jammy/main armhf ca-certificates all 20211016 [148 kB] Get:126 http://ftpmaster.internal/ubuntu jammy/main armhf readline-common all 8.1.2-1 [53.5 kB] Get:127 http://ftpmaster.internal/ubuntu jammy/main armhf libreadline8 armhf 8.1.2-1 [128 kB] Get:128 http://ftpmaster.internal/ubuntu jammy/main armhf libsqlite3-0 armhf 3.37.2-2 [549 kB] Get:129 http://ftpmaster.internal/ubuntu jammy/main armhf tzdata all 2022a-0ubuntu1 [342 kB] Get:130 http://ftpmaster.internal/ubuntu jammy/main armhf libpng16-16 armhf 1.6.37-3build5 [170 kB] Get:131 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf xz-utils armhf 5.2.5-2ubuntu1 [84.6 kB] Get:132 http://ftpmaster.internal/ubuntu jammy/main armhf advancecomp armhf 2.1-2.1ubuntu2 [185 kB] Get:133 http://ftpmaster.internal/ubuntu jammy/main armhf libctf0 armhf 2.38-3ubuntu1 [93.6 kB] Get:134 http://ftpmaster.internal/ubuntu jammy/main armhf libctf-nobfd0 armhf 2.38-3ubuntu1 [93.5 kB] Get:135 http://ftpmaster.internal/ubuntu jammy/main armhf binutils-arm-linux-gnueabihf armhf 2.38-3ubuntu1 [3061 kB] Get:136 http://ftpmaster.internal/ubuntu jammy/main armhf libbinutils armhf 2.38-3ubuntu1 [497 kB] Get:137 http://ftpmaster.internal/ubuntu jammy/main armhf binutils armhf 2.38-3ubuntu1 [3162 B] Get:138 http://ftpmaster.internal/ubuntu jammy/main armhf binutils-common armhf 2.38-3ubuntu1 [221 kB] Get:139 http://ftpmaster.internal/ubuntu jammy/main armhf make armhf 4.3-4.1build1 [163 kB] Get:140 http://ftpmaster.internal/ubuntu jammy/main armhf dpkg-dev all 1.21.1ubuntu2 [922 kB] Get:141 http://ftpmaster.internal/ubuntu jammy/main armhf libdpkg-perl all 1.21.1ubuntu2 [236 kB] Get:142 http://ftpmaster.internal/ubuntu jammy/main armhf patch armhf 2.7.6-7build2 [111 kB] Get:143 http://ftpmaster.internal/ubuntu jammy/main armhf lto-disabled-list all 24 [12.5 kB] Get:144 http://ftpmaster.internal/ubuntu jammy/main armhf build-essential armhf 12.9ubuntu3 [4744 B] Get:145 http://ftpmaster.internal/ubuntu jammy/main armhf libubsan1 armhf 12-20220319-1ubuntu1 [959 kB] Get:146 http://ftpmaster.internal/ubuntu jammy/main armhf libgomp1 armhf 12-20220319-1ubuntu1 [110 kB] Get:147 http://ftpmaster.internal/ubuntu jammy/main armhf libatomic1 armhf 12-20220319-1ubuntu1 [7620 B] Get:148 http://ftpmaster.internal/ubuntu jammy/main armhf libasan6 armhf 11.2.0-19ubuntu1 [2242 kB] Get:149 http://ftpmaster.internal/ubuntu jammy/main armhf g++-11 armhf 11.2.0-19ubuntu1 [9018 kB] Get:150 http://ftpmaster.internal/ubuntu jammy/main armhf gcc-11 armhf 11.2.0-19ubuntu1 [15.8 MB] Get:151 http://ftpmaster.internal/ubuntu jammy/main armhf libstdc++-11-dev armhf 11.2.0-19ubuntu1 [2134 kB] Get:152 http://ftpmaster.internal/ubuntu jammy/main armhf libgcc-11-dev armhf 11.2.0-19ubuntu1 [835 kB] Get:153 http://ftpmaster.internal/ubuntu jammy/main armhf libcc1-0 armhf 12-20220319-1ubuntu1 [39.1 kB] Get:154 http://ftpmaster.internal/ubuntu jammy/main armhf cpp-11 armhf 11.2.0-19ubuntu1 [7841 kB] Get:155 http://ftpmaster.internal/ubuntu jammy/main armhf gcc-11-base armhf 11.2.0-19ubuntu1 [20.8 kB] Get:156 http://ftpmaster.internal/ubuntu jammy/main armhf libisl23 armhf 0.24-2build1 [581 kB] Get:157 http://ftpmaster.internal/ubuntu jammy/main armhf libmpfr6 armhf 4.1.0-3build3 [217 kB] Get:158 http://ftpmaster.internal/ubuntu jammy/main armhf libmpc3 armhf 1.2.1-2build1 [39.5 kB] Get:159 http://ftpmaster.internal/ubuntu jammy/main armhf libfakeroot armhf 1.28-1ubuntu1 [26.3 kB] Get:160 http://ftpmaster.internal/ubuntu jammy/main armhf fakeroot armhf 1.28-1ubuntu1 [62.2 kB] Get:161 http://ftpmaster.internal/ubuntu jammy/main armhf libassuan0 armhf 2.5.5-1build1 [31.3 kB] Get:162 http://ftpmaster.internal/ubuntu jammy/main armhf pinentry-curses armhf 1.1.1-1build2 [35.6 kB] Get:163 http://ftpmaster.internal/ubuntu jammy/main armhf libnpth0 armhf 1.6-3build2 [7230 B] Get:164 http://ftpmaster.internal/ubuntu jammy/main armhf gpg armhf 2.2.27-3ubuntu2 [483 kB] Get:165 http://ftpmaster.internal/ubuntu jammy/main armhf gpgconf armhf 2.2.27-3ubuntu2 [115 kB] Get:166 http://ftpmaster.internal/ubuntu jammy/main armhf gpg-agent armhf 2.2.27-3ubuntu2 [227 kB] Get:167 http://ftpmaster.internal/ubuntu jammy/main armhf liblockfile-bin armhf 1.17-1build2 [11.0 kB] Get:168 http://ftpmaster.internal/ubuntu jammy/main armhf liblockfile1 armhf 1.17-1build2 [5930 B] Get:169 http://ftpmaster.internal/ubuntu jammy/main armhf lockfile-progs armhf 0.1.19build1 [9506 B] Get:170 http://ftpmaster.internal/ubuntu jammy/main armhf optipng armhf 0.7.7-2build1 [84.8 kB] Get:171 http://ftpmaster.internal/ubuntu jammy/main armhf pkgbinarymangler all 149 [32.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 89.9 MB in 3s (29.0 MB/s) (Reading database ... 12985 files and directories currently installed.) Preparing to unpack .../0-rpcsvc-proto_1.4.2-0ubuntu6_armhf.deb ... Unpacking rpcsvc-proto (1.4.2-0ubuntu6) over (1.4.2-0ubuntu5) ... Preparing to unpack .../1-libnsl-dev_1.3.0-2build2_armhf.deb ... Unpacking libnsl-dev:armhf (1.3.0-2build2) over (1.3.0-2build1) ... Preparing to unpack .../2-libcrypt-dev_1%3a4.4.27-1_armhf.deb ... Unpacking libcrypt-dev:armhf (1:4.4.27-1) over (1:4.4.18-4ubuntu2) ... Preparing to unpack .../3-libc6-dev_2.35-0ubuntu3_armhf.deb ... Unpacking libc6-dev:armhf (2.35-0ubuntu3) over (2.34-0ubuntu3) ... Preparing to unpack .../4-libc-dev-bin_2.35-0ubuntu3_armhf.deb ... Unpacking libc-dev-bin (2.35-0ubuntu3) over (2.34-0ubuntu3) ... Preparing to unpack .../5-libtirpc-common_1.3.2-2build1_all.deb ... Unpacking libtirpc-common (1.3.2-2build1) over (1.3.2-2) ... Setting up libtirpc-common (1.3.2-2build1) ... (Reading database ... 12990 files and directories currently installed.) Preparing to unpack .../libtirpc-dev_1.3.2-2build1_armhf.deb ... Unpacking libtirpc-dev:armhf (1.3.2-2build1) over (1.3.2-2) ... Selecting previously unselected package libssl3:armhf. Preparing to unpack .../libssl3_3.0.2-0ubuntu1_armhf.deb ... Unpacking libssl3:armhf (3.0.2-0ubuntu1) ... Setting up libssl3:armhf (3.0.2-0ubuntu1) ... (Reading database ... 13001 files and directories currently installed.) Preparing to unpack .../libk5crypto3_1.19.2-2_armhf.deb ... Unpacking libk5crypto3:armhf (1.19.2-2) over (1.18.3-6) ... Setting up libk5crypto3:armhf (1.19.2-2) ... (Reading database ... 13001 files and directories currently installed.) Preparing to unpack .../libkrb5support0_1.19.2-2_armhf.deb ... Unpacking libkrb5support0:armhf (1.19.2-2) over (1.18.3-6) ... Setting up libkrb5support0:armhf (1.19.2-2) ... (Reading database ... 13001 files and directories currently installed.) Preparing to unpack .../libkrb5-3_1.19.2-2_armhf.deb ... Unpacking libkrb5-3:armhf (1.19.2-2) over (1.18.3-6) ... Setting up libkrb5-3:armhf (1.19.2-2) ... (Reading database ... 13001 files and directories currently installed.) Preparing to unpack .../libgssapi-krb5-2_1.19.2-2_armhf.deb ... Unpacking libgssapi-krb5-2:armhf (1.19.2-2) over (1.18.3-6) ... Setting up libgssapi-krb5-2:armhf (1.19.2-2) ... (Reading database ... 13001 files and directories currently installed.) Preparing to unpack .../libc6_2.35-0ubuntu3_armhf.deb ... Unpacking libc6:armhf (2.35-0ubuntu3) over (2.34-0ubuntu3) ... Setting up libc6:armhf (2.35-0ubuntu3) ... (Reading database ... 13000 files and directories currently installed.) Preparing to unpack .../libc-bin_2.35-0ubuntu3_armhf.deb ... Unpacking libc-bin (2.35-0ubuntu3) over (2.34-0ubuntu3) ... Setting up libc-bin (2.35-0ubuntu3) ... (Reading database ... 12998 files and directories currently installed.) Preparing to unpack .../perl_5.34.0-3ubuntu1_armhf.deb ... Unpacking perl (5.34.0-3ubuntu1) over (5.32.1-3ubuntu3) ... Selecting previously unselected package perl-modules-5.34. Preparing to unpack .../perl-modules-5.34_5.34.0-3ubuntu1_all.deb ... Unpacking perl-modules-5.34 (5.34.0-3ubuntu1) ... Selecting previously unselected package libperl5.34:armhf. Preparing to unpack .../libperl5.34_5.34.0-3ubuntu1_armhf.deb ... Unpacking libperl5.34:armhf (5.34.0-3ubuntu1) ... Preparing to unpack .../perl-base_5.34.0-3ubuntu1_armhf.deb ... Unpacking perl-base (5.34.0-3ubuntu1) over (5.32.1-3ubuntu3) ... Setting up perl-base (5.34.0-3ubuntu1) ... (Reading database ... 14906 files and directories currently installed.) Preparing to unpack .../bzip2_1.0.8-5build1_armhf.deb ... Unpacking bzip2 (1.0.8-5build1) over (1.0.8-4ubuntu4) ... Preparing to unpack .../libbz2-1.0_1.0.8-5build1_armhf.deb ... Unpacking libbz2-1.0:armhf (1.0.8-5build1) over (1.0.8-4ubuntu4) ... Setting up libbz2-1.0:armhf (1.0.8-5build1) ... (Reading database ... 14906 files and directories currently installed.) Preparing to unpack .../libaudit-common_1%3a3.0.7-1build1_all.deb ... Unpacking libaudit-common (1:3.0.7-1build1) over (1:3.0-2ubuntu3) ... Setting up libaudit-common (1:3.0.7-1build1) ... (Reading database ... 14906 files and directories currently installed.) Preparing to unpack .../libcap-ng0_0.7.9-2.2build3_armhf.deb ... Unpacking libcap-ng0:armhf (0.7.9-2.2build3) over (0.7.9-2.2build2) ... Setting up libcap-ng0:armhf (0.7.9-2.2build3) ... (Reading database ... 14906 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a3.0.7-1build1_armhf.deb ... Unpacking libaudit1:armhf (1:3.0.7-1build1) over (1:3.0-2ubuntu3) ... Setting up libaudit1:armhf (1:3.0.7-1build1) ... (Reading database ... 14906 files and directories currently installed.) Preparing to unpack .../libpam0g_1.4.0-11ubuntu2_armhf.deb ... Unpacking libpam0g:armhf (1.4.0-11ubuntu2) over (1.3.1-5ubuntu11) ... Setting up libpam0g:armhf (1.4.0-11ubuntu2) ... Checking for services that may need to be restarted...Checking init scripts... Nothing to restart. (Reading database ... 14906 files and directories currently installed.) Preparing to unpack .../libcrypt1_1%3a4.4.27-1_armhf.deb ... Unpacking libcrypt1:armhf (1:4.4.27-1) over (1:4.4.18-4ubuntu2) ... Setting up libcrypt1:armhf (1:4.4.27-1) ... (Reading database ... 14906 files and directories currently installed.) Preparing to unpack .../libdb5.3_5.3.28+dfsg1-0.8ubuntu3_armhf.deb ... Unpacking libdb5.3:armhf (5.3.28+dfsg1-0.8ubuntu3) over (5.3.28+dfsg1-0.8ubuntu2) ... Setting up libdb5.3:armhf (5.3.28+dfsg1-0.8ubuntu3) ... (Reading database ... 14906 files and directories currently installed.) Preparing to unpack .../libgdbm6_1.23-1_armhf.deb ... Unpacking libgdbm6:armhf (1.23-1) over (1.19-2build1) ... Preparing to unpack .../libgdbm-compat4_1.23-1_armhf.deb ... Unpacking libgdbm-compat4:armhf (1.23-1) over (1.19-2build1) ... Preparing to unpack .../zlib1g_1%3a1.2.11.dfsg-2ubuntu9_armhf.deb ... Unpacking zlib1g:armhf (1:1.2.11.dfsg-2ubuntu9) over (1:1.2.11.dfsg-2ubuntu7) ... Setting up zlib1g:armhf (1:1.2.11.dfsg-2ubuntu9) ... (Reading database ... 14906 files and directories currently installed.) Preparing to unpack .../debconf_1.5.79ubuntu1_all.deb ... Unpacking debconf (1.5.79ubuntu1) over (1.5.77) ... Setting up debconf (1.5.79ubuntu1) ... (Reading database ... 14905 files and directories currently installed.) Preparing to unpack .../libcom-err2_1.46.5-2ubuntu1_armhf.deb ... Unpacking libcom-err2:armhf (1.46.5-2ubuntu1) over (1.46.3-1ubuntu3) ... Setting up libcom-err2:armhf (1.46.5-2ubuntu1) ... (Reading database ... 14905 files and directories currently installed.) Preparing to unpack .../libkeyutils1_1.6.1-2ubuntu3_armhf.deb ... Unpacking libkeyutils1:armhf (1.6.1-2ubuntu3) over (1.6.1-2ubuntu2) ... Setting up libkeyutils1:armhf (1.6.1-2ubuntu3) ... (Reading database ... 14905 files and directories currently installed.) Preparing to unpack .../libtirpc3_1.3.2-2build1_armhf.deb ... Unpacking libtirpc3:armhf (1.3.2-2build1) over (1.3.2-2) ... Setting up libtirpc3:armhf (1.3.2-2build1) ... (Reading database ... 14905 files and directories currently installed.) Preparing to unpack .../libnsl2_1.3.0-2build2_armhf.deb ... Unpacking libnsl2:armhf (1.3.0-2build2) over (1.3.0-2build1) ... Setting up libnsl2:armhf (1.3.0-2build2) ... (Reading database ... 14905 files and directories currently installed.) Preparing to unpack .../linux-libc-dev_5.15.0-25.25_armhf.deb ... Unpacking linux-libc-dev:armhf (5.15.0-25.25) over (5.13.0-19.19) ... Selecting previously unselected package gcc-12-base:armhf. Preparing to unpack .../gcc-12-base_12-20220319-1ubuntu1_armhf.deb ... Unpacking gcc-12-base:armhf (12-20220319-1ubuntu1) ... Setting up gcc-12-base:armhf (12-20220319-1ubuntu1) ... (Reading database ... 14921 files and directories currently installed.) Preparing to unpack .../libgcc-s1_12-20220319-1ubuntu1_armhf.deb ... Unpacking libgcc-s1:armhf (12-20220319-1ubuntu1) over (11.2.0-7ubuntu2) ... Setting up libgcc-s1:armhf (12-20220319-1ubuntu1) ... (Reading database ... 14921 files and directories currently installed.) Preparing to unpack .../base-files_12ubuntu3_armhf.deb ... Unpacking base-files (12ubuntu3) over (12ubuntu1) ... Setting up base-files (12ubuntu3) ... (Reading database ... 14921 files and directories currently installed.) Preparing to unpack .../debianutils_5.5-1ubuntu2_armhf.deb ... Unpacking debianutils (5.5-1ubuntu2) over (4.11.2build1) ... Setting up debianutils (5.5-1ubuntu2) ... update-alternatives: using /usr/bin/which.debianutils to provide /usr/bin/which (which) in auto mode (Reading database ... 14925 files and directories currently installed.) Preparing to unpack .../bash_5.1-6ubuntu1_armhf.deb ... Unpacking bash (5.1-6ubuntu1) over (5.1-3ubuntu2) ... Setting up bash (5.1-6ubuntu1) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... 14925 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.37.2-4ubuntu3_armhf.deb ... Unpacking bsdutils (1:2.37.2-4ubuntu3) over (1:2.36.1-8ubuntu1) ... Setting up bsdutils (1:2.37.2-4ubuntu3) ... (Reading database ... 14925 files and directories currently installed.) Preparing to unpack .../coreutils_8.32-4.1ubuntu1_armhf.deb ... Unpacking coreutils (8.32-4.1ubuntu1) over (8.32-4ubuntu3) ... Setting up coreutils (8.32-4.1ubuntu1) ... (Reading database ... 14925 files and directories currently installed.) Preparing to unpack .../libgpg-error0_1.43-3_armhf.deb ... Unpacking libgpg-error0:armhf (1.43-3) over (1.38-2build2) ... Setting up libgpg-error0:armhf (1.43-3) ... (Reading database ... 14925 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.9.4-3ubuntu3_armhf.deb ... Unpacking libgcrypt20:armhf (1.9.4-3ubuntu3) over (1.8.7-5ubuntu2) ... Setting up libgcrypt20:armhf (1.9.4-3ubuntu3) ... (Reading database ... 14925 files and directories currently installed.) Preparing to unpack .../liblz4-1_1.9.3-2build2_armhf.deb ... Unpacking liblz4-1:armhf (1.9.3-2build2) over (1.9.3-2build1) ... Setting up liblz4-1:armhf (1.9.3-2build2) ... (Reading database ... 14925 files and directories currently installed.) Preparing to unpack .../liblzma5_5.2.5-2ubuntu1_armhf.deb ... Unpacking liblzma5:armhf (5.2.5-2ubuntu1) over (5.2.5-2build1) ... Setting up liblzma5:armhf (5.2.5-2ubuntu1) ... (Reading database ... 14925 files and directories currently installed.) Preparing to unpack .../libstdc++6_12-20220319-1ubuntu1_armhf.deb ... Unpacking libstdc++6:armhf (12-20220319-1ubuntu1) over (11.2.0-7ubuntu2) ... Setting up libstdc++6:armhf (12-20220319-1ubuntu1) ... (Reading database ... 14925 files and directories currently installed.) Preparing to unpack .../libargon2-1_0~20171227-0.3_armhf.deb ... Unpacking libargon2-1:armhf (0~20171227-0.3) over (0~20171227-0.2build22) ... Preparing to unpack .../libblkid1_2.37.2-4ubuntu3_armhf.deb ... Unpacking libblkid1:armhf (2.37.2-4ubuntu3) over (2.36.1-8ubuntu1) ... Setting up libblkid1:armhf (2.37.2-4ubuntu3) ... (Reading database ... 14925 files and directories currently installed.) Preparing to unpack .../libpcre2-8-0_10.39-3build1_armhf.deb ... Unpacking libpcre2-8-0:armhf (10.39-3build1) over (10.37-0ubuntu2) ... Setting up libpcre2-8-0:armhf (10.39-3build1) ... (Reading database ... 14925 files and directories currently installed.) Preparing to unpack .../libselinux1_3.3-1build2_armhf.deb ... Unpacking libselinux1:armhf (3.3-1build2) over (3.1-3build2) ... Setting up libselinux1:armhf (3.3-1build2) ... (Reading database ... 14925 files and directories currently installed.) Preparing to unpack .../libudev1_249.11-0ubuntu3_armhf.deb ... Unpacking libudev1:armhf (249.11-0ubuntu3) over (248.3-1ubuntu8) ... Setting up libudev1:armhf (249.11-0ubuntu3) ... (Reading database ... 14925 files and directories currently installed.) Preparing to unpack .../libdevmapper1.02.1_2%3a1.02.175-2.1ubuntu4_armhf.deb ... Unpacking libdevmapper1.02.1:armhf (2:1.02.175-2.1ubuntu4) over (2:1.02.175-2.1ubuntu3) ... Preparing to unpack .../libjson-c5_0.15-2build4_armhf.deb ... Unpacking libjson-c5:armhf (0.15-2build4) over (0.15-2build3) ... Preparing to unpack .../libuuid1_2.37.2-4ubuntu3_armhf.deb ... Unpacking libuuid1:armhf (2.37.2-4ubuntu3) over (2.36.1-8ubuntu1) ... Setting up libuuid1:armhf (2.37.2-4ubuntu3) ... (Reading database ... 14925 files and directories currently installed.) Preparing to unpack .../libcryptsetup12_2%3a2.4.3-1ubuntu1_armhf.deb ... Unpacking libcryptsetup12:armhf (2:2.4.3-1ubuntu1) over (2:2.3.6-0ubuntu1) ... Preparing to unpack .../libgmp10_2%3a6.2.1+dfsg-3ubuntu1_armhf.deb ... Unpacking libgmp10:armhf (2:6.2.1+dfsg-3ubuntu1) over (2:6.2.1+dfsg-1ubuntu3) ... Setting up libgmp10:armhf (2:6.2.1+dfsg-3ubuntu1) ... (Reading database ... 14927 files and directories currently installed.) Preparing to unpack .../libnettle8_3.7.3-1build2_armhf.deb ... Unpacking libnettle8:armhf (3.7.3-1build2) over (3.7.3-1build1) ... Setting up libnettle8:armhf (3.7.3-1build2) ... (Reading database ... 14927 files and directories currently installed.) Preparing to unpack .../libhogweed6_3.7.3-1build2_armhf.deb ... Unpacking libhogweed6:armhf (3.7.3-1build2) over (3.7.3-1build1) ... Setting up libhogweed6:armhf (3.7.3-1build2) ... (Reading database ... 14927 files and directories currently installed.) Preparing to unpack .../libunistring2_1.0-1_armhf.deb ... Unpacking libunistring2:armhf (1.0-1) over (0.9.10-6) ... Setting up libunistring2:armhf (1.0-1) ... (Reading database ... 14927 files and directories currently installed.) Preparing to unpack .../libidn2-0_2.3.2-2build1_armhf.deb ... Unpacking libidn2-0:armhf (2.3.2-2build1) over (2.3.1-1build1) ... Setting up libidn2-0:armhf (2.3.2-2build1) ... (Reading database ... 14927 files and directories currently installed.) Preparing to unpack .../libffi8_3.4.2-4_armhf.deb ... Unpacking libffi8:armhf (3.4.2-4) over (3.4.2-1ubuntu5) ... Setting up libffi8:armhf (3.4.2-4) ... (Reading database ... 14927 files and directories currently installed.) Preparing to unpack .../libp11-kit0_0.24.0-6build1_armhf.deb ... Unpacking libp11-kit0:armhf (0.24.0-6build1) over (0.23.22-1build1) ... Setting up libp11-kit0:armhf (0.24.0-6build1) ... (Reading database ... 14927 files and directories currently installed.) Preparing to unpack .../libtasn1-6_4.18.0-4build1_armhf.deb ... Unpacking libtasn1-6:armhf (4.18.0-4build1) over (4.16.0-2build1) ... Setting up libtasn1-6:armhf (4.18.0-4build1) ... (Reading database ... 14927 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.7.3-4ubuntu1_armhf.deb ... Unpacking libgnutls30:armhf (3.7.3-4ubuntu1) over (3.7.1-5ubuntu1) ... Setting up libgnutls30:armhf (3.7.3-4ubuntu1) ... (Reading database ... 14927 files and directories currently installed.) Preparing to unpack .../systemd-sysv_249.11-0ubuntu3_armhf.deb ... Unpacking systemd-sysv (249.11-0ubuntu3) over (248.3-1ubuntu8) ... Preparing to unpack .../systemd-timesyncd_249.11-0ubuntu3_armhf.deb ... Unpacking systemd-timesyncd (249.11-0ubuntu3) over (248.3-1ubuntu8) ... Preparing to unpack .../libacl1_2.3.1-1_armhf.deb ... Unpacking libacl1:armhf (2.3.1-1) over (2.2.53-10ubuntu2) ... Setting up libacl1:armhf (2.3.1-1) ... (Reading database ... 14928 files and directories currently installed.) Preparing to unpack .../libapparmor1_3.0.4-2ubuntu2_armhf.deb ... Unpacking libapparmor1:armhf (3.0.4-2ubuntu2) over (3.0.3-0ubuntu1) ... Preparing to unpack .../libip4tc2_1.8.7-1ubuntu5_armhf.deb ... Unpacking libip4tc2:armhf (1.8.7-1ubuntu5) over (1.8.7-1ubuntu3) ... Preparing to unpack .../libzstd1_1.4.8+dfsg-3build1_armhf.deb ... Unpacking libzstd1:armhf (1.4.8+dfsg-3build1) over (1.4.8+dfsg-2.1build1) ... Setting up libzstd1:armhf (1.4.8+dfsg-3build1) ... (Reading database ... 14927 files and directories currently installed.) Preparing to unpack .../libkmod2_29-1ubuntu1_armhf.deb ... Unpacking libkmod2:armhf (29-1ubuntu1) over (28-1ubuntu4) ... Preparing to unpack .../libmount1_2.37.2-4ubuntu3_armhf.deb ... Unpacking libmount1:armhf (2.37.2-4ubuntu3) over (2.36.1-8ubuntu1) ... Setting up libmount1:armhf (2.37.2-4ubuntu3) ... (Reading database ... 14927 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.5.3-2ubuntu2_armhf.deb ... Unpacking libseccomp2:armhf (2.5.3-2ubuntu2) over (2.5.1-1ubuntu1) ... Setting up libseccomp2:armhf (2.5.3-2ubuntu2) ... (Reading database ... 14927 files and directories currently installed.) Preparing to unpack .../login_1%3a4.8.1-2ubuntu2_armhf.deb ... Unpacking login (1:4.8.1-2ubuntu2) over (1:4.8.1-1ubuntu9) ... Setting up login (1:4.8.1-2ubuntu2) ... (Reading database ... 14927 files and directories currently installed.) Preparing to unpack .../util-linux_2.37.2-4ubuntu3_armhf.deb ... Unpacking util-linux (2.37.2-4ubuntu3) over (2.36.1-8ubuntu1) ... Setting up util-linux (2.37.2-4ubuntu3) ... (Reading database ... 14922 files and directories currently installed.) Preparing to unpack .../mount_2.37.2-4ubuntu3_armhf.deb ... Unpacking mount (2.37.2-4ubuntu3) over (2.36.1-8ubuntu1) ... Preparing to unpack .../systemd_249.11-0ubuntu3_armhf.deb ... Unpacking systemd (249.11-0ubuntu3) over (248.3-1ubuntu8) ... Preparing to unpack .../libsystemd0_249.11-0ubuntu3_armhf.deb ... Unpacking libsystemd0:armhf (249.11-0ubuntu3) over (248.3-1ubuntu8) ... Setting up libsystemd0:armhf (249.11-0ubuntu3) ... (Reading database ... 14926 files and directories currently installed.) Preparing to unpack .../libxxhash0_0.8.1-1_armhf.deb ... Unpacking libxxhash0:armhf (0.8.1-1) over (0.8.0-2build1) ... Setting up libxxhash0:armhf (0.8.1-1) ... (Reading database ... 14926 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0_2.4.3_armhf.deb ... Unpacking libapt-pkg6.0:armhf (2.4.3) over (2.3.9) ... Setting up libapt-pkg6.0:armhf (2.4.3) ... (Reading database ... 14926 files and directories currently installed.) Preparing to unpack .../tar_1.34+dfsg-1build3_armhf.deb ... Unpacking tar (1.34+dfsg-1build3) over (1.34+dfsg-1build2) ... Setting up tar (1.34+dfsg-1build3) ... (Reading database ... 14926 files and directories currently installed.) Preparing to unpack .../dpkg_1.21.1ubuntu2_armhf.deb ... Unpacking dpkg (1.21.1ubuntu2) over (1.20.9ubuntu2) ... Setting up dpkg (1.21.1ubuntu2) ... Installing new version of config file /etc/cron.daily/dpkg ... Created symlink /etc/systemd/system/timers.target.wants/dpkg-db-backup.timer -> /lib/systemd/system/dpkg-db-backup.timer. (Reading database ... 14927 files and directories currently installed.) Preparing to unpack .../dash_0.5.11+git20210903+057cd650a4ed-3build1_armhf.deb ... Unpacking dash (0.5.11+git20210903+057cd650a4ed-3build1) over (0.5.11+git20210120+802ebd4-1build1) ... Setting up dash (0.5.11+git20210903+057cd650a4ed-3build1) ... (Reading database ... 14927 files and directories currently installed.) Preparing to unpack .../diffutils_1%3a3.8-0ubuntu2_armhf.deb ... Unpacking diffutils (1:3.8-0ubuntu2) over (1:3.8-0ubuntu1) ... Setting up diffutils (1:3.8-0ubuntu2) ... (Reading database ... 14927 files and directories currently installed.) Preparing to unpack .../findutils_4.8.0-1ubuntu3_armhf.deb ... Unpacking findutils (4.8.0-1ubuntu3) over (4.8.0-1ubuntu2) ... Setting up findutils (4.8.0-1ubuntu3) ... (Reading database ... 14927 files and directories currently installed.) Preparing to unpack .../grep_3.7-1build1_armhf.deb ... Unpacking grep (3.7-1build1) over (3.7-0ubuntu1) ... Setting up grep (3.7-1build1) ... (Reading database ... 14927 files and directories currently installed.) Preparing to unpack .../gzip_1.10-4ubuntu4_armhf.deb ... Unpacking gzip (1.10-4ubuntu4) over (1.10-4ubuntu2) ... Setting up gzip (1.10-4ubuntu4) ... (Reading database ... 14927 files and directories currently installed.) Preparing to unpack .../hostname_3.23ubuntu2_armhf.deb ... Unpacking hostname (3.23ubuntu2) over (3.23ubuntu1) ... Setting up hostname (3.23ubuntu2) ... (Reading database ... 14927 files and directories currently installed.) Preparing to unpack .../libncurses6_6.3-2_armhf.deb ... Unpacking libncurses6:armhf (6.3-2) over (6.2+20201114-2build2) ... Preparing to unpack .../libncursesw6_6.3-2_armhf.deb ... Unpacking libncursesw6:armhf (6.3-2) over (6.2+20201114-2build2) ... Preparing to unpack .../libtinfo6_6.3-2_armhf.deb ... Unpacking libtinfo6:armhf (6.3-2) over (6.2+20201114-2build2) ... Setting up libtinfo6:armhf (6.3-2) ... (Reading database ... 14926 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.3-2_armhf.deb ... Unpacking ncurses-bin (6.3-2) over (6.2+20201114-2build2) ... Setting up ncurses-bin (6.3-2) ... (Reading database ... 14926 files and directories currently installed.) Preparing to unpack .../sed_4.8-1ubuntu2_armhf.deb ... Unpacking sed (4.8-1ubuntu2) over (4.7-1ubuntu2) ... Setting up sed (4.8-1ubuntu2) ... (Reading database ... 14926 files and directories currently installed.) Preparing to unpack .../libdebconfclient0_0.261ubuntu1_armhf.deb ... Unpacking libdebconfclient0:armhf (0.261ubuntu1) over (0.256ubuntu4) ... Setting up libdebconfclient0:armhf (0.261ubuntu1) ... (Reading database ... 14926 files and directories currently installed.) Preparing to unpack .../base-passwd_3.5.52build1_armhf.deb ... Unpacking base-passwd (3.5.52build1) over (3.5.52) ... Setting up base-passwd (3.5.52build1) ... (Reading database ... 14926 files and directories currently installed.) Preparing to unpack .../init-system-helpers_1.62_all.deb ... Unpacking init-system-helpers (1.62) over (1.60build1) ... Setting up init-system-helpers (1.62) ... (Reading database ... 14926 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.3-2_all.deb ... Unpacking ncurses-base (6.3-2) over (6.2+20201114-2build2) ... Setting up ncurses-base (6.3-2) ... (Reading database ... 14927 files and directories currently installed.) Preparing to unpack .../lsb-base_11.1.0ubuntu4_all.deb ... Unpacking lsb-base (11.1.0ubuntu4) over (11.1.0ubuntu3) ... Setting up lsb-base (11.1.0ubuntu4) ... (Reading database ... 14927 files and directories currently installed.) Preparing to unpack .../sysvinit-utils_3.01-1ubuntu1_armhf.deb ... Unpacking sysvinit-utils (3.01-1ubuntu1) over (2.96-7ubuntu2) ... Setting up sysvinit-utils (3.01-1ubuntu1) ... (Reading database ... 14927 files and directories currently installed.) Preparing to unpack .../gpgv_2.2.27-3ubuntu2_armhf.deb ... Unpacking gpgv (2.2.27-3ubuntu2) over (2.2.20-1ubuntu4) ... Setting up gpgv (2.2.27-3ubuntu2) ... (Reading database ... 14927 files and directories currently installed.) Preparing to unpack .../archives/apt_2.4.3_armhf.deb ... Unpacking apt (2.4.3) over (2.3.9) ... Setting up apt (2.4.3) ... Installing new version of config file /etc/cron.daily/apt-compat ... Selecting previously unselected package libsepol2:armhf. (Reading database ... 14923 files and directories currently installed.) Preparing to unpack .../libsepol2_3.3-1build1_armhf.deb ... Unpacking libsepol2:armhf (3.3-1build1) ... Setting up libsepol2:armhf (3.3-1build1) ... (Reading database ... 14927 files and directories currently installed.) Preparing to unpack .../libsemanage-common_3.3-1build2_all.deb ... Unpacking libsemanage-common (3.3-1build2) over (3.1-1ubuntu3) ... Setting up libsemanage-common (3.3-1build2) ... Selecting previously unselected package libsemanage2:armhf. (Reading database ... 14927 files and directories currently installed.) Preparing to unpack .../libsemanage2_3.3-1build2_armhf.deb ... Unpacking libsemanage2:armhf (3.3-1build2) ... Setting up libsemanage2:armhf (3.3-1build2) ... (Reading database ... 14931 files and directories currently installed.) Preparing to unpack .../passwd_1%3a4.8.1-2ubuntu2_armhf.deb ... Unpacking passwd (1:4.8.1-2ubuntu2) over (1:4.8.1-1ubuntu9) ... Setting up passwd (1:4.8.1-2ubuntu2) ... (Reading database ... 14938 files and directories currently installed.) Removing libsemanage1:armhf (3.1-1ubuntu3) ... (Reading database ... 14934 files and directories currently installed.) Preparing to unpack .../libpam-modules-bin_1.4.0-11ubuntu2_armhf.deb ... Unpacking libpam-modules-bin (1.4.0-11ubuntu2) over (1.3.1-5ubuntu11) ... Setting up libpam-modules-bin (1.4.0-11ubuntu2) ... (Reading database ... 14932 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.4.0-11ubuntu2_armhf.deb ... Unpacking libpam-modules:armhf (1.4.0-11ubuntu2) over (1.3.1-5ubuntu11) ... Setting up libpam-modules:armhf (1.4.0-11ubuntu2) ... Installing new version of config file /etc/security/namespace.conf ... Installing new version of config file /etc/security/pam_env.conf ... (Reading database ... 14933 files and directories currently installed.) Preparing to unpack .../logsave_1.46.5-2ubuntu1_armhf.deb ... Unpacking logsave (1.46.5-2ubuntu1) over (1.46.3-1ubuntu3) ... Preparing to unpack .../libext2fs2_1.46.5-2ubuntu1_armhf.deb ... Unpacking libext2fs2:armhf (1.46.5-2ubuntu1) over (1.46.3-1ubuntu3) ... Setting up libext2fs2:armhf (1.46.5-2ubuntu1) ... (Reading database ... 14933 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.46.5-2ubuntu1_armhf.deb ... Unpacking e2fsprogs (1.46.5-2ubuntu1) over (1.46.3-1ubuntu3) ... Setting up libapparmor1:armhf (3.0.4-2ubuntu2) ... Setting up libargon2-1:armhf (0~20171227-0.3) ... Setting up libdevmapper1.02.1:armhf (2:1.02.175-2.1ubuntu4) ... Setting up libjson-c5:armhf (0.15-2build4) ... Setting up libcryptsetup12:armhf (2:2.4.3-1ubuntu1) ... Setting up libip4tc2:armhf (1.8.7-1ubuntu5) ... Setting up libkmod2:armhf (29-1ubuntu1) ... Setting up mount (2.37.2-4ubuntu3) ... Setting up systemd (249.11-0ubuntu3) ... Installing new version of config file /etc/systemd/logind.conf ... Installing new version of config file /etc/systemd/networkd.conf ... Installing new version of config file /etc/systemd/resolved.conf ... Initializing machine ID from random generator. Setting up systemd-sysv (249.11-0ubuntu3) ... (Reading database ... 14933 files and directories currently installed.) Preparing to unpack .../archives/init_1.62_armhf.deb ... Unpacking init (1.62) over (1.60build1) ... Preparing to unpack .../libattr1_1%3a2.5.1-1build1_armhf.deb ... Unpacking libattr1:armhf (1:2.5.1-1build1) over (1:2.4.48-6build2) ... Setting up libattr1:armhf (1:2.5.1-1build1) ... Installing new version of config file /etc/xattr.conf ... (Reading database ... 14933 files and directories currently installed.) Preparing to unpack .../libcap2_1%3a2.44-1build3_armhf.deb ... Unpacking libcap2:armhf (1:2.44-1build3) over (1:2.44-1build2) ... Setting up libcap2:armhf (1:2.44-1build3) ... (Reading database ... 14933 files and directories currently installed.) Preparing to unpack .../libpam-runtime_1.4.0-11ubuntu2_all.deb ... Unpacking libpam-runtime (1.4.0-11ubuntu2) over (1.3.1-5ubuntu11) ... Setting up libpam-runtime (1.4.0-11ubuntu2) ... (Reading database ... 14933 files and directories currently installed.) Preparing to unpack .../libpcre3_2%3a8.39-13build5_armhf.deb ... Unpacking libpcre3:armhf (2:8.39-13build5) over (2:8.39-13build4) ... Setting up libpcre3:armhf (2:8.39-13build5) ... (Reading database ... 14933 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.37.2-4ubuntu3_armhf.deb ... Unpacking libsmartcols1:armhf (2.37.2-4ubuntu3) over (2.36.1-8ubuntu1) ... Setting up libsmartcols1:armhf (2.37.2-4ubuntu3) ... (Reading database ... 14933 files and directories currently installed.) Preparing to unpack .../00-libprocps8_2%3a3.3.17-6ubuntu2_armhf.deb ... Unpacking libprocps8:armhf (2:3.3.17-6ubuntu2) over (2:3.3.17-5ubuntu3) ... Preparing to unpack .../01-libss2_1.46.5-2ubuntu1_armhf.deb ... Unpacking libss2:armhf (1.46.5-2ubuntu1) over (1.46.3-1ubuntu3) ... Preparing to unpack .../02-mawk_1.3.4.20200120-3_armhf.deb ... Unpacking mawk (1.3.4.20200120-3) over (1.3.4.20200120-2build1) ... Preparing to unpack .../03-procps_2%3a3.3.17-6ubuntu2_armhf.deb ... Unpacking procps (2:3.3.17-6ubuntu2) over (2:3.3.17-5ubuntu3) ... Preparing to unpack .../04-sensible-utils_0.0.17_all.deb ... Unpacking sensible-utils (0.0.17) over (0.0.14) ... Preparing to unpack .../05-usrmerge_25ubuntu2_all.deb ... Unpacking usrmerge (25ubuntu2) over (25ubuntu1) ... Preparing to unpack .../06-openssl_3.0.2-0ubuntu1_armhf.deb ... Unpacking openssl (3.0.2-0ubuntu1) over (1.1.1l-1ubuntu1) ... Preparing to unpack .../07-ca-certificates_20211016_all.deb ... Unpacking ca-certificates (20211016) over (20210119ubuntu1) ... Preparing to unpack .../08-readline-common_8.1.2-1_all.deb ... Unpacking readline-common (8.1.2-1) over (8.1-2build1) ... Preparing to unpack .../09-libreadline8_8.1.2-1_armhf.deb ... Unpacking libreadline8:armhf (8.1.2-1) over (8.1-2build1) ... Preparing to unpack .../10-libsqlite3-0_3.37.2-2_armhf.deb ... Unpacking libsqlite3-0:armhf (3.37.2-2) over (3.35.5-1) ... Preparing to unpack .../11-tzdata_2022a-0ubuntu1_all.deb ... Unpacking tzdata (2022a-0ubuntu1) over (2021a-2ubuntu1) ... Preparing to unpack .../12-libpng16-16_1.6.37-3build5_armhf.deb ... Unpacking libpng16-16:armhf (1.6.37-3build5) over (1.6.37-3build4) ... Preparing to unpack .../13-xz-utils_5.2.5-2ubuntu1_armhf.deb ... Unpacking xz-utils (5.2.5-2ubuntu1) over (5.2.5-2build1) ... Preparing to unpack .../14-advancecomp_2.1-2.1ubuntu2_armhf.deb ... Unpacking advancecomp (2.1-2.1ubuntu2) over (2.1-2.1ubuntu1) ... Preparing to unpack .../15-libctf0_2.38-3ubuntu1_armhf.deb ... Unpacking libctf0:armhf (2.38-3ubuntu1) over (2.37-7ubuntu1) ... Preparing to unpack .../16-libctf-nobfd0_2.38-3ubuntu1_armhf.deb ... Unpacking libctf-nobfd0:armhf (2.38-3ubuntu1) over (2.37-7ubuntu1) ... Preparing to unpack .../17-binutils-arm-linux-gnueabihf_2.38-3ubuntu1_armhf.deb ... Unpacking binutils-arm-linux-gnueabihf (2.38-3ubuntu1) over (2.37-7ubuntu1) ... Preparing to unpack .../18-libbinutils_2.38-3ubuntu1_armhf.deb ... Unpacking libbinutils:armhf (2.38-3ubuntu1) over (2.37-7ubuntu1) ... Preparing to unpack .../19-binutils_2.38-3ubuntu1_armhf.deb ... Unpacking binutils (2.38-3ubuntu1) over (2.37-7ubuntu1) ... Preparing to unpack .../20-binutils-common_2.38-3ubuntu1_armhf.deb ... Unpacking binutils-common:armhf (2.38-3ubuntu1) over (2.37-7ubuntu1) ... Preparing to unpack .../21-make_4.3-4.1build1_armhf.deb ... Unpacking make (4.3-4.1build1) over (4.3-4ubuntu1) ... Preparing to unpack .../22-dpkg-dev_1.21.1ubuntu2_all.deb ... Unpacking dpkg-dev (1.21.1ubuntu2) over (1.20.9ubuntu2) ... Preparing to unpack .../23-libdpkg-perl_1.21.1ubuntu2_all.deb ... Unpacking libdpkg-perl (1.21.1ubuntu2) over (1.20.9ubuntu2) ... Preparing to unpack .../24-patch_2.7.6-7build2_armhf.deb ... Unpacking patch (2.7.6-7build2) over (2.7.6-7build1) ... Preparing to unpack .../25-lto-disabled-list_24_all.deb ... Unpacking lto-disabled-list (24) over (16) ... Preparing to unpack .../26-build-essential_12.9ubuntu3_armhf.deb ... Unpacking build-essential (12.9ubuntu3) over (12.9ubuntu2) ... Preparing to unpack .../27-libubsan1_12-20220319-1ubuntu1_armhf.deb ... Unpacking libubsan1:armhf (12-20220319-1ubuntu1) over (11.2.0-7ubuntu2) ... Preparing to unpack .../28-libgomp1_12-20220319-1ubuntu1_armhf.deb ... Unpacking libgomp1:armhf (12-20220319-1ubuntu1) over (11.2.0-7ubuntu2) ... Preparing to unpack .../29-libatomic1_12-20220319-1ubuntu1_armhf.deb ... Unpacking libatomic1:armhf (12-20220319-1ubuntu1) over (11.2.0-7ubuntu2) ... Preparing to unpack .../30-libasan6_11.2.0-19ubuntu1_armhf.deb ... Unpacking libasan6:armhf (11.2.0-19ubuntu1) over (11.2.0-7ubuntu2) ... Preparing to unpack .../31-g++-11_11.2.0-19ubuntu1_armhf.deb ... Unpacking g++-11 (11.2.0-19ubuntu1) over (11.2.0-7ubuntu2) ... Preparing to unpack .../32-gcc-11_11.2.0-19ubuntu1_armhf.deb ... Unpacking gcc-11 (11.2.0-19ubuntu1) over (11.2.0-7ubuntu2) ... Preparing to unpack .../33-libstdc++-11-dev_11.2.0-19ubuntu1_armhf.deb ... Unpacking libstdc++-11-dev:armhf (11.2.0-19ubuntu1) over (11.2.0-7ubuntu2) ... Preparing to unpack .../34-libgcc-11-dev_11.2.0-19ubuntu1_armhf.deb ... Unpacking libgcc-11-dev:armhf (11.2.0-19ubuntu1) over (11.2.0-7ubuntu2) ... Preparing to unpack .../35-libcc1-0_12-20220319-1ubuntu1_armhf.deb ... Unpacking libcc1-0:armhf (12-20220319-1ubuntu1) over (11.2.0-7ubuntu2) ... Preparing to unpack .../36-cpp-11_11.2.0-19ubuntu1_armhf.deb ... Unpacking cpp-11 (11.2.0-19ubuntu1) over (11.2.0-7ubuntu2) ... Preparing to unpack .../37-gcc-11-base_11.2.0-19ubuntu1_armhf.deb ... Unpacking gcc-11-base:armhf (11.2.0-19ubuntu1) over (11.2.0-7ubuntu2) ... Preparing to unpack .../38-libisl23_0.24-2build1_armhf.deb ... Unpacking libisl23:armhf (0.24-2build1) over (0.24-1build1) ... Preparing to unpack .../39-libmpfr6_4.1.0-3build3_armhf.deb ... Unpacking libmpfr6:armhf (4.1.0-3build3) over (4.1.0-3build2) ... Preparing to unpack .../40-libmpc3_1.2.1-2build1_armhf.deb ... Unpacking libmpc3:armhf (1.2.1-2build1) over (1.2.0-1build2) ... Preparing to unpack .../41-libfakeroot_1.28-1ubuntu1_armhf.deb ... Unpacking libfakeroot:armhf (1.28-1ubuntu1) over (1.25.3-1.1ubuntu3) ... Preparing to unpack .../42-fakeroot_1.28-1ubuntu1_armhf.deb ... Unpacking fakeroot (1.28-1ubuntu1) over (1.25.3-1.1ubuntu3) ... Preparing to unpack .../43-libassuan0_2.5.5-1build1_armhf.deb ... Unpacking libassuan0:armhf (2.5.5-1build1) over (2.5.5-1) ... Preparing to unpack .../44-pinentry-curses_1.1.1-1build2_armhf.deb ... Unpacking pinentry-curses (1.1.1-1build2) over (1.1.1-1build1) ... Preparing to unpack .../45-libnpth0_1.6-3build2_armhf.deb ... Unpacking libnpth0:armhf (1.6-3build2) over (1.6-3build1) ... Preparing to unpack .../46-gpg_2.2.27-3ubuntu2_armhf.deb ... Unpacking gpg (2.2.27-3ubuntu2) over (2.2.20-1ubuntu4) ... Preparing to unpack .../47-gpgconf_2.2.27-3ubuntu2_armhf.deb ... Unpacking gpgconf (2.2.27-3ubuntu2) over (2.2.20-1ubuntu4) ... Preparing to unpack .../48-gpg-agent_2.2.27-3ubuntu2_armhf.deb ... Unpacking gpg-agent (2.2.27-3ubuntu2) over (2.2.20-1ubuntu4) ... Preparing to unpack .../49-liblockfile-bin_1.17-1build2_armhf.deb ... Unpacking liblockfile-bin (1.17-1build2) over (1.17-1build1) ... Preparing to unpack .../50-liblockfile1_1.17-1build2_armhf.deb ... Unpacking liblockfile1:armhf (1.17-1build2) over (1.17-1build1) ... Preparing to unpack .../51-lockfile-progs_0.1.19build1_armhf.deb ... Unpacking lockfile-progs (0.1.19build1) over (0.1.18build1) ... Preparing to unpack .../52-optipng_0.7.7-2build1_armhf.deb ... Unpacking optipng (0.7.7-2build1) over (0.7.7-2) ... Preparing to unpack .../53-pkgbinarymangler_149_all.deb ... Unpacking pkgbinarymangler (149) over (148) ... Setting up gcc-11-base:armhf (11.2.0-19ubuntu1) ... Setting up lto-disabled-list (24) ... Setting up liblockfile-bin (1.17-1build2) ... Setting up init (1.62) ... Setting up libsqlite3-0:armhf (3.37.2-2) ... Setting up binutils-common:armhf (2.38-3ubuntu1) ... Setting up linux-libc-dev:armhf (5.15.0-25.25) ... Setting up libctf-nobfd0:armhf (2.38-3ubuntu1) ... Setting up libnpth0:armhf (1.6-3build2) ... Setting up libassuan0:armhf (2.5.5-1build1) ... Setting up libgomp1:armhf (12-20220319-1ubuntu1) ... Setting up perl-modules-5.34 (5.34.0-3ubuntu1) ... Setting up bzip2 (1.0.8-5build1) ... Setting up libfakeroot:armhf (1.28-1ubuntu1) ... Setting up libasan6:armhf (11.2.0-19ubuntu1) ... Setting up tzdata (2022a-0ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Apr 9 09:09:06 UTC 2022. Universal Time is now: Sat Apr 9 09:09:06 UTC 2022. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.28-1ubuntu1) ... Setting up libtirpc-dev:armhf (1.3.2-2build1) ... Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... Setting up make (4.3-4.1build1) ... Setting up libmpfr6:armhf (4.1.0-3build3) ... Setting up libncurses6:armhf (6.3-2) ... Setting up xz-utils (5.2.5-2ubuntu1) ... Setting up libpng16-16:armhf (1.6.37-3build5) ... Setting up libmpc3:armhf (1.2.1-2build1) ... Setting up systemd-timesyncd (249.11-0ubuntu3) ... Setting up libatomic1:armhf (12-20220319-1ubuntu1) ... Setting up usrmerge (25ubuntu2) ... Setting up patch (2.7.6-7build2) ... Setting up libss2:armhf (1.46.5-2ubuntu1) ... Setting up libncursesw6:armhf (6.3-2) ... Setting up logsave (1.46.5-2ubuntu1) ... Setting up libubsan1:armhf (12-20220319-1ubuntu1) ... Setting up advancecomp (2.1-2.1ubuntu2) ... Setting up libgcc-11-dev:armhf (11.2.0-19ubuntu1) ... Setting up libnsl-dev:armhf (1.3.0-2build2) ... Setting up sensible-utils (0.0.17) ... Setting up libcrypt-dev:armhf (1:4.4.27-1) ... Setting up mawk (1.3.4.20200120-3) ... Setting up liblockfile1:armhf (1.17-1build2) ... Setting up libbinutils:armhf (2.38-3ubuntu1) ... Setting up libisl23:armhf (0.24-2build1) ... Setting up libc-dev-bin (2.35-0ubuntu3) ... Setting up openssl (3.0.2-0ubuntu1) ... Installing new version of config file /etc/ssl/openssl.cnf ... Setting up readline-common (8.1.2-1) ... Setting up libcc1-0:armhf (12-20220319-1ubuntu1) ... Setting up libprocps8:armhf (2:3.3.17-6ubuntu2) ... Setting up libgdbm6:armhf (1.23-1) ... Setting up libctf0:armhf (2.38-3ubuntu1) ... Setting up pinentry-curses (1.1.1-1build2) ... Setting up cpp-11 (11.2.0-19ubuntu1) ... Setting up libreadline8:armhf (8.1.2-1) ... Setting up e2fsprogs (1.46.5-2ubuntu1) ... Installing new version of config file /etc/mke2fs.conf ... Setting up ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 7 added, 8 removed; done. Setting up optipng (0.7.7-2build1) ... Setting up lockfile-progs (0.1.19build1) ... Setting up libgdbm-compat4:armhf (1.23-1) ... Setting up procps (2:3.3.17-6ubuntu2) ... Installing new version of config file /etc/init.d/procps ... Installing new version of config file /etc/sysctl.d/README.sysctl ... Setting up gpgconf (2.2.27-3ubuntu2) ... Setting up libc6-dev:armhf (2.35-0ubuntu3) ... Setting up binutils-arm-linux-gnueabihf (2.38-3ubuntu1) ... Setting up gpg (2.2.27-3ubuntu2) ... Setting up libperl5.34:armhf (5.34.0-3ubuntu1) ... Setting up gpg-agent (2.2.27-3ubuntu2) ... Setting up pkgbinarymangler (149) ... Setting up binutils (2.38-3ubuntu1) ... Setting up perl (5.34.0-3ubuntu1) ... Setting up libdpkg-perl (1.21.1ubuntu2) ... Setting up libstdc++-11-dev:armhf (11.2.0-19ubuntu1) ... Setting up gcc-11 (11.2.0-19ubuntu1) ... Setting up g++-11 (11.2.0-19ubuntu1) ... Setting up dpkg-dev (1.21.1ubuntu2) ... Setting up build-essential (12.9ubuntu3) ... Processing triggers for libc-bin (2.35-0ubuntu3) ... Processing triggers for ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-22372247 armhf jammy-proposed -c chroot:build-PACKAGEBUILD-22372247 --arch=armhf --dist=jammy-proposed --nolog python-cogent_2021.10.12a1+dfsg-1.dsc Initiating build PACKAGEBUILD-22372247 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-107-generic #121-Ubuntu SMP Thu Mar 24 16:07:22 UTC 2022 armv7l sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos02-arm64-066.buildd +==============================================================================+ | python-cogent 2021.10.12a1+dfsg-1 (armhf) Sat, 09 Apr 2022 09:09:15 +0000 | +==============================================================================+ Package: python-cogent Version: 2021.10.12a1+dfsg-1 Source Version: 2021.10.12a1+dfsg-1 Distribution: jammy-proposed Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-22372247/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/python-cogent-nwRRaE/resolver-4YlyMh' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- python-cogent_2021.10.12a1+dfsg-1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/python-cogent-nwRRaE/python-cogent-2021.10.12a1+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/python-cogent-nwRRaE' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-python, flit, python3-all-dev, python3-matplotlib, python3-numba, python3-numpy, python3-pandas, python3-scitrack, python3-tqdm, python3-tinydb, python3-sphinx, python3-numpydoc, python3-nbsphinx, python3-sphinx-bootstrap-theme, python3-sphinx-gallery, python3-pytest, cython3, pandoc, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), dh-python, flit, python3-all-dev, python3-matplotlib, python3-numba, python3-numpy, python3-pandas, python3-scitrack, python3-tqdm, python3-tinydb, python3-sphinx, python3-numpydoc, python3-nbsphinx, python3-sphinx-bootstrap-theme, python3-sphinx-gallery, python3-pytest, cython3, pandoc, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [483 B] Get:5 copy:/<>/apt_archive ./ Packages [559 B] Fetched 1999 B in 0s (80.1 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libperl5.32 perl-modules-5.32 systemd-timesyncd Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev blt bsdextrautils cython3 debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dwz file flit fontconfig-config fonts-dejavu-core fonts-lyx gettext gettext-base groff-base intltool-debian libarchive-zip-perl libblas3 libbrotli1 libbsd0 libcmark-gfm-extensions0.29.0.gfm.3 libcmark-gfm0.29.0.gfm.3 libdebhelper-perl libdeflate0 libdw1 libedit2 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libicu70 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblcms2-2 libllvm11 libmagic-mgc libmagic1 libmd0 libmpdec3 libnorm1 libopenjp2-7 libpfm4 libpgm-5.3-0 libpipeline1 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.10 libpython3.10-dev libpython3.10-minimal libpython3.10-stdlib libqhull-r8.0 libraqm0 libsigsegv2 libsodium23 libsub-override-perl libtbb12 libtbbmalloc2 libtcl8.6 libtiff5 libtk8.6 libtool libuchardet0 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 libzmq5 llvm-11 llvm-11-linker-tools llvm-11-runtime m4 man-db media-types pandoc pandoc-data po-debconf python-babel-localedata python-matplotlib-data python3 python3-alabaster python3-all python3-all-dev python3-appdirs python3-attr python3-babel python3-bleach python3-brotli python3-certifi python3-cffi-backend python3-chardet python3-cycler python3-dateutil python3-decorator python3-defusedxml python3-dev python3-distutils python3-docutils python3-entrypoints python3-fonttools python3-fs python3-html5lib python3-idna python3-imagesize python3-importlib-metadata python3-iniconfig python3-ipython-genutils python3-jinja2 python3-jsonschema python3-jupyter-client python3-jupyter-core python3-jupyterlab-pygments python3-kiwisolver python3-lib2to3 python3-llvmlite python3-lxml python3-lz4 python3-markupsafe python3-matplotlib python3-minimal python3-more-itertools python3-mpmath python3-nbclient python3-nbconvert python3-nbformat python3-nbsphinx python3-nest-asyncio python3-numba python3-numpy python3-numpydoc python3-packaging python3-pandas python3-pandas-lib python3-pandocfilters python3-pil python3-pil.imagetk python3-pkg-resources python3-pluggy python3-py python3-pygments python3-pyparsing python3-pyrsistent python3-pytest python3-requests python3-roman python3-scipy python3-scitrack python3-setuptools python3-six python3-snowballstemmer python3-sphinx python3-sphinx-bootstrap-theme python3-sphinx-gallery python3-sympy python3-testpath python3-tinydb python3-tk python3-toml python3-tomli python3-tomli-w python3-tornado python3-tqdm python3-traitlets python3-tz python3-ufolib2 python3-unicodedata2 python3-urllib3 python3-webencodings python3-zipp python3-zmq python3.10 python3.10-dev python3.10-minimal sgml-base sphinx-common tk8.6-blt2.5 ucf unicode-data x11-common xml-core zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc blt-demo cython-doc dh-make python3-build python3-installer gettext-doc libasprintf-dev libgettextpo-dev groff libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk llvm-11-doc m4-doc apparmor less www-browser texlive-latex-recommended texlive-xetex texlive-luatex pandoc-citeproc texlive-latex-extra context wkhtmltopdf librsvg2-bin ghc nodejs php python ruby r-base-core libjs-mathjax libjs-katex citation-style-language-styles libmail-box-perl python3-doc python3-venv python-attr-doc python-bleach-doc python-cycler-doc docutils-doc fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french texlive-latex-base python3-genshi python-jinja2-doc python-jsonschema-doc python3-pip llvmlite-doc python-lxml-doc dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip texlive-extra-utils python-mpmath-doc python3-gmpy2 python-nbconvert-doc texlive-fonts-recommended texlive-plain-generic python-nbsphinx-doc gfortran python-numpy-doc python-pandas-doc python3-statsmodels python-pil-doc subversion python-pygments-doc ttf-bitstream-vera python-pyparsing-doc python3-cryptography python3-openssl python3-socks python-requests-doc python-scipy-doc python-setuptools-doc python3-stemmer fonts-freefont-otf imagemagick-6.q16 latexmk python3-sphinx-rtd-theme sphinx-doc tex-gyre python-sphinx-gallery-doc python3-seaborn texlive-fonts-extra python-sympy-doc tix python3-tk-dbg python3-pycurl python-tornado-doc python3-twisted python3.10-venv python3.10-doc binfmt-support sgml-base-doc Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs javascript-common libltdl-dev llvm-11-dev binfmt-support libmail-sendmail-perl libpaper-utils python3-bs4 python3-sphinxcontrib.bibtex numba-doc python3-pip python3-bottleneck python3-numexpr python3-odf python3-openpyxl python3-xlwt python3-tables python3-olefile The following NEW packages will be installed: autoconf automake autopoint autotools-dev blt bsdextrautils cython3 debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dwz file flit fontconfig-config fonts-dejavu-core fonts-lyx gettext gettext-base groff-base intltool-debian libarchive-zip-perl libblas3 libbrotli1 libbsd0 libcmark-gfm-extensions0.29.0.gfm.3 libcmark-gfm0.29.0.gfm.3 libdebhelper-perl libdeflate0 libdw1 libedit2 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libicu70 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblcms2-2 libllvm11 libmagic-mgc libmagic1 libmd0 libmpdec3 libnorm1 libopenjp2-7 libpfm4 libpgm-5.3-0 libpipeline1 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.10 libpython3.10-dev libpython3.10-minimal libpython3.10-stdlib libqhull-r8.0 libraqm0 libsigsegv2 libsodium23 libsub-override-perl libtbb12 libtbbmalloc2 libtcl8.6 libtiff5 libtk8.6 libtool libuchardet0 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 libzmq5 llvm-11 llvm-11-linker-tools llvm-11-runtime m4 man-db media-types pandoc pandoc-data po-debconf python-babel-localedata python-matplotlib-data python3 python3-alabaster python3-all python3-all-dev python3-appdirs python3-attr python3-babel python3-bleach python3-brotli python3-certifi python3-cffi-backend python3-chardet python3-cycler python3-dateutil python3-decorator python3-defusedxml python3-dev python3-distutils python3-docutils python3-entrypoints python3-fonttools python3-fs python3-html5lib python3-idna python3-imagesize python3-importlib-metadata python3-iniconfig python3-ipython-genutils python3-jinja2 python3-jsonschema python3-jupyter-client python3-jupyter-core python3-jupyterlab-pygments python3-kiwisolver python3-lib2to3 python3-llvmlite python3-lxml python3-lz4 python3-markupsafe python3-matplotlib python3-minimal python3-more-itertools python3-mpmath python3-nbclient python3-nbconvert python3-nbformat python3-nbsphinx python3-nest-asyncio python3-numba python3-numpy python3-numpydoc python3-packaging python3-pandas python3-pandas-lib python3-pandocfilters python3-pil python3-pil.imagetk python3-pkg-resources python3-pluggy python3-py python3-pygments python3-pyparsing python3-pyrsistent python3-pytest python3-requests python3-roman python3-scipy python3-scitrack python3-setuptools python3-six python3-snowballstemmer python3-sphinx python3-sphinx-bootstrap-theme python3-sphinx-gallery python3-sympy python3-testpath python3-tinydb python3-tk python3-toml python3-tomli python3-tomli-w python3-tornado python3-tqdm python3-traitlets python3-tz python3-ufolib2 python3-unicodedata2 python3-urllib3 python3-webencodings python3-zipp python3-zmq python3.10 python3.10-dev python3.10-minimal sbuild-build-depends-main-dummy sgml-base sphinx-common tk8.6-blt2.5 ucf unicode-data x11-common xml-core zlib1g-dev 0 upgraded, 214 newly installed, 0 to remove and 0 not upgraded. Need to get 154 MB of archives. After this operation, 657 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [780 B] Get:2 http://ftpmaster.internal/ubuntu jammy/main armhf libpython3.10-minimal armhf 3.10.4-3 [793 kB] Get:3 http://ftpmaster.internal/ubuntu jammy/main armhf libexpat1 armhf 2.4.7-1 [66.5 kB] Get:4 http://ftpmaster.internal/ubuntu jammy/main armhf python3.10-minimal armhf 3.10.4-3 [1932 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main armhf python3-minimal armhf 3.10.4-0ubuntu2 [24.4 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main armhf media-types all 7.0.0 [25.5 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/main armhf libmpdec3 armhf 2.5.1-2build2 [76.5 kB] Get:8 http://ftpmaster.internal/ubuntu jammy/main armhf libpython3.10-stdlib armhf 3.10.4-3 [1748 kB] Get:9 http://ftpmaster.internal/ubuntu jammy/main armhf python3.10 armhf 3.10.4-3 [488 kB] Get:10 http://ftpmaster.internal/ubuntu jammy/main armhf libpython3-stdlib armhf 3.10.4-0ubuntu2 [6990 B] Get:11 http://ftpmaster.internal/ubuntu jammy/main armhf python3 armhf 3.10.4-0ubuntu2 [22.8 kB] Get:12 http://ftpmaster.internal/ubuntu jammy/main armhf sgml-base all 1.30 [12.5 kB] Get:13 http://ftpmaster.internal/ubuntu jammy/main armhf libmd0 armhf 1.0.4-1build1 [22.5 kB] Get:14 http://ftpmaster.internal/ubuntu jammy/main armhf libbsd0 armhf 0.11.5-1 [39.8 kB] Get:15 http://ftpmaster.internal/ubuntu jammy/main armhf libelf1 armhf 0.186-1build1 [42.7 kB] Get:16 http://ftpmaster.internal/ubuntu jammy/main armhf libfribidi0 armhf 1.0.8-2ubuntu3 [23.5 kB] Get:17 http://ftpmaster.internal/ubuntu jammy/main armhf libglib2.0-0 armhf 2.72.0-1 [1322 kB] Get:18 http://ftpmaster.internal/ubuntu jammy/main armhf libicu70 armhf 70.1-2 [10.3 MB] Get:19 http://ftpmaster.internal/ubuntu jammy/main armhf libxml2 armhf 2.9.13+dfsg-1build1 [600 kB] Get:20 http://ftpmaster.internal/ubuntu jammy/main armhf python3-pkg-resources all 59.6.0-1.2 [132 kB] Get:21 http://ftpmaster.internal/ubuntu jammy/main armhf ucf all 3.0043 [56.1 kB] Get:22 http://ftpmaster.internal/ubuntu jammy/main armhf bsdextrautils armhf 2.37.2-4ubuntu3 [77.1 kB] Get:23 http://ftpmaster.internal/ubuntu jammy/main armhf libmagic-mgc armhf 1:5.41-3 [257 kB] Get:24 http://ftpmaster.internal/ubuntu jammy/main armhf libmagic1 armhf 1:5.41-3 [80.2 kB] Get:25 http://ftpmaster.internal/ubuntu jammy/main armhf file armhf 1:5.41-3 [20.6 kB] Get:26 http://ftpmaster.internal/ubuntu jammy/main armhf gettext-base armhf 0.21-4ubuntu4 [38.0 kB] Get:27 http://ftpmaster.internal/ubuntu jammy/main armhf libuchardet0 armhf 0.0.7-1build2 [75.7 kB] Get:28 http://ftpmaster.internal/ubuntu jammy/main armhf groff-base armhf 1.22.4-8build1 [870 kB] Get:29 http://ftpmaster.internal/ubuntu jammy/main armhf libedit2 armhf 3.1-20210910-1build1 [78.7 kB] Get:30 http://ftpmaster.internal/ubuntu jammy/main armhf libpipeline1 armhf 1.5.5-1 [25.6 kB] Get:31 http://ftpmaster.internal/ubuntu jammy/main armhf libxau6 armhf 1:1.0.9-1build5 [6622 B] Get:32 http://ftpmaster.internal/ubuntu jammy/main armhf libxdmcp6 armhf 1:1.1.3-0ubuntu5 [9452 B] Get:33 http://ftpmaster.internal/ubuntu jammy/main armhf libxcb1 armhf 1.14-3ubuntu3 [46.1 kB] Get:34 http://ftpmaster.internal/ubuntu jammy/main armhf libx11-data all 2:1.7.5-1 [119 kB] Get:35 http://ftpmaster.internal/ubuntu jammy/main armhf libx11-6 armhf 2:1.7.5-1 [604 kB] Get:36 http://ftpmaster.internal/ubuntu jammy/main armhf libxext6 armhf 2:1.3.4-1build1 [26.4 kB] Get:37 http://ftpmaster.internal/ubuntu jammy/main armhf man-db armhf 2.10.2-1 [1151 kB] Get:38 http://ftpmaster.internal/ubuntu jammy/main armhf libsigsegv2 armhf 2.13-1ubuntu3 [13.7 kB] Get:39 http://ftpmaster.internal/ubuntu jammy/main armhf m4 armhf 1.4.18-5ubuntu2 [191 kB] Get:40 http://ftpmaster.internal/ubuntu jammy/main armhf autoconf all 2.71-2 [338 kB] Get:41 http://ftpmaster.internal/ubuntu jammy/main armhf autotools-dev all 20220109.1 [44.9 kB] Get:42 http://ftpmaster.internal/ubuntu jammy/main armhf automake all 1:1.16.5-1.3 [558 kB] Get:43 http://ftpmaster.internal/ubuntu jammy/main armhf autopoint all 0.21-4ubuntu4 [422 kB] Get:44 http://ftpmaster.internal/ubuntu jammy/main armhf libtcl8.6 armhf 8.6.12+dfsg-1build1 [911 kB] Get:45 http://ftpmaster.internal/ubuntu jammy/main armhf libbrotli1 armhf 1.0.9-2build6 [306 kB] Get:46 http://ftpmaster.internal/ubuntu jammy/main armhf libfreetype6 armhf 2.11.1+dfsg-1build1 [326 kB] Get:47 http://ftpmaster.internal/ubuntu jammy/main armhf fonts-dejavu-core all 2.37-2build1 [1041 kB] Get:48 http://ftpmaster.internal/ubuntu jammy/main armhf fontconfig-config all 2.13.1-4.2ubuntu5 [29.1 kB] Get:49 http://ftpmaster.internal/ubuntu jammy/main armhf libfontconfig1 armhf 2.13.1-4.2ubuntu5 [109 kB] Get:50 http://ftpmaster.internal/ubuntu jammy/main armhf libxrender1 armhf 1:0.9.10-1build4 [16.2 kB] Get:51 http://ftpmaster.internal/ubuntu jammy/main armhf libxft2 armhf 2.3.3-0ubuntu5 [34.7 kB] Get:52 http://ftpmaster.internal/ubuntu jammy/main armhf x11-common all 1:7.7+23ubuntu2 [23.4 kB] Get:53 http://ftpmaster.internal/ubuntu jammy/main armhf libxss1 armhf 1:1.2.3-1build2 [7580 B] Get:54 http://ftpmaster.internal/ubuntu jammy/main armhf libtk8.6 armhf 8.6.12-1build1 [689 kB] Get:55 http://ftpmaster.internal/ubuntu jammy/main armhf tk8.6-blt2.5 armhf 2.5.3+dfsg-4.1build2 [538 kB] Get:56 http://ftpmaster.internal/ubuntu jammy/main armhf blt armhf 2.5.3+dfsg-4.1build2 [4838 B] Get:57 http://ftpmaster.internal/ubuntu jammy/universe armhf cython3 armhf 0.29.28-1ubuntu3 [1295 kB] Get:58 http://ftpmaster.internal/ubuntu jammy/main armhf libdebhelper-perl all 13.6ubuntu1 [67.2 kB] Get:59 http://ftpmaster.internal/ubuntu jammy/main armhf libtool all 2.4.6-15build2 [164 kB] Get:60 http://ftpmaster.internal/ubuntu jammy/main armhf dh-autoreconf all 20 [16.1 kB] Get:61 http://ftpmaster.internal/ubuntu jammy/main armhf libarchive-zip-perl all 1.68-1 [90.2 kB] Get:62 http://ftpmaster.internal/ubuntu jammy/main armhf libsub-override-perl all 0.09-2 [9532 B] Get:63 http://ftpmaster.internal/ubuntu jammy/main armhf libfile-stripnondeterminism-perl all 1.13.0-1 [18.1 kB] Get:64 http://ftpmaster.internal/ubuntu jammy/main armhf dh-strip-nondeterminism all 1.13.0-1 [5344 B] Get:65 http://ftpmaster.internal/ubuntu jammy/main armhf libdw1 armhf 0.186-1build1 [228 kB] Get:66 http://ftpmaster.internal/ubuntu jammy/main armhf debugedit armhf 1:5.0-4build1 [43.3 kB] Get:67 http://ftpmaster.internal/ubuntu jammy/main armhf dwz armhf 0.14-1build2 [99.2 kB] Get:68 http://ftpmaster.internal/ubuntu jammy/main armhf gettext armhf 0.21-4ubuntu4 [805 kB] Get:69 http://ftpmaster.internal/ubuntu jammy/main armhf intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:70 http://ftpmaster.internal/ubuntu jammy/main armhf po-debconf all 1.0.21+nmu1 [233 kB] Get:71 http://ftpmaster.internal/ubuntu jammy/main armhf debhelper all 13.6ubuntu1 [923 kB] Get:72 http://ftpmaster.internal/ubuntu jammy/main armhf python3-lib2to3 all 3.10.4-0ubuntu1 [76.2 kB] Get:73 http://ftpmaster.internal/ubuntu jammy/main armhf python3-distutils all 3.10.4-0ubuntu1 [138 kB] Get:74 http://ftpmaster.internal/ubuntu jammy/universe armhf dh-python all 5.20220403 [106 kB] Get:75 http://ftpmaster.internal/ubuntu jammy/main armhf xml-core all 0.18+nmu1 [21.6 kB] Get:76 http://ftpmaster.internal/ubuntu jammy/main armhf docutils-common all 0.17.1+dfsg-2 [117 kB] Get:77 http://ftpmaster.internal/ubuntu jammy/main armhf python3-roman all 3.3-1 [10.6 kB] Get:78 http://ftpmaster.internal/ubuntu jammy/main armhf python3-docutils all 0.17.1+dfsg-2 [387 kB] Get:79 http://ftpmaster.internal/ubuntu jammy/main armhf python3-certifi all 2020.6.20-1 [150 kB] Get:80 http://ftpmaster.internal/ubuntu jammy/main armhf python3-chardet all 4.0.0-1 [98.0 kB] Get:81 http://ftpmaster.internal/ubuntu jammy/main armhf python3-idna all 3.3-1 [49.3 kB] Get:82 http://ftpmaster.internal/ubuntu jammy/main armhf python3-six all 1.16.0-3 [12.5 kB] Get:83 http://ftpmaster.internal/ubuntu jammy/main armhf python3-urllib3 all 1.26.5-1~exp1 [96.4 kB] Get:84 http://ftpmaster.internal/ubuntu jammy/main armhf python3-requests all 2.25.1+dfsg-2 [47.9 kB] Get:85 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-tomli all 1.2.2-2 [12.9 kB] Get:86 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-tomli-w all 1.0.0-1 [7266 B] Get:87 http://ftpmaster.internal/ubuntu jammy/universe armhf flit all 3.6.0-1 [86.4 kB] Get:88 http://ftpmaster.internal/ubuntu jammy/universe armhf fonts-lyx all 2.3.6-1 [159 kB] Get:89 http://ftpmaster.internal/ubuntu jammy/main armhf libblas3 armhf 3.10.0-2ubuntu1 [118 kB] Get:90 http://ftpmaster.internal/ubuntu jammy/universe armhf libcmark-gfm0.29.0.gfm.3 armhf 0.29.0.gfm.3-3 [95.2 kB] Get:91 http://ftpmaster.internal/ubuntu jammy/universe armhf libcmark-gfm-extensions0.29.0.gfm.3 armhf 0.29.0.gfm.3-3 [22.4 kB] Get:92 http://ftpmaster.internal/ubuntu jammy/main armhf libdeflate0 armhf 1.10-2 [59.2 kB] Get:93 http://ftpmaster.internal/ubuntu jammy/main armhf libexpat1-dev armhf 2.4.7-1 [126 kB] Get:94 http://ftpmaster.internal/ubuntu jammy/main armhf libgfortran5 armhf 12-20220319-1ubuntu1 [294 kB] Get:95 http://ftpmaster.internal/ubuntu jammy/main armhf libgraphite2-3 armhf 1.3.14-1build2 [65.2 kB] Get:96 http://ftpmaster.internal/ubuntu jammy/main armhf libharfbuzz0b armhf 2.7.4-1ubuntu3 [335 kB] Get:97 http://ftpmaster.internal/ubuntu jammy/main armhf libimagequant0 armhf 2.17.0-1 [28.8 kB] Get:98 http://ftpmaster.internal/ubuntu jammy/main armhf libjpeg-turbo8 armhf 2.1.2-0ubuntu1 [116 kB] Get:99 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libjpeg8 armhf 8c-2ubuntu10 [2266 B] Get:100 http://ftpmaster.internal/ubuntu jammy/main armhf libjs-jquery all 3.6.0+dfsg+~3.5.13-1 [321 kB] Get:101 http://ftpmaster.internal/ubuntu jammy/universe armhf libjs-jquery-ui all 1.13.1+dfsg-1 [253 kB] Get:102 http://ftpmaster.internal/ubuntu jammy/main armhf libjs-underscore all 1.13.2~dfsg-2 [118 kB] Get:103 http://ftpmaster.internal/ubuntu jammy/main armhf libjs-sphinxdoc all 4.3.2-1 [139 kB] Get:104 http://ftpmaster.internal/ubuntu jammy/main armhf liblapack3 armhf 3.10.0-2ubuntu1 [1932 kB] Get:105 http://ftpmaster.internal/ubuntu jammy/universe armhf liblbfgsb0 armhf 3.0+dfsg.3-10 [26.9 kB] Get:106 http://ftpmaster.internal/ubuntu jammy/main armhf liblcms2-2 armhf 2.12~rc1-2build2 [131 kB] Get:107 http://ftpmaster.internal/ubuntu jammy/universe armhf libllvm11 armhf 1:11.1.0-6 [18.2 MB] Get:108 http://ftpmaster.internal/ubuntu jammy/universe armhf libnorm1 armhf 1.5.9+dfsg-2 [185 kB] Get:109 http://ftpmaster.internal/ubuntu jammy/universe armhf libpgm-5.3-0 armhf 5.3.128~dfsg-2 [155 kB] Get:110 http://ftpmaster.internal/ubuntu jammy/main armhf libpython3.10 armhf 3.10.4-3 [1727 kB] Get:111 http://ftpmaster.internal/ubuntu jammy/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2ubuntu9 [157 kB] Get:112 http://ftpmaster.internal/ubuntu jammy/main armhf libpython3.10-dev armhf 3.10.4-3 [3599 kB] Get:113 http://ftpmaster.internal/ubuntu jammy/main armhf libpython3-dev armhf 3.10.4-0ubuntu2 [7250 B] Get:114 http://ftpmaster.internal/ubuntu jammy/main armhf libpython3-all-dev armhf 3.10.4-0ubuntu2 [918 B] Get:115 http://ftpmaster.internal/ubuntu jammy/universe armhf libqhull-r8.0 armhf 2020.2-4 [175 kB] Get:116 http://ftpmaster.internal/ubuntu jammy/main armhf libraqm0 armhf 0.7.0-4ubuntu1 [10.1 kB] Get:117 http://ftpmaster.internal/ubuntu jammy/main armhf libsodium23 armhf 1.0.18-1build2 [141 kB] Get:118 http://ftpmaster.internal/ubuntu jammy/universe armhf libtbbmalloc2 armhf 2021.5.0-7ubuntu2 [42.2 kB] Get:119 http://ftpmaster.internal/ubuntu jammy/universe armhf libtbb12 armhf 2021.5.0-7ubuntu2 [70.2 kB] Get:120 http://ftpmaster.internal/ubuntu jammy/main armhf libjbig0 armhf 2.1-3.1build3 [25.1 kB] Get:121 http://ftpmaster.internal/ubuntu jammy/main armhf libwebp7 armhf 1.2.2-2 [166 kB] Get:122 http://ftpmaster.internal/ubuntu jammy/main armhf libtiff5 armhf 4.3.0-6 [165 kB] Get:123 http://ftpmaster.internal/ubuntu jammy/main armhf libwebpdemux2 armhf 1.2.2-2 [8878 B] Get:124 http://ftpmaster.internal/ubuntu jammy/main armhf libwebpmux3 armhf 1.2.2-2 [16.8 kB] Get:125 http://ftpmaster.internal/ubuntu jammy/main armhf libxslt1.1 armhf 1.1.34-4build2 [147 kB] Get:126 http://ftpmaster.internal/ubuntu jammy/universe armhf libzmq5 armhf 4.3.4-2 [261 kB] Get:127 http://ftpmaster.internal/ubuntu jammy/universe armhf llvm-11-runtime armhf 1:11.1.0-6 [165 kB] Get:128 http://ftpmaster.internal/ubuntu jammy/universe armhf llvm-11-linker-tools armhf 1:11.1.0-6 [1073 kB] Get:129 http://ftpmaster.internal/ubuntu jammy/main armhf libpfm4 armhf 4.11.1+git32-gd0b85fb-1 [39.3 kB] Get:130 http://ftpmaster.internal/ubuntu jammy/universe armhf llvm-11 armhf 1:11.1.0-6 [7968 kB] Get:131 http://ftpmaster.internal/ubuntu jammy/universe armhf pandoc-data all 2.9.2.1-3ubuntu2 [81.8 kB] Get:132 http://ftpmaster.internal/ubuntu jammy/universe armhf pandoc armhf 2.9.2.1-3ubuntu2 [20.8 MB] Get:133 http://ftpmaster.internal/ubuntu jammy/main armhf python-babel-localedata all 2.8.0+dfsg.1-7 [4982 kB] Get:134 http://ftpmaster.internal/ubuntu jammy/universe armhf python-matplotlib-data all 3.5.1-2build1 [2942 kB] Get:135 http://ftpmaster.internal/ubuntu jammy/main armhf python3-all armhf 3.10.4-0ubuntu2 [916 B] Get:136 http://ftpmaster.internal/ubuntu jammy/main armhf python3.10-dev armhf 3.10.4-3 [508 kB] Get:137 http://ftpmaster.internal/ubuntu jammy/main armhf python3-dev armhf 3.10.4-0ubuntu2 [26.0 kB] Get:138 http://ftpmaster.internal/ubuntu jammy/main armhf python3-all-dev armhf 3.10.4-0ubuntu2 [916 B] Get:139 http://ftpmaster.internal/ubuntu jammy/main armhf python3-appdirs all 1.4.4-2 [11.4 kB] Get:140 http://ftpmaster.internal/ubuntu jammy/main armhf python3-attr all 21.2.0-1 [44.0 kB] Get:141 http://ftpmaster.internal/ubuntu jammy/main armhf python3-tz all 2022.1-1 [33.3 kB] Get:142 http://ftpmaster.internal/ubuntu jammy/main armhf python3-babel all 2.8.0+dfsg.1-7 [85.1 kB] Get:143 http://ftpmaster.internal/ubuntu jammy/main armhf python3-pyparsing all 2.4.7-1 [61.4 kB] Get:144 http://ftpmaster.internal/ubuntu jammy/main armhf python3-packaging all 21.3-1 [30.7 kB] Get:145 http://ftpmaster.internal/ubuntu jammy/main armhf python3-webencodings all 0.5.1-4 [11.8 kB] Get:146 http://ftpmaster.internal/ubuntu jammy/main armhf python3-html5lib all 1.1-3 [87.0 kB] Get:147 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-bleach all 4.1.0-1 [40.7 kB] Get:148 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-brotli armhf 1.0.9-2build6 [309 kB] Get:149 http://ftpmaster.internal/ubuntu jammy/main armhf python3-cffi-backend armhf 1.15.0-1build2 [67.6 kB] Get:150 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-cycler all 0.11.0-1 [8156 B] Get:151 http://ftpmaster.internal/ubuntu jammy/main armhf python3-dateutil all 2.8.1-6 [78.4 kB] Get:152 http://ftpmaster.internal/ubuntu jammy/main armhf python3-decorator all 4.4.2-0ubuntu1 [10.3 kB] Get:153 http://ftpmaster.internal/ubuntu jammy/main armhf python3-defusedxml all 0.7.1-1 [43.2 kB] Get:154 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-entrypoints all 0.4-1 [7112 B] Get:155 http://ftpmaster.internal/ubuntu jammy/main armhf python3-numpy armhf 1:1.21.5-1build2 [3787 kB] Get:156 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-scipy armhf 1.8.0-1exp2ubuntu1 [14.0 MB] Get:157 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-ufolib2 all 0.13.1+dfsg1-1 [32.2 kB] Get:158 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-mpmath all 1.2.1-2 [419 kB] Get:159 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-sympy all 1.9-1 [4312 kB] Get:160 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-fs all 2.4.12-1 [84.9 kB] Get:161 http://ftpmaster.internal/ubuntu jammy/main armhf python3-lxml armhf 4.8.0-1build1 [1097 kB] Get:162 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-lz4 armhf 3.1.3+dfsg-1build3 [30.9 kB] Get:163 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-unicodedata2 armhf 14.0.0+ds-8 [379 kB] Get:164 http://ftpmaster.internal/ubuntu jammy/universe armhf unicode-data all 14.0.0-1.1 [8206 kB] Get:165 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-fonttools armhf 4.29.1-2build1 [804 kB] Get:166 http://ftpmaster.internal/ubuntu jammy/main armhf python3-imagesize all 1.3.0-1 [6458 B] Get:167 http://ftpmaster.internal/ubuntu jammy/main armhf python3-more-itertools all 8.10.0-2 [47.9 kB] Get:168 http://ftpmaster.internal/ubuntu jammy/main armhf python3-zipp all 1.0.0-3 [5440 B] Get:169 http://ftpmaster.internal/ubuntu jammy/main armhf python3-importlib-metadata all 4.6.4-1 [16.2 kB] Get:170 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-iniconfig all 1.1.1-2 [6024 B] Get:171 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-ipython-genutils all 0.2.0-5 [21.9 kB] Get:172 http://ftpmaster.internal/ubuntu jammy/main armhf python3-markupsafe armhf 2.0.1-2build1 [12.0 kB] Get:173 http://ftpmaster.internal/ubuntu jammy/main armhf python3-jinja2 all 3.0.3-1 [108 kB] Get:174 http://ftpmaster.internal/ubuntu jammy/main armhf python3-setuptools all 59.6.0-1.2 [339 kB] Get:175 http://ftpmaster.internal/ubuntu jammy/main armhf python3-pyrsistent armhf 0.18.1-1build1 [52.6 kB] Get:176 http://ftpmaster.internal/ubuntu jammy/main armhf python3-jsonschema all 3.2.0-0ubuntu2 [43.1 kB] Get:177 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-traitlets all 5.1.1-1 [81.2 kB] Get:178 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-jupyter-core all 4.9.1-1 [20.3 kB] Get:179 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-nest-asyncio all 1.5.4-1 [6256 B] Get:180 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-tornado armhf 6.1.0-3build1 [287 kB] Get:181 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-py all 1.10.0-1 [71.9 kB] Get:182 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-zmq armhf 22.3.0-1build1 [269 kB] Get:183 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-jupyter-client all 7.1.2-1 [87.2 kB] Get:184 http://ftpmaster.internal/ubuntu jammy/main armhf python3-pygments all 2.11.2+dfsg-2 [750 kB] Get:185 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-jupyterlab-pygments all 0.1.2-8 [5006 B] Get:186 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-kiwisolver armhf 1.3.2-1build1 [51.3 kB] Get:187 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-llvmlite armhf 0.38.0-1 [119 kB] Get:188 http://ftpmaster.internal/ubuntu jammy/main armhf libopenjp2-7 armhf 2.4.0-6 [147 kB] Get:189 http://ftpmaster.internal/ubuntu jammy/main armhf python3-pil armhf 9.0.1-1build1 [386 kB] Get:190 http://ftpmaster.internal/ubuntu jammy/main armhf python3-tk armhf 3.10.4-0ubuntu1 [98.8 kB] Get:191 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-pil.imagetk armhf 9.0.1-1build1 [9062 B] Get:192 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-matplotlib armhf 3.5.1-2build1 [5777 kB] Get:193 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-nbformat all 5.1.3-1 [31.4 kB] Get:194 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-nbclient all 0.5.6-2 [52.2 kB] Get:195 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-pandocfilters all 1.5.0-1 [24.0 kB] Get:196 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-testpath all 0.5.0+dfsg-1 [9900 B] Get:197 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-nbconvert all 6.4.0-1 [183 kB] Get:198 http://ftpmaster.internal/ubuntu jammy/main armhf sphinx-common all 4.3.2-1 [680 kB] Get:199 http://ftpmaster.internal/ubuntu jammy/main armhf python3-alabaster all 0.7.12-1 [17.8 kB] Get:200 http://ftpmaster.internal/ubuntu jammy/main armhf python3-snowballstemmer all 2.2.0-1build1 [60.2 kB] Get:201 http://ftpmaster.internal/ubuntu jammy/main armhf python3-sphinx all 4.3.2-1 [541 kB] Get:202 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-nbsphinx all 0.8.7+ds-1 [36.3 kB] Get:203 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-numba armhf 0.55.1-0ubuntu2 [1570 kB] Get:204 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-numpydoc all 1.2-1 [43.5 kB] Get:205 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-pandas-lib armhf 1.3.5+dfsg-3 [3708 kB] Get:206 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-pandas all 1.3.5+dfsg-3 [2680 kB] Get:207 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-pluggy all 0.13.0-7.1 [19.0 kB] Get:208 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-toml all 0.10.2-1 [16.5 kB] Get:209 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-pytest all 6.2.5-1ubuntu2 [214 kB] Get:210 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-scitrack all 2021.5.3-2 [9246 B] Get:211 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-sphinx-bootstrap-theme all 0.8.1-1 [430 kB] Get:212 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-sphinx-gallery all 0.10.1-1 [95.6 kB] Get:213 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-tinydb all 3.15.2-2 [16.2 kB] Get:214 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-tqdm all 4.57.0-2 [93.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 154 MB in 3s (46.7 MB/s) Selecting previously unselected package libpython3.10-minimal:armhf. (Reading database ... 15097 files and directories currently installed.) Preparing to unpack .../libpython3.10-minimal_3.10.4-3_armhf.deb ... Unpacking libpython3.10-minimal:armhf (3.10.4-3) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.4.7-1_armhf.deb ... Unpacking libexpat1:armhf (2.4.7-1) ... Selecting previously unselected package python3.10-minimal. Preparing to unpack .../python3.10-minimal_3.10.4-3_armhf.deb ... Unpacking python3.10-minimal (3.10.4-3) ... Setting up libpython3.10-minimal:armhf (3.10.4-3) ... Setting up libexpat1:armhf (2.4.7-1) ... Setting up python3.10-minimal (3.10.4-3) ... Selecting previously unselected package python3-minimal. (Reading database ... 15399 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.10.4-0ubuntu2_armhf.deb ... Unpacking python3-minimal (3.10.4-0ubuntu2) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_7.0.0_all.deb ... Unpacking media-types (7.0.0) ... Selecting previously unselected package libmpdec3:armhf. Preparing to unpack .../2-libmpdec3_2.5.1-2build2_armhf.deb ... Unpacking libmpdec3:armhf (2.5.1-2build2) ... Selecting previously unselected package libpython3.10-stdlib:armhf. Preparing to unpack .../3-libpython3.10-stdlib_3.10.4-3_armhf.deb ... Unpacking libpython3.10-stdlib:armhf (3.10.4-3) ... Selecting previously unselected package python3.10. Preparing to unpack .../4-python3.10_3.10.4-3_armhf.deb ... Unpacking python3.10 (3.10.4-3) ... Selecting previously unselected package libpython3-stdlib:armhf. Preparing to unpack .../5-libpython3-stdlib_3.10.4-0ubuntu2_armhf.deb ... Unpacking libpython3-stdlib:armhf (3.10.4-0ubuntu2) ... Setting up python3-minimal (3.10.4-0ubuntu2) ... Selecting previously unselected package python3. (Reading database ... 15800 files and directories currently installed.) Preparing to unpack .../000-python3_3.10.4-0ubuntu2_armhf.deb ... Unpacking python3 (3.10.4-0ubuntu2) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.30_all.deb ... Unpacking sgml-base (1.30) ... Selecting previously unselected package libmd0:armhf. Preparing to unpack .../002-libmd0_1.0.4-1build1_armhf.deb ... Unpacking libmd0:armhf (1.0.4-1build1) ... Selecting previously unselected package libbsd0:armhf. Preparing to unpack .../003-libbsd0_0.11.5-1_armhf.deb ... Unpacking libbsd0:armhf (0.11.5-1) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../004-libelf1_0.186-1build1_armhf.deb ... Unpacking libelf1:armhf (0.186-1build1) ... Selecting previously unselected package libfribidi0:armhf. Preparing to unpack .../005-libfribidi0_1.0.8-2ubuntu3_armhf.deb ... Unpacking libfribidi0:armhf (1.0.8-2ubuntu3) ... Selecting previously unselected package libglib2.0-0:armhf. Preparing to unpack .../006-libglib2.0-0_2.72.0-1_armhf.deb ... Unpacking libglib2.0-0:armhf (2.72.0-1) ... Selecting previously unselected package libicu70:armhf. Preparing to unpack .../007-libicu70_70.1-2_armhf.deb ... Unpacking libicu70:armhf (70.1-2) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../008-libxml2_2.9.13+dfsg-1build1_armhf.deb ... Unpacking libxml2:armhf (2.9.13+dfsg-1build1) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../009-python3-pkg-resources_59.6.0-1.2_all.deb ... Unpacking python3-pkg-resources (59.6.0-1.2) ... Selecting previously unselected package ucf. Preparing to unpack .../010-ucf_3.0043_all.deb ... Moving old data out of the way Unpacking ucf (3.0043) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../011-bsdextrautils_2.37.2-4ubuntu3_armhf.deb ... Unpacking bsdextrautils (2.37.2-4ubuntu3) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../012-libmagic-mgc_1%3a5.41-3_armhf.deb ... Unpacking libmagic-mgc (1:5.41-3) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../013-libmagic1_1%3a5.41-3_armhf.deb ... Unpacking libmagic1:armhf (1:5.41-3) ... Selecting previously unselected package file. Preparing to unpack .../014-file_1%3a5.41-3_armhf.deb ... Unpacking file (1:5.41-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../015-gettext-base_0.21-4ubuntu4_armhf.deb ... Unpacking gettext-base (0.21-4ubuntu4) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../016-libuchardet0_0.0.7-1build2_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1build2) ... Selecting previously unselected package groff-base. Preparing to unpack .../017-groff-base_1.22.4-8build1_armhf.deb ... Unpacking groff-base (1.22.4-8build1) ... Selecting previously unselected package libedit2:armhf. Preparing to unpack .../018-libedit2_3.1-20210910-1build1_armhf.deb ... Unpacking libedit2:armhf (3.1-20210910-1build1) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../019-libpipeline1_1.5.5-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.5-1) ... Selecting previously unselected package libxau6:armhf. Preparing to unpack .../020-libxau6_1%3a1.0.9-1build5_armhf.deb ... Unpacking libxau6:armhf (1:1.0.9-1build5) ... Selecting previously unselected package libxdmcp6:armhf. Preparing to unpack .../021-libxdmcp6_1%3a1.1.3-0ubuntu5_armhf.deb ... Unpacking libxdmcp6:armhf (1:1.1.3-0ubuntu5) ... Selecting previously unselected package libxcb1:armhf. Preparing to unpack .../022-libxcb1_1.14-3ubuntu3_armhf.deb ... Unpacking libxcb1:armhf (1.14-3ubuntu3) ... Selecting previously unselected package libx11-data. Preparing to unpack .../023-libx11-data_2%3a1.7.5-1_all.deb ... Unpacking libx11-data (2:1.7.5-1) ... Selecting previously unselected package libx11-6:armhf. Preparing to unpack .../024-libx11-6_2%3a1.7.5-1_armhf.deb ... Unpacking libx11-6:armhf (2:1.7.5-1) ... Selecting previously unselected package libxext6:armhf. Preparing to unpack .../025-libxext6_2%3a1.3.4-1build1_armhf.deb ... Unpacking libxext6:armhf (2:1.3.4-1build1) ... Selecting previously unselected package man-db. Preparing to unpack .../026-man-db_2.10.2-1_armhf.deb ... Unpacking man-db (2.10.2-1) ... Selecting previously unselected package libsigsegv2:armhf. Preparing to unpack .../027-libsigsegv2_2.13-1ubuntu3_armhf.deb ... Unpacking libsigsegv2:armhf (2.13-1ubuntu3) ... Selecting previously unselected package m4. Preparing to unpack .../028-m4_1.4.18-5ubuntu2_armhf.deb ... Unpacking m4 (1.4.18-5ubuntu2) ... Selecting previously unselected package autoconf. Preparing to unpack .../029-autoconf_2.71-2_all.deb ... Unpacking autoconf (2.71-2) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../030-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../031-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../032-autopoint_0.21-4ubuntu4_all.deb ... Unpacking autopoint (0.21-4ubuntu4) ... Selecting previously unselected package libtcl8.6:armhf. Preparing to unpack .../033-libtcl8.6_8.6.12+dfsg-1build1_armhf.deb ... Unpacking libtcl8.6:armhf (8.6.12+dfsg-1build1) ... Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../034-libbrotli1_1.0.9-2build6_armhf.deb ... Unpacking libbrotli1:armhf (1.0.9-2build6) ... Selecting previously unselected package libfreetype6:armhf. Preparing to unpack .../035-libfreetype6_2.11.1+dfsg-1build1_armhf.deb ... Unpacking libfreetype6:armhf (2.11.1+dfsg-1build1) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../036-fonts-dejavu-core_2.37-2build1_all.deb ... Unpacking fonts-dejavu-core (2.37-2build1) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../037-fontconfig-config_2.13.1-4.2ubuntu5_all.deb ... Unpacking fontconfig-config (2.13.1-4.2ubuntu5) ... Selecting previously unselected package libfontconfig1:armhf. Preparing to unpack .../038-libfontconfig1_2.13.1-4.2ubuntu5_armhf.deb ... Unpacking libfontconfig1:armhf (2.13.1-4.2ubuntu5) ... Selecting previously unselected package libxrender1:armhf. Preparing to unpack .../039-libxrender1_1%3a0.9.10-1build4_armhf.deb ... Unpacking libxrender1:armhf (1:0.9.10-1build4) ... Selecting previously unselected package libxft2:armhf. Preparing to unpack .../040-libxft2_2.3.3-0ubuntu5_armhf.deb ... Unpacking libxft2:armhf (2.3.3-0ubuntu5) ... Selecting previously unselected package x11-common. Preparing to unpack .../041-x11-common_1%3a7.7+23ubuntu2_all.deb ... Unpacking x11-common (1:7.7+23ubuntu2) ... Selecting previously unselected package libxss1:armhf. Preparing to unpack .../042-libxss1_1%3a1.2.3-1build2_armhf.deb ... Unpacking libxss1:armhf (1:1.2.3-1build2) ... Selecting previously unselected package libtk8.6:armhf. Preparing to unpack .../043-libtk8.6_8.6.12-1build1_armhf.deb ... Unpacking libtk8.6:armhf (8.6.12-1build1) ... Selecting previously unselected package tk8.6-blt2.5. Preparing to unpack .../044-tk8.6-blt2.5_2.5.3+dfsg-4.1build2_armhf.deb ... Unpacking tk8.6-blt2.5 (2.5.3+dfsg-4.1build2) ... Selecting previously unselected package blt. Preparing to unpack .../045-blt_2.5.3+dfsg-4.1build2_armhf.deb ... Unpacking blt (2.5.3+dfsg-4.1build2) ... Selecting previously unselected package cython3. Preparing to unpack .../046-cython3_0.29.28-1ubuntu3_armhf.deb ... Unpacking cython3 (0.29.28-1ubuntu3) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../047-libdebhelper-perl_13.6ubuntu1_all.deb ... Unpacking libdebhelper-perl (13.6ubuntu1) ... Selecting previously unselected package libtool. Preparing to unpack .../048-libtool_2.4.6-15build2_all.deb ... Unpacking libtool (2.4.6-15build2) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../049-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../050-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../051-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../052-libfile-stripnondeterminism-perl_1.13.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../053-dh-strip-nondeterminism_1.13.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.0-1) ... Selecting previously unselected package libdw1:armhf. Preparing to unpack .../054-libdw1_0.186-1build1_armhf.deb ... Unpacking libdw1:armhf (0.186-1build1) ... Selecting previously unselected package debugedit. Preparing to unpack .../055-debugedit_1%3a5.0-4build1_armhf.deb ... Unpacking debugedit (1:5.0-4build1) ... Selecting previously unselected package dwz. Preparing to unpack .../056-dwz_0.14-1build2_armhf.deb ... Unpacking dwz (0.14-1build2) ... Selecting previously unselected package gettext. Preparing to unpack .../057-gettext_0.21-4ubuntu4_armhf.deb ... Unpacking gettext (0.21-4ubuntu4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../058-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../059-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../060-debhelper_13.6ubuntu1_all.deb ... Unpacking debhelper (13.6ubuntu1) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../061-python3-lib2to3_3.10.4-0ubuntu1_all.deb ... Unpacking python3-lib2to3 (3.10.4-0ubuntu1) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../062-python3-distutils_3.10.4-0ubuntu1_all.deb ... Unpacking python3-distutils (3.10.4-0ubuntu1) ... Selecting previously unselected package dh-python. Preparing to unpack .../063-dh-python_5.20220403_all.deb ... Unpacking dh-python (5.20220403) ... Selecting previously unselected package xml-core. Preparing to unpack .../064-xml-core_0.18+nmu1_all.deb ... Unpacking xml-core (0.18+nmu1) ... Selecting previously unselected package docutils-common. Preparing to unpack .../065-docutils-common_0.17.1+dfsg-2_all.deb ... Unpacking docutils-common (0.17.1+dfsg-2) ... Selecting previously unselected package python3-roman. Preparing to unpack .../066-python3-roman_3.3-1_all.deb ... Unpacking python3-roman (3.3-1) ... Selecting previously unselected package python3-docutils. Preparing to unpack .../067-python3-docutils_0.17.1+dfsg-2_all.deb ... Unpacking python3-docutils (0.17.1+dfsg-2) ... Selecting previously unselected package python3-certifi. Preparing to unpack .../068-python3-certifi_2020.6.20-1_all.deb ... Unpacking python3-certifi (2020.6.20-1) ... Selecting previously unselected package python3-chardet. Preparing to unpack .../069-python3-chardet_4.0.0-1_all.deb ... Unpacking python3-chardet (4.0.0-1) ... Selecting previously unselected package python3-idna. Preparing to unpack .../070-python3-idna_3.3-1_all.deb ... Unpacking python3-idna (3.3-1) ... Selecting previously unselected package python3-six. Preparing to unpack .../071-python3-six_1.16.0-3_all.deb ... Unpacking python3-six (1.16.0-3) ... Selecting previously unselected package python3-urllib3. Preparing to unpack .../072-python3-urllib3_1.26.5-1~exp1_all.deb ... Unpacking python3-urllib3 (1.26.5-1~exp1) ... Selecting previously unselected package python3-requests. Preparing to unpack .../073-python3-requests_2.25.1+dfsg-2_all.deb ... Unpacking python3-requests (2.25.1+dfsg-2) ... Selecting previously unselected package python3-tomli. Preparing to unpack .../074-python3-tomli_1.2.2-2_all.deb ... Unpacking python3-tomli (1.2.2-2) ... Selecting previously unselected package python3-tomli-w. Preparing to unpack .../075-python3-tomli-w_1.0.0-1_all.deb ... Unpacking python3-tomli-w (1.0.0-1) ... Selecting previously unselected package flit. Preparing to unpack .../076-flit_3.6.0-1_all.deb ... Unpacking flit (3.6.0-1) ... Selecting previously unselected package fonts-lyx. Preparing to unpack .../077-fonts-lyx_2.3.6-1_all.deb ... Unpacking fonts-lyx (2.3.6-1) ... Selecting previously unselected package libblas3:armhf. Preparing to unpack .../078-libblas3_3.10.0-2ubuntu1_armhf.deb ... Unpacking libblas3:armhf (3.10.0-2ubuntu1) ... Selecting previously unselected package libcmark-gfm0.29.0.gfm.3:armhf. Preparing to unpack .../079-libcmark-gfm0.29.0.gfm.3_0.29.0.gfm.3-3_armhf.deb ... Unpacking libcmark-gfm0.29.0.gfm.3:armhf (0.29.0.gfm.3-3) ... Selecting previously unselected package libcmark-gfm-extensions0.29.0.gfm.3:armhf. Preparing to unpack .../080-libcmark-gfm-extensions0.29.0.gfm.3_0.29.0.gfm.3-3_armhf.deb ... Unpacking libcmark-gfm-extensions0.29.0.gfm.3:armhf (0.29.0.gfm.3-3) ... Selecting previously unselected package libdeflate0:armhf. Preparing to unpack .../081-libdeflate0_1.10-2_armhf.deb ... Unpacking libdeflate0:armhf (1.10-2) ... Selecting previously unselected package libexpat1-dev:armhf. Preparing to unpack .../082-libexpat1-dev_2.4.7-1_armhf.deb ... Unpacking libexpat1-dev:armhf (2.4.7-1) ... Selecting previously unselected package libgfortran5:armhf. Preparing to unpack .../083-libgfortran5_12-20220319-1ubuntu1_armhf.deb ... Unpacking libgfortran5:armhf (12-20220319-1ubuntu1) ... Selecting previously unselected package libgraphite2-3:armhf. Preparing to unpack .../084-libgraphite2-3_1.3.14-1build2_armhf.deb ... Unpacking libgraphite2-3:armhf (1.3.14-1build2) ... Selecting previously unselected package libharfbuzz0b:armhf. Preparing to unpack .../085-libharfbuzz0b_2.7.4-1ubuntu3_armhf.deb ... Unpacking libharfbuzz0b:armhf (2.7.4-1ubuntu3) ... Selecting previously unselected package libimagequant0:armhf. Preparing to unpack .../086-libimagequant0_2.17.0-1_armhf.deb ... Unpacking libimagequant0:armhf (2.17.0-1) ... Selecting previously unselected package libjpeg-turbo8:armhf. Preparing to unpack .../087-libjpeg-turbo8_2.1.2-0ubuntu1_armhf.deb ... Unpacking libjpeg-turbo8:armhf (2.1.2-0ubuntu1) ... Selecting previously unselected package libjpeg8:armhf. Preparing to unpack .../088-libjpeg8_8c-2ubuntu10_armhf.deb ... Unpacking libjpeg8:armhf (8c-2ubuntu10) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../089-libjs-jquery_3.6.0+dfsg+~3.5.13-1_all.deb ... Unpacking libjs-jquery (3.6.0+dfsg+~3.5.13-1) ... Selecting previously unselected package libjs-jquery-ui. Preparing to unpack .../090-libjs-jquery-ui_1.13.1+dfsg-1_all.deb ... Unpacking libjs-jquery-ui (1.13.1+dfsg-1) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../091-libjs-underscore_1.13.2~dfsg-2_all.deb ... Unpacking libjs-underscore (1.13.2~dfsg-2) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../092-libjs-sphinxdoc_4.3.2-1_all.deb ... Unpacking libjs-sphinxdoc (4.3.2-1) ... Selecting previously unselected package liblapack3:armhf. Preparing to unpack .../093-liblapack3_3.10.0-2ubuntu1_armhf.deb ... Unpacking liblapack3:armhf (3.10.0-2ubuntu1) ... Selecting previously unselected package liblbfgsb0:armhf. Preparing to unpack .../094-liblbfgsb0_3.0+dfsg.3-10_armhf.deb ... Unpacking liblbfgsb0:armhf (3.0+dfsg.3-10) ... Selecting previously unselected package liblcms2-2:armhf. Preparing to unpack .../095-liblcms2-2_2.12~rc1-2build2_armhf.deb ... Unpacking liblcms2-2:armhf (2.12~rc1-2build2) ... Selecting previously unselected package libllvm11:armhf. Preparing to unpack .../096-libllvm11_1%3a11.1.0-6_armhf.deb ... Unpacking libllvm11:armhf (1:11.1.0-6) ... Selecting previously unselected package libnorm1:armhf. Preparing to unpack .../097-libnorm1_1.5.9+dfsg-2_armhf.deb ... Unpacking libnorm1:armhf (1.5.9+dfsg-2) ... Selecting previously unselected package libpgm-5.3-0:armhf. Preparing to unpack .../098-libpgm-5.3-0_5.3.128~dfsg-2_armhf.deb ... Unpacking libpgm-5.3-0:armhf (5.3.128~dfsg-2) ... Selecting previously unselected package libpython3.10:armhf. Preparing to unpack .../099-libpython3.10_3.10.4-3_armhf.deb ... Unpacking libpython3.10:armhf (3.10.4-3) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../100-zlib1g-dev_1%3a1.2.11.dfsg-2ubuntu9_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-2ubuntu9) ... Selecting previously unselected package libpython3.10-dev:armhf. Preparing to unpack .../101-libpython3.10-dev_3.10.4-3_armhf.deb ... Unpacking libpython3.10-dev:armhf (3.10.4-3) ... Selecting previously unselected package libpython3-dev:armhf. Preparing to unpack .../102-libpython3-dev_3.10.4-0ubuntu2_armhf.deb ... Unpacking libpython3-dev:armhf (3.10.4-0ubuntu2) ... Selecting previously unselected package libpython3-all-dev:armhf. Preparing to unpack .../103-libpython3-all-dev_3.10.4-0ubuntu2_armhf.deb ... Unpacking libpython3-all-dev:armhf (3.10.4-0ubuntu2) ... Selecting previously unselected package libqhull-r8.0:armhf. Preparing to unpack .../104-libqhull-r8.0_2020.2-4_armhf.deb ... Unpacking libqhull-r8.0:armhf (2020.2-4) ... Selecting previously unselected package libraqm0:armhf. Preparing to unpack .../105-libraqm0_0.7.0-4ubuntu1_armhf.deb ... Unpacking libraqm0:armhf (0.7.0-4ubuntu1) ... Selecting previously unselected package libsodium23:armhf. Preparing to unpack .../106-libsodium23_1.0.18-1build2_armhf.deb ... Unpacking libsodium23:armhf (1.0.18-1build2) ... Selecting previously unselected package libtbbmalloc2:armhf. Preparing to unpack .../107-libtbbmalloc2_2021.5.0-7ubuntu2_armhf.deb ... Unpacking libtbbmalloc2:armhf (2021.5.0-7ubuntu2) ... Selecting previously unselected package libtbb12:armhf. Preparing to unpack .../108-libtbb12_2021.5.0-7ubuntu2_armhf.deb ... Unpacking libtbb12:armhf (2021.5.0-7ubuntu2) ... Selecting previously unselected package libjbig0:armhf. Preparing to unpack .../109-libjbig0_2.1-3.1build3_armhf.deb ... Unpacking libjbig0:armhf (2.1-3.1build3) ... Selecting previously unselected package libwebp7:armhf. Preparing to unpack .../110-libwebp7_1.2.2-2_armhf.deb ... Unpacking libwebp7:armhf (1.2.2-2) ... Selecting previously unselected package libtiff5:armhf. Preparing to unpack .../111-libtiff5_4.3.0-6_armhf.deb ... Unpacking libtiff5:armhf (4.3.0-6) ... Selecting previously unselected package libwebpdemux2:armhf. Preparing to unpack .../112-libwebpdemux2_1.2.2-2_armhf.deb ... Unpacking libwebpdemux2:armhf (1.2.2-2) ... Selecting previously unselected package libwebpmux3:armhf. Preparing to unpack .../113-libwebpmux3_1.2.2-2_armhf.deb ... Unpacking libwebpmux3:armhf (1.2.2-2) ... Selecting previously unselected package libxslt1.1:armhf. Preparing to unpack .../114-libxslt1.1_1.1.34-4build2_armhf.deb ... Unpacking libxslt1.1:armhf (1.1.34-4build2) ... Selecting previously unselected package libzmq5:armhf. Preparing to unpack .../115-libzmq5_4.3.4-2_armhf.deb ... Unpacking libzmq5:armhf (4.3.4-2) ... Selecting previously unselected package llvm-11-runtime. Preparing to unpack .../116-llvm-11-runtime_1%3a11.1.0-6_armhf.deb ... Unpacking llvm-11-runtime (1:11.1.0-6) ... Selecting previously unselected package llvm-11-linker-tools. Preparing to unpack .../117-llvm-11-linker-tools_1%3a11.1.0-6_armhf.deb ... Unpacking llvm-11-linker-tools (1:11.1.0-6) ... Selecting previously unselected package libpfm4:armhf. Preparing to unpack .../118-libpfm4_4.11.1+git32-gd0b85fb-1_armhf.deb ... Unpacking libpfm4:armhf (4.11.1+git32-gd0b85fb-1) ... Selecting previously unselected package llvm-11. Preparing to unpack .../119-llvm-11_1%3a11.1.0-6_armhf.deb ... Unpacking llvm-11 (1:11.1.0-6) ... Selecting previously unselected package pandoc-data. Preparing to unpack .../120-pandoc-data_2.9.2.1-3ubuntu2_all.deb ... Unpacking pandoc-data (2.9.2.1-3ubuntu2) ... Selecting previously unselected package pandoc. Preparing to unpack .../121-pandoc_2.9.2.1-3ubuntu2_armhf.deb ... Unpacking pandoc (2.9.2.1-3ubuntu2) ... Selecting previously unselected package python-babel-localedata. Preparing to unpack .../122-python-babel-localedata_2.8.0+dfsg.1-7_all.deb ... Unpacking python-babel-localedata (2.8.0+dfsg.1-7) ... Selecting previously unselected package python-matplotlib-data. Preparing to unpack .../123-python-matplotlib-data_3.5.1-2build1_all.deb ... Unpacking python-matplotlib-data (3.5.1-2build1) ... Selecting previously unselected package python3-all. Preparing to unpack .../124-python3-all_3.10.4-0ubuntu2_armhf.deb ... Unpacking python3-all (3.10.4-0ubuntu2) ... Selecting previously unselected package python3.10-dev. Preparing to unpack .../125-python3.10-dev_3.10.4-3_armhf.deb ... Unpacking python3.10-dev (3.10.4-3) ... Selecting previously unselected package python3-dev. Preparing to unpack .../126-python3-dev_3.10.4-0ubuntu2_armhf.deb ... Unpacking python3-dev (3.10.4-0ubuntu2) ... Selecting previously unselected package python3-all-dev. Preparing to unpack .../127-python3-all-dev_3.10.4-0ubuntu2_armhf.deb ... Unpacking python3-all-dev (3.10.4-0ubuntu2) ... Selecting previously unselected package python3-appdirs. Preparing to unpack .../128-python3-appdirs_1.4.4-2_all.deb ... Unpacking python3-appdirs (1.4.4-2) ... Selecting previously unselected package python3-attr. Preparing to unpack .../129-python3-attr_21.2.0-1_all.deb ... Unpacking python3-attr (21.2.0-1) ... Selecting previously unselected package python3-tz. Preparing to unpack .../130-python3-tz_2022.1-1_all.deb ... Unpacking python3-tz (2022.1-1) ... Selecting previously unselected package python3-babel. Preparing to unpack .../131-python3-babel_2.8.0+dfsg.1-7_all.deb ... Unpacking python3-babel (2.8.0+dfsg.1-7) ... Selecting previously unselected package python3-pyparsing. Preparing to unpack .../132-python3-pyparsing_2.4.7-1_all.deb ... Unpacking python3-pyparsing (2.4.7-1) ... Selecting previously unselected package python3-packaging. Preparing to unpack .../133-python3-packaging_21.3-1_all.deb ... Unpacking python3-packaging (21.3-1) ... Selecting previously unselected package python3-webencodings. Preparing to unpack .../134-python3-webencodings_0.5.1-4_all.deb ... Unpacking python3-webencodings (0.5.1-4) ... Selecting previously unselected package python3-html5lib. Preparing to unpack .../135-python3-html5lib_1.1-3_all.deb ... Unpacking python3-html5lib (1.1-3) ... Selecting previously unselected package python3-bleach. Preparing to unpack .../136-python3-bleach_4.1.0-1_all.deb ... Unpacking python3-bleach (4.1.0-1) ... Selecting previously unselected package python3-brotli. Preparing to unpack .../137-python3-brotli_1.0.9-2build6_armhf.deb ... Unpacking python3-brotli (1.0.9-2build6) ... Selecting previously unselected package python3-cffi-backend:armhf. Preparing to unpack .../138-python3-cffi-backend_1.15.0-1build2_armhf.deb ... Unpacking python3-cffi-backend:armhf (1.15.0-1build2) ... Selecting previously unselected package python3-cycler. Preparing to unpack .../139-python3-cycler_0.11.0-1_all.deb ... Unpacking python3-cycler (0.11.0-1) ... Selecting previously unselected package python3-dateutil. Preparing to unpack .../140-python3-dateutil_2.8.1-6_all.deb ... Unpacking python3-dateutil (2.8.1-6) ... Selecting previously unselected package python3-decorator. Preparing to unpack .../141-python3-decorator_4.4.2-0ubuntu1_all.deb ... Unpacking python3-decorator (4.4.2-0ubuntu1) ... Selecting previously unselected package python3-defusedxml. Preparing to unpack .../142-python3-defusedxml_0.7.1-1_all.deb ... Unpacking python3-defusedxml (0.7.1-1) ... Selecting previously unselected package python3-entrypoints. Preparing to unpack .../143-python3-entrypoints_0.4-1_all.deb ... Unpacking python3-entrypoints (0.4-1) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../144-python3-numpy_1%3a1.21.5-1build2_armhf.deb ... Unpacking python3-numpy (1:1.21.5-1build2) ... Selecting previously unselected package python3-scipy. Preparing to unpack .../145-python3-scipy_1.8.0-1exp2ubuntu1_armhf.deb ... Unpacking python3-scipy (1.8.0-1exp2ubuntu1) ... Selecting previously unselected package python3-ufolib2. Preparing to unpack .../146-python3-ufolib2_0.13.1+dfsg1-1_all.deb ... Unpacking python3-ufolib2 (0.13.1+dfsg1-1) ... Selecting previously unselected package python3-mpmath. Preparing to unpack .../147-python3-mpmath_1.2.1-2_all.deb ... Unpacking python3-mpmath (1.2.1-2) ... Selecting previously unselected package python3-sympy. Preparing to unpack .../148-python3-sympy_1.9-1_all.deb ... Unpacking python3-sympy (1.9-1) ... Selecting previously unselected package python3-fs. Preparing to unpack .../149-python3-fs_2.4.12-1_all.deb ... Unpacking python3-fs (2.4.12-1) ... Selecting previously unselected package python3-lxml:armhf. Preparing to unpack .../150-python3-lxml_4.8.0-1build1_armhf.deb ... Unpacking python3-lxml:armhf (4.8.0-1build1) ... Selecting previously unselected package python3-lz4. Preparing to unpack .../151-python3-lz4_3.1.3+dfsg-1build3_armhf.deb ... Unpacking python3-lz4 (3.1.3+dfsg-1build3) ... Selecting previously unselected package python3-unicodedata2. Preparing to unpack .../152-python3-unicodedata2_14.0.0+ds-8_armhf.deb ... Unpacking python3-unicodedata2 (14.0.0+ds-8) ... Selecting previously unselected package unicode-data. Preparing to unpack .../153-unicode-data_14.0.0-1.1_all.deb ... Unpacking unicode-data (14.0.0-1.1) ... Selecting previously unselected package python3-fonttools. Preparing to unpack .../154-python3-fonttools_4.29.1-2build1_armhf.deb ... Unpacking python3-fonttools (4.29.1-2build1) ... Selecting previously unselected package python3-imagesize. Preparing to unpack .../155-python3-imagesize_1.3.0-1_all.deb ... Unpacking python3-imagesize (1.3.0-1) ... Selecting previously unselected package python3-more-itertools. Preparing to unpack .../156-python3-more-itertools_8.10.0-2_all.deb ... Unpacking python3-more-itertools (8.10.0-2) ... Selecting previously unselected package python3-zipp. Preparing to unpack .../157-python3-zipp_1.0.0-3_all.deb ... Unpacking python3-zipp (1.0.0-3) ... Selecting previously unselected package python3-importlib-metadata. Preparing to unpack .../158-python3-importlib-metadata_4.6.4-1_all.deb ... Unpacking python3-importlib-metadata (4.6.4-1) ... Selecting previously unselected package python3-iniconfig. Preparing to unpack .../159-python3-iniconfig_1.1.1-2_all.deb ... Unpacking python3-iniconfig (1.1.1-2) ... Selecting previously unselected package python3-ipython-genutils. Preparing to unpack .../160-python3-ipython-genutils_0.2.0-5_all.deb ... Unpacking python3-ipython-genutils (0.2.0-5) ... Selecting previously unselected package python3-markupsafe. Preparing to unpack .../161-python3-markupsafe_2.0.1-2build1_armhf.deb ... Unpacking python3-markupsafe (2.0.1-2build1) ... Selecting previously unselected package python3-jinja2. Preparing to unpack .../162-python3-jinja2_3.0.3-1_all.deb ... Unpacking python3-jinja2 (3.0.3-1) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../163-python3-setuptools_59.6.0-1.2_all.deb ... Unpacking python3-setuptools (59.6.0-1.2) ... Selecting previously unselected package python3-pyrsistent:armhf. Preparing to unpack .../164-python3-pyrsistent_0.18.1-1build1_armhf.deb ... Unpacking python3-pyrsistent:armhf (0.18.1-1build1) ... Selecting previously unselected package python3-jsonschema. Preparing to unpack .../165-python3-jsonschema_3.2.0-0ubuntu2_all.deb ... Unpacking python3-jsonschema (3.2.0-0ubuntu2) ... Selecting previously unselected package python3-traitlets. Preparing to unpack .../166-python3-traitlets_5.1.1-1_all.deb ... Unpacking python3-traitlets (5.1.1-1) ... Selecting previously unselected package python3-jupyter-core. Preparing to unpack .../167-python3-jupyter-core_4.9.1-1_all.deb ... Unpacking python3-jupyter-core (4.9.1-1) ... Selecting previously unselected package python3-nest-asyncio. Preparing to unpack .../168-python3-nest-asyncio_1.5.4-1_all.deb ... Unpacking python3-nest-asyncio (1.5.4-1) ... Selecting previously unselected package python3-tornado. Preparing to unpack .../169-python3-tornado_6.1.0-3build1_armhf.deb ... Unpacking python3-tornado (6.1.0-3build1) ... Selecting previously unselected package python3-py. Preparing to unpack .../170-python3-py_1.10.0-1_all.deb ... Unpacking python3-py (1.10.0-1) ... Selecting previously unselected package python3-zmq. Preparing to unpack .../171-python3-zmq_22.3.0-1build1_armhf.deb ... Unpacking python3-zmq (22.3.0-1build1) ... Selecting previously unselected package python3-jupyter-client. Preparing to unpack .../172-python3-jupyter-client_7.1.2-1_all.deb ... Unpacking python3-jupyter-client (7.1.2-1) ... Selecting previously unselected package python3-pygments. Preparing to unpack .../173-python3-pygments_2.11.2+dfsg-2_all.deb ... Unpacking python3-pygments (2.11.2+dfsg-2) ... Selecting previously unselected package python3-jupyterlab-pygments. Preparing to unpack .../174-python3-jupyterlab-pygments_0.1.2-8_all.deb ... Unpacking python3-jupyterlab-pygments (0.1.2-8) ... Selecting previously unselected package python3-kiwisolver. Preparing to unpack .../175-python3-kiwisolver_1.3.2-1build1_armhf.deb ... Unpacking python3-kiwisolver (1.3.2-1build1) ... Selecting previously unselected package python3-llvmlite. Preparing to unpack .../176-python3-llvmlite_0.38.0-1_armhf.deb ... Unpacking python3-llvmlite (0.38.0-1) ... Selecting previously unselected package libopenjp2-7:armhf. Preparing to unpack .../177-libopenjp2-7_2.4.0-6_armhf.deb ... Unpacking libopenjp2-7:armhf (2.4.0-6) ... Selecting previously unselected package python3-pil:armhf. Preparing to unpack .../178-python3-pil_9.0.1-1build1_armhf.deb ... Unpacking python3-pil:armhf (9.0.1-1build1) ... Selecting previously unselected package python3-tk:armhf. Preparing to unpack .../179-python3-tk_3.10.4-0ubuntu1_armhf.deb ... Unpacking python3-tk:armhf (3.10.4-0ubuntu1) ... Selecting previously unselected package python3-pil.imagetk:armhf. Preparing to unpack .../180-python3-pil.imagetk_9.0.1-1build1_armhf.deb ... Unpacking python3-pil.imagetk:armhf (9.0.1-1build1) ... Selecting previously unselected package python3-matplotlib. Preparing to unpack .../181-python3-matplotlib_3.5.1-2build1_armhf.deb ... Unpacking python3-matplotlib (3.5.1-2build1) ... Selecting previously unselected package python3-nbformat. Preparing to unpack .../182-python3-nbformat_5.1.3-1_all.deb ... Unpacking python3-nbformat (5.1.3-1) ... Selecting previously unselected package python3-nbclient. Preparing to unpack .../183-python3-nbclient_0.5.6-2_all.deb ... Unpacking python3-nbclient (0.5.6-2) ... Selecting previously unselected package python3-pandocfilters. Preparing to unpack .../184-python3-pandocfilters_1.5.0-1_all.deb ... Unpacking python3-pandocfilters (1.5.0-1) ... Selecting previously unselected package python3-testpath. Preparing to unpack .../185-python3-testpath_0.5.0+dfsg-1_all.deb ... Unpacking python3-testpath (0.5.0+dfsg-1) ... Selecting previously unselected package python3-nbconvert. Preparing to unpack .../186-python3-nbconvert_6.4.0-1_all.deb ... Unpacking python3-nbconvert (6.4.0-1) ... Selecting previously unselected package sphinx-common. Preparing to unpack .../187-sphinx-common_4.3.2-1_all.deb ... Unpacking sphinx-common (4.3.2-1) ... Selecting previously unselected package python3-alabaster. Preparing to unpack .../188-python3-alabaster_0.7.12-1_all.deb ... Unpacking python3-alabaster (0.7.12-1) ... Selecting previously unselected package python3-snowballstemmer. Preparing to unpack .../189-python3-snowballstemmer_2.2.0-1build1_all.deb ... Unpacking python3-snowballstemmer (2.2.0-1build1) ... Selecting previously unselected package python3-sphinx. Preparing to unpack .../190-python3-sphinx_4.3.2-1_all.deb ... Unpacking python3-sphinx (4.3.2-1) ... Selecting previously unselected package python3-nbsphinx. Preparing to unpack .../191-python3-nbsphinx_0.8.7+ds-1_all.deb ... Unpacking python3-nbsphinx (0.8.7+ds-1) ... Selecting previously unselected package python3-numba. Preparing to unpack .../192-python3-numba_0.55.1-0ubuntu2_armhf.deb ... Unpacking python3-numba (0.55.1-0ubuntu2) ... Selecting previously unselected package python3-numpydoc. Preparing to unpack .../193-python3-numpydoc_1.2-1_all.deb ... Unpacking python3-numpydoc (1.2-1) ... Selecting previously unselected package python3-pandas-lib:armhf. Preparing to unpack .../194-python3-pandas-lib_1.3.5+dfsg-3_armhf.deb ... Unpacking python3-pandas-lib:armhf (1.3.5+dfsg-3) ... Selecting previously unselected package python3-pandas. Preparing to unpack .../195-python3-pandas_1.3.5+dfsg-3_all.deb ... Unpacking python3-pandas (1.3.5+dfsg-3) ... Selecting previously unselected package python3-pluggy. Preparing to unpack .../196-python3-pluggy_0.13.0-7.1_all.deb ... Unpacking python3-pluggy (0.13.0-7.1) ... Selecting previously unselected package python3-toml. Preparing to unpack .../197-python3-toml_0.10.2-1_all.deb ... Unpacking python3-toml (0.10.2-1) ... Selecting previously unselected package python3-pytest. Preparing to unpack .../198-python3-pytest_6.2.5-1ubuntu2_all.deb ... Unpacking python3-pytest (6.2.5-1ubuntu2) ... Selecting previously unselected package python3-scitrack. Preparing to unpack .../199-python3-scitrack_2021.5.3-2_all.deb ... Unpacking python3-scitrack (2021.5.3-2) ... Selecting previously unselected package python3-sphinx-bootstrap-theme. Preparing to unpack .../200-python3-sphinx-bootstrap-theme_0.8.1-1_all.deb ... Unpacking python3-sphinx-bootstrap-theme (0.8.1-1) ... Selecting previously unselected package python3-sphinx-gallery. Preparing to unpack .../201-python3-sphinx-gallery_0.10.1-1_all.deb ... Unpacking python3-sphinx-gallery (0.10.1-1) ... Selecting previously unselected package python3-tinydb. Preparing to unpack .../202-python3-tinydb_3.15.2-2_all.deb ... Unpacking python3-tinydb (3.15.2-2) ... Selecting previously unselected package python3-tqdm. Preparing to unpack .../203-python3-tqdm_4.57.0-2_all.deb ... Unpacking python3-tqdm (4.57.0-2) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../204-sbuild-build-depends-main-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up media-types (7.0.0) ... Setting up libpipeline1:armhf (1.5.5-1) ... Setting up libgraphite2-3:armhf (1.3.14-1build2) ... Setting up liblcms2-2:armhf (2.12~rc1-2build2) ... Setting up libtbbmalloc2:armhf (2021.5.0-7ubuntu2) ... Setting up libxau6:armhf (1:1.0.9-1build5) ... Setting up libsodium23:armhf (1.0.18-1build2) ... Setting up bsdextrautils (2.37.2-4ubuntu3) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libmagic-mgc (1:5.41-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:armhf (2.72.0-1) ... No schema files found: doing nothing. Setting up libpgm-5.3-0:armhf (5.3.128~dfsg-2) ... Setting up fonts-lyx (2.3.6-1) ... Setting up libdebhelper-perl (13.6ubuntu1) ... Setting up libbrotli1:armhf (1.0.9-2build6) ... Setting up libnorm1:armhf (1.5.9+dfsg-2) ... Setting up x11-common (1:7.7+23ubuntu2) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libmagic1:armhf (1:5.41-3) ... Setting up libdeflate0:armhf (1.10-2) ... Setting up gettext-base (0.21-4ubuntu4) ... Setting up libqhull-r8.0:armhf (2020.2-4) ... Setting up libtbb12:armhf (2021.5.0-7ubuntu2) ... Setting up file (1:5.41-3) ... Setting up libjbig0:armhf (2.1-3.1build3) ... Setting up python-babel-localedata (2.8.0+dfsg.1-7) ... Setting up unicode-data (14.0.0-1.1) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:armhf (3.10.0-2ubuntu1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up libpfm4:armhf (4.11.1+git32-gd0b85fb-1) ... Setting up libexpat1-dev:armhf (2.4.7-1) ... Setting up libfreetype6:armhf (2.11.1+dfsg-1build1) ... Setting up libx11-data (2:1.7.5-1) ... Setting up libsigsegv2:armhf (2.13-1ubuntu3) ... Setting up libfribidi0:armhf (1.0.8-2ubuntu3) ... Setting up libimagequant0:armhf (2.17.0-1) ... Setting up libtcl8.6:armhf (8.6.12+dfsg-1build1) ... Setting up autopoint (0.21-4ubuntu4) ... Setting up fonts-dejavu-core (2.37-2build1) ... Setting up ucf (3.0043) ... Setting up libjpeg-turbo8:armhf (2.1.2-0ubuntu1) ... Setting up libgfortran5:armhf (12-20220319-1ubuntu1) ... Setting up libwebp7:armhf (1.2.2-2) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2ubuntu9) ... Setting up libcmark-gfm0.29.0.gfm.3:armhf (0.29.0.gfm.3-3) ... Setting up libmd0:armhf (1.0.4-1build1) ... Setting up libuchardet0:armhf (0.0.7-1build2) ... Setting up libmpdec3:armhf (2.5.1-2build2) ... Setting up libopenjp2-7:armhf (2.4.0-6) ... Setting up libsub-override-perl (0.09-2) ... Setting up libharfbuzz0b:armhf (2.7.4-1ubuntu3) ... Setting up libcmark-gfm-extensions0.29.0.gfm.3:armhf (0.29.0.gfm.3-3) ... Setting up sgml-base (1.30) ... Setting up pandoc-data (2.9.2.1-3ubuntu2) ... Setting up libjs-jquery (3.6.0+dfsg+~3.5.13-1) ... Setting up python-matplotlib-data (3.5.1-2build1) ... Setting up libwebpmux3:armhf (1.2.2-2) ... Setting up libbsd0:armhf (0.11.5-1) ... Setting up libelf1:armhf (0.186-1build1) ... Setting up libjs-underscore (1.13.2~dfsg-2) ... Setting up libicu70:armhf (70.1-2) ... Setting up libjpeg8:armhf (8c-2ubuntu10) ... Setting up libfile-stripnondeterminism-perl (1.13.0-1) ... Setting up libdw1:armhf (0.186-1build1) ... Setting up libxdmcp6:armhf (1:1.1.3-0ubuntu5) ... Setting up liblapack3:armhf (3.10.0-2ubuntu1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up libxcb1:armhf (1.14-3ubuntu3) ... Setting up libzmq5:armhf (4.3.4-2) ... Setting up libtool (2.4.6-15build2) ... Setting up fontconfig-config (2.13.1-4.2ubuntu5) ... Setting up libwebpdemux2:armhf (1.2.2-2) ... Setting up libedit2:armhf (3.1-20210910-1build1) ... Setting up m4 (1.4.18-5ubuntu2) ... Setting up libpython3.10-stdlib:armhf (3.10.4-3) ... Setting up libjs-jquery-ui (1.13.1+dfsg-1) ... Setting up pandoc (2.9.2.1-3ubuntu2) ... Setting up libraqm0:armhf (0.7.0-4ubuntu1) ... Setting up libjs-sphinxdoc (4.3.2-1) ... Setting up autoconf (2.71-2) ... Setting up dh-strip-nondeterminism (1.13.0-1) ... Setting up dwz (0.14-1build2) ... Setting up groff-base (1.22.4-8build1) ... Setting up xml-core (0.18+nmu1) ... Setting up debugedit (1:5.0-4build1) ... Setting up libx11-6:armhf (2:1.7.5-1) ... Setting up libtiff5:armhf (4.3.0-6) ... Setting up libfontconfig1:armhf (2.13.1-4.2ubuntu5) ... Setting up libxml2:armhf (2.9.13+dfsg-1build1) ... Setting up libpython3-stdlib:armhf (3.10.4-0ubuntu2) ... Setting up liblbfgsb0:armhf (3.0+dfsg.3-10) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libpython3.10:armhf (3.10.4-3) ... Setting up gettext (0.21-4ubuntu4) ... Setting up python3.10 (3.10.4-3) ... Setting up libxrender1:armhf (1:0.9.10-1build4) ... Setting up libxext6:armhf (2:1.3.4-1build1) ... Setting up python3 (3.10.4-0ubuntu2) ... Setting up python3-pandocfilters (1.5.0-1) ... Setting up man-db (2.10.2-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up python3-markupsafe (2.0.1-2build1) ... Setting up python3-webencodings (0.5.1-4) ... Setting up python3-tz (2022.1-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up python3-six (1.16.0-3) ... Setting up dh-autoreconf (20) ... Setting up python3-roman (3.3-1) ... Setting up python3-decorator (4.4.2-0ubuntu1) ... Setting up libllvm11:armhf (1:11.1.0-6) ... Setting up python3-pyparsing (2.4.7-1) ... Setting up python3-certifi (2020.6.20-1) ... Setting up python3-sphinx-bootstrap-theme (0.8.1-1) ... Setting up python3-snowballstemmer (2.2.0-1build1) ... Setting up python3-testpath (0.5.0+dfsg-1) ... Setting up python3-nest-asyncio (1.5.4-1) ... Setting up python3-brotli (1.0.9-2build6) ... Setting up sphinx-common (4.3.2-1) ... Setting up python3-cycler (0.11.0-1) ... Setting up python3-kiwisolver (1.3.2-1build1) ... Setting up python3-idna (3.3-1) ... Setting up cython3 (0.29.28-1ubuntu3) ... Setting up libpython3.10-dev:armhf (3.10.4-3) ... Setting up python3-html5lib (1.1-3) ... Setting up python3-toml (0.10.2-1) ... Setting up python3-urllib3 (1.26.5-1~exp1) ... Setting up llvm-11-linker-tools (1:11.1.0-6) ... Setting up python3.10-dev (3.10.4-3) ... Setting up python3-pyrsistent:armhf (0.18.1-1build1) ... Setting up python3-traitlets (5.1.1-1) ... Setting up python3-scitrack (2021.5.3-2) ... Setting up libxslt1.1:armhf (1.1.34-4build2) ... Setting up python3-dateutil (2.8.1-6) ... Setting up libxss1:armhf (1:1.2.3-1build2) ... Setting up python3-mpmath (1.2.1-2) ... Setting up python3-lib2to3 (3.10.4-0ubuntu1) ... Setting up python3-tomli-w (1.0.0-1) ... Setting up python3-appdirs (1.4.4-2) ... Setting up python3-cffi-backend:armhf (1.15.0-1build2) ... Setting up python3-imagesize (1.3.0-1) ... Setting up python3-pkg-resources (59.6.0-1.2) ... Setting up python3-entrypoints (0.4-1) ... Setting up python3-distutils (3.10.4-0ubuntu1) ... Setting up dh-python (5.20220403) ... Setting up python3-more-itertools (8.10.0-2) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-sympy (1.9-1) ... Setting up python3-attr (21.2.0-1) ... Setting up python3-tornado (6.1.0-3build1) ... Setting up libxft2:armhf (2.3.3-0ubuntu5) ... Setting up llvm-11-runtime (1:11.1.0-6) ... Setting up libpython3-dev:armhf (3.10.4-0ubuntu2) ... Setting up python3-setuptools (59.6.0-1.2) ... Setting up python3-tomli (1.2.2-2) ... Setting up python3-py (1.10.0-1) ... Setting up python3-babel (2.8.0+dfsg.1-7) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-lz4 (3.1.3+dfsg-1build3) ... Setting up python3-defusedxml (0.7.1-1) ... Setting up python3-ipython-genutils (0.2.0-5) ... Setting up python3-alabaster (0.7.12-1) ... Setting up python3-unicodedata2 (14.0.0+ds-8) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libtk8.6:armhf (8.6.12-1build1) ... Setting up python3-tqdm (4.57.0-2) ... Setting up python3-tinydb (3.15.2-2) ... Setting up llvm-11 (1:11.1.0-6) ... Setting up python3-all (3.10.4-0ubuntu2) ... Setting up debhelper (13.6ubuntu1) ... Setting up python3-zipp (1.0.0-3) ... Setting up python3-fs (2.4.12-1) ... Setting up python3-llvmlite (0.38.0-1) ... Setting up python3-jinja2 (3.0.3-1) ... Setting up python3-pygments (2.11.2+dfsg-2) ... Setting up python3-packaging (21.3-1) ... Setting up python3-chardet (4.0.0-1) ... Setting up libpython3-all-dev:armhf (3.10.4-0ubuntu2) ... Setting up python3-zmq (22.3.0-1build1) ... Setting up python3-dev (3.10.4-0ubuntu2) ... Setting up python3-requests (2.25.1+dfsg-2) ... Setting up python3-numpy (1:1.21.5-1build2) ... Setting up python3-lxml:armhf (4.8.0-1build1) ... Setting up python3-jupyter-core (4.9.1-1) ... Setting up python3-all-dev (3.10.4-0ubuntu2) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-4.1build2) ... Setting up python3-scipy (1.8.0-1exp2ubuntu1) ... Setting up python3-importlib-metadata (4.6.4-1) ... Setting up blt (2.5.3+dfsg-4.1build2) ... Setting up python3-pandas-lib:armhf (1.3.5+dfsg-3) ... Setting up python3-tk:armhf (3.10.4-0ubuntu1) ... Setting up python3-numba (0.55.1-0ubuntu2) ... update-alternatives: using /usr/share/python3-numba/numba to provide /usr/bin/numba (numba) in auto mode Setting up python3-bleach (4.1.0-1) ... Setting up python3-jupyterlab-pygments (0.1.2-8) ... Setting up python3-pandas (1.3.5+dfsg-3) ... Setting up python3-jsonschema (3.2.0-0ubuntu2) ... Setting up python3-pluggy (0.13.0-7.1) ... Setting up python3-jupyter-client (7.1.2-1) ... Setting up python3-pytest (6.2.5-1ubuntu2) ... Setting up python3-nbformat (5.1.3-1) ... Setting up python3-nbclient (0.5.6-2) ... Setting up python3-nbconvert (6.4.0-1) ... Setting up python3-fonttools (4.29.1-2build1) ... Setting up python3-pil.imagetk:armhf (9.0.1-1build1) ... Setting up python3-ufolib2 (0.13.1+dfsg1-1) ... Setting up python3-pil:armhf (9.0.1-1build1) ... Setting up python3-matplotlib (3.5.1-2build1) ... Processing triggers for libc-bin (2.35-0ubuntu3) ... Processing triggers for sgml-base (1.30) ... Setting up docutils-common (0.17.1+dfsg-2) ... Processing triggers for sgml-base (1.30) ... Setting up python3-docutils (0.17.1+dfsg-2) ... Setting up flit (3.6.0-1) ... Setting up python3-sphinx (4.3.2-1) ... Setting up python3-sphinx-gallery (0.10.1-1) ... Setting up python3-nbsphinx (0.8.7+ds-1) ... Setting up python3-numpydoc (1.2-1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armhf included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-107-generic #121-Ubuntu SMP Thu Mar 24 16:07:22 UTC 2022 arm64 (armv7l) Toolchain package versions: binutils_2.38-3ubuntu1 dpkg-dev_1.21.1ubuntu2 g++-11_11.2.0-19ubuntu1 gcc-11_11.2.0-19ubuntu1 libc6-dev_2.35-0ubuntu3 libstdc++-11-dev_11.2.0-19ubuntu1 libstdc++6_12-20220319-1ubuntu1 linux-libc-dev_5.15.0-25.25 Package versions: adduser_3.118ubuntu5 advancecomp_2.1-2.1ubuntu2 apt_2.4.3 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-4ubuntu4 autotools-dev_20220109.1 base-files_12ubuntu3 base-passwd_3.5.52build1 bash_5.1-6ubuntu1 binutils_2.38-3ubuntu1 binutils-arm-linux-gnueabihf_2.38-3ubuntu1 binutils-common_2.38-3ubuntu1 blt_2.5.3+dfsg-4.1build2 bsdextrautils_2.37.2-4ubuntu3 bsdutils_1:2.37.2-4ubuntu3 build-essential_12.9ubuntu3 bzip2_1.0.8-5build1 ca-certificates_20211016 coreutils_8.32-4.1ubuntu1 cpp_4:11.2.0-1ubuntu1 cpp-11_11.2.0-19ubuntu1 cython3_0.29.28-1ubuntu3 dash_0.5.11+git20210903+057cd650a4ed-3build1 debconf_1.5.79ubuntu1 debhelper_13.6ubuntu1 debianutils_5.5-1ubuntu2 debugedit_1:5.0-4build1 dh-autoreconf_20 dh-python_5.20220403 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-0ubuntu2 docutils-common_0.17.1+dfsg-2 dpkg_1.21.1ubuntu2 dpkg-dev_1.21.1ubuntu2 dwz_0.14-1build2 e2fsprogs_1.46.5-2ubuntu1 fakeroot_1.28-1ubuntu1 file_1:5.41-3 findutils_4.8.0-1ubuntu3 flit_3.6.0-1 fontconfig-config_2.13.1-4.2ubuntu5 fonts-dejavu-core_2.37-2build1 fonts-lyx_2.3.6-1 g++_4:11.2.0-1ubuntu1 g++-11_11.2.0-19ubuntu1 gcc_4:11.2.0-1ubuntu1 gcc-11_11.2.0-19ubuntu1 gcc-11-base_11.2.0-19ubuntu1 gcc-12-base_12-20220319-1ubuntu1 gettext_0.21-4ubuntu4 gettext-base_0.21-4ubuntu4 gpg_2.2.27-3ubuntu2 gpg-agent_2.2.27-3ubuntu2 gpgconf_2.2.27-3ubuntu2 gpgv_2.2.27-3ubuntu2 grep_3.7-1build1 groff-base_1.22.4-8build1 gzip_1.10-4ubuntu4 hostname_3.23ubuntu2 init_1.62 init-system-helpers_1.62 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapparmor1_3.0.4-2ubuntu2 libapt-pkg6.0_2.4.3 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.3 libasan6_11.2.0-19ubuntu1 libassuan0_2.5.5-1build1 libatomic1_12-20220319-1ubuntu1 libattr1_1:2.5.1-1build1 libaudit-common_1:3.0.7-1build1 libaudit1_1:3.0.7-1build1 libbinutils_2.38-3ubuntu1 libblas3_3.10.0-2ubuntu1 libblkid1_2.37.2-4ubuntu3 libbrotli1_1.0.9-2build6 libbsd0_0.11.5-1 libbz2-1.0_1.0.8-5build1 libc-bin_2.35-0ubuntu3 libc-dev-bin_2.35-0ubuntu3 libc6_2.35-0ubuntu3 libc6-dev_2.35-0ubuntu3 libcap-ng0_0.7.9-2.2build3 libcap2_1:2.44-1build3 libcc1-0_12-20220319-1ubuntu1 libcmark-gfm-extensions0.29.0.gfm.3_0.29.0.gfm.3-3 libcmark-gfm0.29.0.gfm.3_0.29.0.gfm.3-3 libcom-err2_1.46.5-2ubuntu1 libcrypt-dev_1:4.4.27-1 libcrypt1_1:4.4.27-1 libcryptsetup12_2:2.4.3-1ubuntu1 libctf-nobfd0_2.38-3ubuntu1 libctf0_2.38-3ubuntu1 libdb5.3_5.3.28+dfsg1-0.8ubuntu3 libdebconfclient0_0.261ubuntu1 libdebhelper-perl_13.6ubuntu1 libdeflate0_1.10-2 libdevmapper1.02.1_2:1.02.175-2.1ubuntu4 libdpkg-perl_1.21.1ubuntu2 libdw1_0.186-1build1 libedit2_3.1-20210910-1build1 libelf1_0.186-1build1 libexpat1_2.4.7-1 libexpat1-dev_2.4.7-1 libext2fs2_1.46.5-2ubuntu1 libfakeroot_1.28-1ubuntu1 libffi8_3.4.2-4 libfile-stripnondeterminism-perl_1.13.0-1 libfontconfig1_2.13.1-4.2ubuntu5 libfreetype6_2.11.1+dfsg-1build1 libfribidi0_1.0.8-2ubuntu3 libgcc-11-dev_11.2.0-19ubuntu1 libgcc-s1_12-20220319-1ubuntu1 libgcrypt20_1.9.4-3ubuntu3 libgdbm-compat4_1.23-1 libgdbm6_1.23-1 libgfortran5_12-20220319-1ubuntu1 libglib2.0-0_2.72.0-1 libgmp10_2:6.2.1+dfsg-3ubuntu1 libgnutls30_3.7.3-4ubuntu1 libgomp1_12-20220319-1ubuntu1 libgpg-error0_1.43-3 libgraphite2-3_1.3.14-1build2 libgssapi-krb5-2_1.19.2-2 libharfbuzz0b_2.7.4-1ubuntu3 libhogweed6_3.7.3-1build2 libicu70_70.1-2 libidn2-0_2.3.2-2build1 libimagequant0_2.17.0-1 libip4tc2_1.8.7-1ubuntu5 libisl23_0.24-2build1 libjbig0_2.1-3.1build3 libjpeg-turbo8_2.1.2-0ubuntu1 libjpeg8_8c-2ubuntu10 libjs-jquery_3.6.0+dfsg+~3.5.13-1 libjs-jquery-ui_1.13.1+dfsg-1 libjs-sphinxdoc_4.3.2-1 libjs-underscore_1.13.2~dfsg-2 libjson-c5_0.15-2build4 libk5crypto3_1.19.2-2 libkeyutils1_1.6.1-2ubuntu3 libkmod2_29-1ubuntu1 libkrb5-3_1.19.2-2 libkrb5support0_1.19.2-2 liblapack3_3.10.0-2ubuntu1 liblbfgsb0_3.0+dfsg.3-10 liblcms2-2_2.12~rc1-2build2 libllvm11_1:11.1.0-6 liblockfile-bin_1.17-1build2 liblockfile1_1.17-1build2 liblz4-1_1.9.3-2build2 liblzma5_5.2.5-2ubuntu1 libmagic-mgc_1:5.41-3 libmagic1_1:5.41-3 libmd0_1.0.4-1build1 libmount1_2.37.2-4ubuntu3 libmpc3_1.2.1-2build1 libmpdec3_2.5.1-2build2 libmpfr6_4.1.0-3build3 libncurses6_6.3-2 libncursesw6_6.3-2 libnettle8_3.7.3-1build2 libnorm1_1.5.9+dfsg-2 libnpth0_1.6-3build2 libnsl-dev_1.3.0-2build2 libnsl2_1.3.0-2build2 libopenjp2-7_2.4.0-6 libp11-kit0_0.24.0-6build1 libpam-modules_1.4.0-11ubuntu2 libpam-modules-bin_1.4.0-11ubuntu2 libpam-runtime_1.4.0-11ubuntu2 libpam0g_1.4.0-11ubuntu2 libpcre2-8-0_10.39-3build1 libpcre3_2:8.39-13build5 libperl5.32_5.32.1-3ubuntu3 libperl5.34_5.34.0-3ubuntu1 libpfm4_4.11.1+git32-gd0b85fb-1 libpgm-5.3-0_5.3.128~dfsg-2 libpipeline1_1.5.5-1 libpng16-16_1.6.37-3build5 libprocps8_2:3.3.17-6ubuntu2 libpython3-all-dev_3.10.4-0ubuntu2 libpython3-dev_3.10.4-0ubuntu2 libpython3-stdlib_3.10.4-0ubuntu2 libpython3.10_3.10.4-3 libpython3.10-dev_3.10.4-3 libpython3.10-minimal_3.10.4-3 libpython3.10-stdlib_3.10.4-3 libqhull-r8.0_2020.2-4 libraqm0_0.7.0-4ubuntu1 libreadline8_8.1.2-1 libseccomp2_2.5.3-2ubuntu2 libselinux1_3.3-1build2 libsemanage-common_3.3-1build2 libsemanage2_3.3-1build2 libsepol1_3.1-1ubuntu2 libsepol2_3.3-1build1 libsigsegv2_2.13-1ubuntu3 libsmartcols1_2.37.2-4ubuntu3 libsodium23_1.0.18-1build2 libsqlite3-0_3.37.2-2 libss2_1.46.5-2ubuntu1 libssl1.1_1.1.1l-1ubuntu1 libssl3_3.0.2-0ubuntu1 libstdc++-11-dev_11.2.0-19ubuntu1 libstdc++6_12-20220319-1ubuntu1 libsub-override-perl_0.09-2 libsystemd0_249.11-0ubuntu3 libtasn1-6_4.18.0-4build1 libtbb12_2021.5.0-7ubuntu2 libtbbmalloc2_2021.5.0-7ubuntu2 libtcl8.6_8.6.12+dfsg-1build1 libtiff5_4.3.0-6 libtinfo6_6.3-2 libtirpc-common_1.3.2-2build1 libtirpc-dev_1.3.2-2build1 libtirpc3_1.3.2-2build1 libtk8.6_8.6.12-1build1 libtool_2.4.6-15build2 libubsan1_12-20220319-1ubuntu1 libuchardet0_0.0.7-1build2 libudev1_249.11-0ubuntu3 libunistring2_1.0-1 libuuid1_2.37.2-4ubuntu3 libwebp7_1.2.2-2 libwebpdemux2_1.2.2-2 libwebpmux3_1.2.2-2 libx11-6_2:1.7.5-1 libx11-data_2:1.7.5-1 libxau6_1:1.0.9-1build5 libxcb1_1.14-3ubuntu3 libxdmcp6_1:1.1.3-0ubuntu5 libxext6_2:1.3.4-1build1 libxft2_2.3.3-0ubuntu5 libxml2_2.9.13+dfsg-1build1 libxrender1_1:0.9.10-1build4 libxslt1.1_1.1.34-4build2 libxss1_1:1.2.3-1build2 libxxhash0_0.8.1-1 libzmq5_4.3.4-2 libzstd1_1.4.8+dfsg-3build1 linux-libc-dev_5.15.0-25.25 llvm-11_1:11.1.0-6 llvm-11-linker-tools_1:11.1.0-6 llvm-11-runtime_1:11.1.0-6 lockfile-progs_0.1.19build1 login_1:4.8.1-2ubuntu2 logsave_1.46.5-2ubuntu1 lsb-base_11.1.0ubuntu4 lto-disabled-list_24 m4_1.4.18-5ubuntu2 make_4.3-4.1build1 man-db_2.10.2-1 mawk_1.3.4.20200120-3 media-types_7.0.0 mount_2.37.2-4ubuntu3 ncurses-base_6.3-2 ncurses-bin_6.3-2 openssl_3.0.2-0ubuntu1 optipng_0.7.7-2build1 pandoc_2.9.2.1-3ubuntu2 pandoc-data_2.9.2.1-3ubuntu2 passwd_1:4.8.1-2ubuntu2 patch_2.7.6-7build2 perl_5.34.0-3ubuntu1 perl-base_5.34.0-3ubuntu1 perl-modules-5.32_5.32.1-3ubuntu3 perl-modules-5.34_5.34.0-3ubuntu1 pinentry-curses_1.1.1-1build2 pkgbinarymangler_149 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3 procps_2:3.3.17-6ubuntu2 python-babel-localedata_2.8.0+dfsg.1-7 python-matplotlib-data_3.5.1-2build1 python3_3.10.4-0ubuntu2 python3-alabaster_0.7.12-1 python3-all_3.10.4-0ubuntu2 python3-all-dev_3.10.4-0ubuntu2 python3-appdirs_1.4.4-2 python3-attr_21.2.0-1 python3-babel_2.8.0+dfsg.1-7 python3-bleach_4.1.0-1 python3-brotli_1.0.9-2build6 python3-certifi_2020.6.20-1 python3-cffi-backend_1.15.0-1build2 python3-chardet_4.0.0-1 python3-cycler_0.11.0-1 python3-dateutil_2.8.1-6 python3-decorator_4.4.2-0ubuntu1 python3-defusedxml_0.7.1-1 python3-dev_3.10.4-0ubuntu2 python3-distutils_3.10.4-0ubuntu1 python3-docutils_0.17.1+dfsg-2 python3-entrypoints_0.4-1 python3-fonttools_4.29.1-2build1 python3-fs_2.4.12-1 python3-html5lib_1.1-3 python3-idna_3.3-1 python3-imagesize_1.3.0-1 python3-importlib-metadata_4.6.4-1 python3-iniconfig_1.1.1-2 python3-ipython-genutils_0.2.0-5 python3-jinja2_3.0.3-1 python3-jsonschema_3.2.0-0ubuntu2 python3-jupyter-client_7.1.2-1 python3-jupyter-core_4.9.1-1 python3-jupyterlab-pygments_0.1.2-8 python3-kiwisolver_1.3.2-1build1 python3-lib2to3_3.10.4-0ubuntu1 python3-llvmlite_0.38.0-1 python3-lxml_4.8.0-1build1 python3-lz4_3.1.3+dfsg-1build3 python3-markupsafe_2.0.1-2build1 python3-matplotlib_3.5.1-2build1 python3-minimal_3.10.4-0ubuntu2 python3-more-itertools_8.10.0-2 python3-mpmath_1.2.1-2 python3-nbclient_0.5.6-2 python3-nbconvert_6.4.0-1 python3-nbformat_5.1.3-1 python3-nbsphinx_0.8.7+ds-1 python3-nest-asyncio_1.5.4-1 python3-numba_0.55.1-0ubuntu2 python3-numpy_1:1.21.5-1build2 python3-numpydoc_1.2-1 python3-packaging_21.3-1 python3-pandas_1.3.5+dfsg-3 python3-pandas-lib_1.3.5+dfsg-3 python3-pandocfilters_1.5.0-1 python3-pil_9.0.1-1build1 python3-pil.imagetk_9.0.1-1build1 python3-pkg-resources_59.6.0-1.2 python3-pluggy_0.13.0-7.1 python3-py_1.10.0-1 python3-pygments_2.11.2+dfsg-2 python3-pyparsing_2.4.7-1 python3-pyrsistent_0.18.1-1build1 python3-pytest_6.2.5-1ubuntu2 python3-requests_2.25.1+dfsg-2 python3-roman_3.3-1 python3-scipy_1.8.0-1exp2ubuntu1 python3-scitrack_2021.5.3-2 python3-setuptools_59.6.0-1.2 python3-six_1.16.0-3 python3-snowballstemmer_2.2.0-1build1 python3-sphinx_4.3.2-1 python3-sphinx-bootstrap-theme_0.8.1-1 python3-sphinx-gallery_0.10.1-1 python3-sympy_1.9-1 python3-testpath_0.5.0+dfsg-1 python3-tinydb_3.15.2-2 python3-tk_3.10.4-0ubuntu1 python3-toml_0.10.2-1 python3-tomli_1.2.2-2 python3-tomli-w_1.0.0-1 python3-tornado_6.1.0-3build1 python3-tqdm_4.57.0-2 python3-traitlets_5.1.1-1 python3-tz_2022.1-1 python3-ufolib2_0.13.1+dfsg1-1 python3-unicodedata2_14.0.0+ds-8 python3-urllib3_1.26.5-1~exp1 python3-webencodings_0.5.1-4 python3-zipp_1.0.0-3 python3-zmq_22.3.0-1build1 python3.10_3.10.4-3 python3.10-dev_3.10.4-3 python3.10-minimal_3.10.4-3 readline-common_8.1.2-1 rpcsvc-proto_1.4.2-0ubuntu6 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1ubuntu2 sensible-utils_0.0.17 sgml-base_1.30 sphinx-common_4.3.2-1 systemd_249.11-0ubuntu3 systemd-sysv_249.11-0ubuntu3 systemd-timesyncd_249.11-0ubuntu3 sysvinit-utils_3.01-1ubuntu1 tar_1.34+dfsg-1build3 tk8.6-blt2.5_2.5.3+dfsg-4.1build2 tzdata_2022a-0ubuntu1 ubuntu-keyring_2021.03.26 ucf_3.0043 unicode-data_14.0.0-1.1 usrmerge_25ubuntu2 util-linux_2.37.2-4ubuntu3 x11-common_1:7.7+23ubuntu2 xml-core_0.18+nmu1 xz-utils_5.2.5-2ubuntu1 zlib1g_1:1.2.11.dfsg-2ubuntu9 zlib1g-dev_1:1.2.11.dfsg-2ubuntu9 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: python-cogent Binary: python3-cogent3, python-cogent-doc Architecture: any all Version: 2021.10.12a1+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille Homepage: https://github.com/cogent3/cogent3 Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/python-cogent Vcs-Git: https://salsa.debian.org/med-team/python-cogent.git Testsuite: autopkgtest, autopkgtest-pkg-python Testsuite-Triggers: python3-pytest Build-Depends: debhelper-compat (= 13), dh-python, flit, python3-all-dev, python3-matplotlib, python3-numba, python3-numpy, python3-pandas, python3-scitrack, python3-tqdm, python3-tinydb, python3-sphinx, python3-numpydoc, python3-nbsphinx, python3-sphinx-bootstrap-theme, python3-sphinx-gallery, python3-pytest , cython3, pandoc Package-List: python-cogent-doc deb doc optional arch=all python3-cogent3 deb python optional arch=any Checksums-Sha1: 6fcdf10bb1437406af0899fd3c85a3a5e314c349 3012940 python-cogent_2021.10.12a1+dfsg.orig.tar.xz 5b637997c60a4dbbd775590d006ebde8f7548df8 11600 python-cogent_2021.10.12a1+dfsg-1.debian.tar.xz Checksums-Sha256: bea317e2e6722e55788074b417063a8312c56b07f01cf53cc2cf57732933c2f9 3012940 python-cogent_2021.10.12a1+dfsg.orig.tar.xz b7f197f5dc775dd53636d5eecd842fcae556d687d19667f79df8472131cfc693 11600 python-cogent_2021.10.12a1+dfsg-1.debian.tar.xz Files: b14afccdd2e784d2f35ae15d7bc82da9 3012940 python-cogent_2021.10.12a1+dfsg.orig.tar.xz e1528059562364a0d31f31f74bf4b465 11600 python-cogent_2021.10.12a1+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmGDoA4RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEU5Q/+Py9nhE8hR2APFSCcN7QbqnBE9qpkhGw2 haEJGyxQY+Oq88MLfFJd3F9VShy73fmNcQn0aQkwcifxsIN2cY7eBbwgAQNGwJPq 2sqFKarr63DE5a3AObOn48/+HI7+GJ8z/LS6JjaVGae9mwQR5UJbSdcdNvW+00RM ScMzAnCJt2VdcoMfJOVtQUyxQOuRXKayR/AnXFVYYdjYliJNWDSsa/Paq2p76KHR CSbhhNZZkh5kKLj4FlFt+2zkeI0+l8Q0oWO41SEi26cyKzeMWRNazbRY51JX6kjO oGBQX+6w1w5lkkt8+5oZ2yJ1F7VJMgKS7S5Yeu0krKUWah76Jc55sW7t7kkGNjyk 8hLjEyZfOXdadrXjBV9V7nQd3p55Pbri0Eu2p+dNTxAJhx7Dx4EQ9h1Mty2YF3c+ zhKP5xceYrNdN3Hw01ESolmrAEv2oBByRg3RmVodq6mWGzlqR8dM1Eg/hJ2+KwEz 0kkJST+wGagYHBOtdcxqLoYYo9YEdj5PsYYBcQaIaHkzx2Emvnnw2vXx3s2MaEmd 2snhaUEd1XVMQS1iBbw4Oc7m4nNXSUX8Uj79dTm6/wHFz6FpNxeQXNgeDsRQe+Vo hYwiIDrc5YMttBwCNuEn7NdBu5gnvaS1D7YeZc3v3jij4DgdGFRynOfHTZy1pcdb vsmcDGYi+s8= =uHeK -----END PGP SIGNATURE----- gpgv: Signature made Thu Nov 4 08:55:42 2021 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify signature ./python-cogent_2021.10.12a1+dfsg-1.dsc dpkg-source: info: extracting python-cogent in /<> dpkg-source: info: unpacking python-cogent_2021.10.12a1+dfsg.orig.tar.xz dpkg-source: info: unpacking python-cogent_2021.10.12a1+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying sphinx.patch dpkg-source: info: applying fix_interpreter.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-22372247 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-22372247 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-22372247 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -B -rfakeroot dpkg-buildpackage: info: source package python-cogent dpkg-buildpackage: info: source version 2021.10.12a1+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean --with python3 --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild dh_autoreconf_clean -O--buildsystem=pybuild debian/rules override_dh_clean make[1]: Entering directory '/<>' #These files are rebuilt on-the-fly for f in `find -name '*.c'` ; do \ head -n 1 "$f" | grep -q '^/\* Generated by Cython' && rm "$f" ; \ done rm -rf build build-stamp rm -rf doc/_build dh_clean make[1]: Leaving directory '/<>' debian/rules binary-arch dh binary-arch --with python3 --buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_autoreconf -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build W: pybuild validate:127: Couldn't get list of valid classifiers to check against I: pybuild plugin_flit:66: Installing package /<>/src/cogent3 -> /<>/.pybuild/cpython3_3.10_cogent3/build/cogent3 I: pybuild plugin_flit:79: Writing dist-info /<>/.pybuild/cpython3_3.10_cogent3/build/ set -x; cd doc; PYTHONPATH=/<> http_proxy='127.0.0.1:9' /usr/bin/make html + cd doc + PYTHONPATH=/<> http_proxy=127.0.0.1:9 /usr/bin/make html make[2]: Entering directory '/<>/doc' sphinx-build -b html -d _build/doctrees . _build/html Running Sphinx v4.3.2 making output directory... done WARNING: html_static_path entry '_static' does not exist WARNING: The config value `today' has type `date', defaults to `str'. [autosummary] generating autosummary for: api/__init__/cogent3.__init__.available_apps.rst, api/__init__/cogent3.__init__.available_codes.rst, api/__init__/cogent3.__init__.available_models.rst, api/__init__/cogent3.__init__.available_moltypes.rst, api/__init__/cogent3.__init__.get_code.rst, api/__init__/cogent3.__init__.get_model.rst, api/__init__/cogent3.__init__.get_moltype.rst, api/__init__/cogent3.__init__.load_aligned_seqs.rst, api/__init__/cogent3.__init__.load_delimited.rst, api/__init__/cogent3.__init__.load_table.rst, ..., examples/scope_model_params_on_trees.rst, examples/seq_features.rst, examples/simple.rst, examples/simulate_alignment.rst, examples/testing_multi_loci.rst, general.rst, index.rst, install.rst, licenses.rst, pycogent.rst building [mo]: targets for 0 po files that are out of date building [html]: targets for 110 source files that are out of date updating environment: [new config] 110 added, 0 changed, 0 removed reading sources... [ 0%] api/__init__/cogent3.__init__.available_apps reading sources... [ 1%] api/__init__/cogent3.__init__.available_codes reading sources... [ 2%] api/__init__/cogent3.__init__.available_models reading sources... [ 3%] api/__init__/cogent3.__init__.available_moltypes reading sources... [ 4%] api/__init__/cogent3.__init__.get_code reading sources... [ 5%] api/__init__/cogent3.__init__.get_model reading sources... [ 6%] api/__init__/cogent3.__init__.get_moltype reading sources... [ 7%] api/__init__/cogent3.__init__.load_aligned_seqs reading sources... [ 8%] api/__init__/cogent3.__init__.load_delimited reading sources... [ 9%] api/__init__/cogent3.__init__.load_table reading sources... [ 10%] api/__init__/cogent3.__init__.load_tree reading sources... [ 10%] api/__init__/cogent3.__init__.load_unaligned_seqs reading sources... [ 11%] api/__init__/cogent3.__init__.make_aligned_seqs reading sources... [ 12%] api/__init__/cogent3.__init__.make_seq reading sources... [ 13%] api/__init__/cogent3.__init__.make_table reading sources... [ 14%] api/__init__/cogent3.__init__.make_tree reading sources... [ 15%] api/__init__/cogent3.__init__.make_unaligned_seqs reading sources... [ 16%] api/alignment/alignment reading sources... [ 17%] api/alignment/classes/cogent3.core.alignment.Alignment reading sources... [ 18%] api/alignment/classes/cogent3.core.alignment.ArrayAlignment reading sources... [ 19%] api/alignment/classes/cogent3.core.alignment.SequenceCollection reading sources... [ 20%] api/alphabet/alphabet reading sources... [ 20%] api/alphabet/classes/cogent3.core.alphabet.Alphabet reading sources... [ 21%] api/genetic_code/classes/cogent3.core.genetic_code.GeneticCode reading sources... [ 22%] api/genetic_code/genetic_code reading sources... [ 23%] api/index reading sources... [ 24%] api/moltype/classes/cogent3.core.moltype.MolType reading sources... [ 25%] api/moltype/moltype reading sources... [ 26%] api/sequence/classes/cogent3.core.sequence.DnaSequence reading sources... [ 27%] api/sequence/classes/cogent3.core.sequence.ProteinSequence reading sources... [ 28%] api/sequence/classes/cogent3.core.sequence.RnaSequence reading sources... [ 29%] api/sequence/sequence reading sources... [ 30%] api/table/classes/cogent3.parse.table.FilteringParser reading sources... [ 30%] api/table/classes/cogent3.util.table.Columns reading sources... [ 31%] api/table/classes/cogent3.util.table.Table reading sources... [ 32%] api/table/table reading sources... [ 33%] api/tree/classes/cogent3.core.tree.PhyloNode reading sources... [ 34%] api/tree/tree reading sources... [ 35%] app/align-codon reading sources... [ 36%] app/align-nucleotide reading sources... [ 37%] app/align-protein reading sources... [ 38%] app/app-overview reading sources... [ 39%] app/available-apps reading sources... [ 40%] app/dstore reading sources... [ 40%] app/evo-ancestral-states reading sources... [ 41%] app/evo-dt-nuc-model reading sources... [ 42%] app/evo-extract-model-stats reading sources... [ 43%] app/evo-hypothesis reading sources... [ 44%] app/evo-model reading sources... [ 45%] app/evo-model-timehet reading sources... [ 46%] app/evo-model-with-tree reading sources... [ 47%] app/evo-natsel_neutral reading sources... [ 48%] app/evo-natsel_sitehet reading sources... [ 49%] app/evo-natsel_timehet reading sources... [ 50%] app/evo-natsel_zhang reading sources... [ 50%] app/evo-nstat-codon-model reading sources... [ 51%] app/evo-tr-codon-model reading sources... [ 52%] app/evo-tr-nuc-model reading sources... [ 53%] app/index reading sources... [ 54%] app/not-completed reading sources... [ 55%] app/user_function reading sources... [ 56%] app/warning reading sources... [ 57%] cookbook/DNA_and_RNA_sequences reading sources... [ 58%] cookbook/alignments reading sources... [ 59%] cookbook/alphabet reading sources... [ 60%] cookbook/annotations reading sources... [ 60%] cookbook/building_alignments reading sources... [ 61%] cookbook/building_phylogenies reading sources... [ 62%] cookbook/calc_genetic_distance reading sources... [ 63%] cookbook/evo_modelling reading sources... [ 64%] cookbook/genetic_code reading sources... [ 65%] cookbook/index reading sources... [ 66%] cookbook/loading_sequences reading sources... [ 67%] cookbook/loading_tabular reading sources... [ 68%] cookbook/manipulating_biological_data reading sources... [ 69%] cookbook/moltypes reading sources... [ 70%] cookbook/protein_sequences reading sources... [ 70%] cookbook/simple_trees reading sources... [ 71%] cookbook/tables reading sources... [ 72%] cookbook/useful_utilities reading sources... [ 73%] cookbook/what_codes reading sources... [ 74%] data_file_links reading sources... [ 75%] examples/align_codons_to_protein reading sources... [ 76%] examples/calculate_UPGMA_cluster reading sources... [ 77%] examples/calculate_neigbourjoining_tree reading sources... [ 78%] examples/calculate_pairwise_distances reading sources... [ 79%] examples/codon_models reading sources... [ 80%] examples/coevolution reading sources... [ 80%] examples/complete_seq_features reading sources... [ 81%] examples/empirical_protein_models reading sources... [ 82%] examples/hmm_par_heterogeneity reading sources... [ 83%] examples/index reading sources... [ 84%] examples/manipulating_tree_nodes reading sources... [ 85%] examples/neutral_test reading sources... [ 86%] examples/parallel reading sources... [ 87%] examples/parametric_bootstrap reading sources... [ 88%] examples/period_estimation reading sources... [ 89%] examples/phylo_by_ls reading sources... [ 90%] examples/rate_heterogeneity reading sources... [ 90%] examples/relative_rate reading sources... [ 91%] examples/scope_model_params_on_trees reading sources... [ 92%] examples/seq_features reading sources... [ 93%] examples/simple reading sources... [ 94%] examples/simulate_alignment reading sources... [ 95%] examples/testing_multi_loci reading sources... [ 96%] general reading sources... [ 97%] index reading sources... [ 98%] install reading sources... [ 99%] licenses reading sources... [100%] pycogent /<>/doc/../src/cogent3/core/alignment.py:docstring of cogent3.core.alignment.AlignmentI.entropy_per_seq:11: WARNING: Unexpected section title. Notes ----- /<>/doc/../src/cogent3/core/alignment.py:docstring of cogent3.core.alignment.AlignmentI.to_type:11: WARNING: Field list ends without a blank line; unexpected unindent. /<>/doc/../src/cogent3/core/alignment.py:docstring of cogent3.core.alignment.AlignmentI.entropy_per_seq:11: WARNING: Unexpected section title. Notes ----- /<>/doc/../src/cogent3/core/alignment.py:docstring of cogent3.core.alignment.AlignmentI.to_type:11: WARNING: Field list ends without a blank line; unexpected unindent. /<>/doc/app/align-codon.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/align-codon.rst:11: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io reader = io.load_unaligned(format="fasta") seqs = reader("data/SCA1-cds.fasta") /<>/doc/app/align-codon.rst:23: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app.align import progressive_align codon_aligner = progressive_align("codon") aligned = codon_aligner(seqs) aligned /<>/doc/app/align-codon.rst:33: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned.info /<>/doc/app/align-codon.rst:46: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: nt_aligner = progressive_align("codon", distance="paralinear") aligned = nt_aligner(seqs) aligned /<>/doc/app/align-codon.rst:57: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tree = "((Chimp:0.001,Human:0.001):0.0076,Macaque:0.01,((Rat:0.01,Mouse:0.01):0.02,Mouse_Lemur:0.02):0.01)" codon_aligner = progressive_align("codon", guide_tree=tree) aligned = codon_aligner(seqs) aligned /<>/doc/app/align-codon.rst:67: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: codon_aligner = progressive_align( "codon", guide_tree=tree, indel_rate=0.001, indel_length=0.01 ) aligned = codon_aligner(seqs) aligned /<>/doc/app/align-codon.rst:80: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: codon_aligner = progressive_align( "CNFHKY", guide_tree=tree, param_vals=dict(omega=0.1, kappa=3) ) aligned = codon_aligner(seqs) aligned /<>/doc/app/align-codon.rst:91: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned.info /<>/doc/app/align-nucleotide.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/align-nucleotide.rst:11: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io reader = io.load_unaligned(format="fasta") seqs = reader("data/SCA1-cds.fasta") /<>/doc/app/align-nucleotide.rst:23: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app.align import progressive_align nt_aligner = progressive_align("nucleotide") aligned = nt_aligner(seqs) aligned /<>/doc/app/align-nucleotide.rst:36: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: nt_aligner = progressive_align("nucleotide", distance="TN93") aligned = nt_aligner(seqs) aligned /<>/doc/app/align-nucleotide.rst:45: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tree = "((Chimp:0.001,Human:0.001):0.0076,Macaque:0.01,((Rat:0.01,Mouse:0.01):0.02,Mouse_Lemur:0.02):0.01)" nt_aligner = progressive_align("nucleotide", guide_tree=tree) aligned = nt_aligner(seqs) aligned /<>/doc/app/align-nucleotide.rst:59: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tree = "((Chimp:0.001,Human:0.001):0.0076,Macaque:0.01,((Rat:0.01,Mouse:0.01):0.02,Mouse_Lemur:0.02):0.01)" nt_aligner = progressive_align("F81", guide_tree=tree) aligned = nt_aligner(seqs) aligned /<>/doc/app/align-nucleotide.rst:69: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned.info /<>/doc/app/align-protein.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/align-protein.rst:11: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io, translate reader = io.load_unaligned(format="fasta") to_aa = translate.translate_seqs() process = reader + to_aa seqs = process("data/SCA1-cds.fasta") /<>/doc/app/align-protein.rst:25: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app.align import progressive_align aa_aligner = progressive_align("protein") aligned = aa_aligner(seqs) aligned /<>/doc/app/align-protein.rst:40: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aa_aligner = progressive_align("protein", distance="paralinear") aligned = aa_aligner(seqs) aligned /<>/doc/app/align-protein.rst:49: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned.info /<>/doc/app/available-apps.rst:8: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_apps available_apps() /<>/doc/app/dstore.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/dstore.rst:24: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app.io import get_data_store dstore = get_data_store("data/raw.zip", suffix="fa*", limit=5) dstore /<>/doc/app/dstore.rst:36: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: m = dstore[0] m /<>/doc/app/dstore.rst:41: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: m.read()[:20] # truncating /<>/doc/app/dstore.rst:50: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.tail() /<>/doc/app/dstore.rst:57: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.filtered("*ENSG00000067704*") /<>/doc/app/dstore.rst:64: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: for m in dstore: print(m) /<>/doc/app/dstore.rst:85: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore = get_data_store("data/demo-locked.tinydb") dstore.describe /<>/doc/app/dstore.rst:92: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.unlock(force=True) /<>/doc/app/dstore.rst:101: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.summary_logs /<>/doc/app/dstore.rst:107: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.logs /<>/doc/app/dstore.rst:113: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(dstore.logs[0].read()[:225]) # truncated for clarity /<>/doc/app/evo-ancestral-states.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/evo-ancestral-states.rst:13: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io, evo reader = io.load_aligned(format="fasta") aln = reader("data/primate_brca1.fasta") gn = evo.model("GN", tree="data/primate_brca1.tree") result = gn(aln) /<>/doc/app/evo-ancestral-states.rst:25: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: reconstuctor = evo.ancestral_states() states_result = reconstuctor(result) states_result /<>/doc/app/evo-ancestral-states.rst:33: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: states_result["edge.0"] /<>/doc/app/evo-ancestral-states.rst:39: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.tree.get_figure(contemporaneous=True).show(width=500, height=500) /<>/doc/app/evo-dt-nuc-model.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/evo-dt-nuc-model.rst:11: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io, evo loader = io.load_aligned(format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") model = evo.model("BH", tree="data/primate_brca1.tree") result = model(aln) result /<>/doc/app/evo-dt-nuc-model.rst:27: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.lf /<>/doc/app/evo-dt-nuc-model.rst:36: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tree = result.tree fig = tree.get_figure() fig.scale_bar = "top right" fig.show(width=500, height=500) /<>/doc/app/evo-dt-nuc-model.rst:48: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulator = evo.tabulate_stats() stats = tabulator(result) stats /<>/doc/app/evo-dt-nuc-model.rst:54: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: stats["edge motif motif2 params"] /<>/doc/app/evo-extract-model-stats.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/evo-extract-model-stats.rst:13: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io, evo loader = io.load_aligned(format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") model = evo.model("GN", tree="data/primate_brca1.tree") result = model(aln) /<>/doc/app/evo-extract-model-stats.rst:25: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulator = evo.tabulate_stats() tabulated = tabulator(result) tabulated /<>/doc/app/evo-extract-model-stats.rst:38: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulated["edge params"] /<>/doc/app/evo-extract-model-stats.rst:49: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulated["global params"] /<>/doc/app/evo-extract-model-stats.rst:58: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulated["motif params"] /<>/doc/app/evo-hypothesis.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/evo-hypothesis.rst:11: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io, evo, sample loader = io.load_aligned(format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") /<>/doc/app/evo-hypothesis.rst:18: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tree = "data/primate_brca1.tree" sm_args = dict(optimise_motif_probs=True) null = evo.model("GTR", tree=tree, sm_args=sm_args) alt = evo.model("GN", tree=tree, sm_args=sm_args) hyp = evo.hypothesis(null, alt) result = hyp(aln) type(result) /<>/doc/app/evo-hypothesis.rst:31: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result /<>/doc/app/evo-hypothesis.rst:43: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.LR, result.df, result.pvalue /<>/doc/app/evo-hypothesis.rst:52: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.null /<>/doc/app/evo-hypothesis.rst:56: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.null.lf /<>/doc/app/evo-hypothesis.rst:63: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf /<>/doc/app/evo-model.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/evo-model.rst:12: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io, sample reader = io.load_aligned(format="fasta", moltype="dna") select_seqs = sample.take_named_seqs("Human", "Rhesus", "Galago") process = reader + select_seqs aln = process("data/primate_brca1.fasta") aln.names /<>/doc/app/evo-model.rst:26: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import evo gn = evo.model("GN") gn /<>/doc/app/evo-model.rst:35: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted = gn(aln) type(fitted) /<>/doc/app/evo-model.rst:49: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted /<>/doc/app/evo-model.rst:55: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.lf /<>/doc/app/evo-model.rst:59: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.lnL, fitted.nfp /<>/doc/app/evo-model.rst:63: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.source /<>/doc/app/evo-model.rst:69: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.tree, fitted.alignment /<>/doc/app/evo-model.rst:75: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.total_length(length_as="paralinear") /<>/doc/app/evo-model.rst:84: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: gn = evo.model("GN", split_codons=True) fitted = gn(aln) fitted /<>/doc/app/evo-model.rst:95: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted[3] /<>/doc/app/evo-model-timehet.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/evo-model-timehet.rst:13: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.app import io, evo tree = load_tree("data/primate_brca1.tree") fig = tree.get_figure(contemporaneous=True) fig.style_edges( "Human", tip2="Orangutan", outgroup="Galago", line=dict(color="red") ) fig.show(width=500, height=500) /<>/doc/app/evo-model-timehet.rst:32: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: time_het = evo.model( "GN", tree=tree, time_het=[dict(tip_names=["Human", "Orangutan"], outgroup_name="Galago")], ) /<>/doc/app/evo-model-timehet.rst:42: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: reader = io.load_aligned(format="fasta") aln = reader("data/primate_brca1.fasta") result = time_het(aln) /<>/doc/app/evo-model-timehet.rst:50: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.lf /<>/doc/app/evo-model-with-tree.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/evo-model-with-tree.rst:11: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io reader = io.load_aligned(format="fasta", moltype="dna") aln = reader("data/primate_brca1.fasta") aln.names /<>/doc/app/evo-model-with-tree.rst:22: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.app import evo tree = load_tree("data/primate_brca1.tree") gn = evo.model("GN", tree=tree) gn /<>/doc/app/evo-model-with-tree.rst:34: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: gn = evo.model("GN", tree="data/primate_brca1.tree") gn /<>/doc/app/evo-model-with-tree.rst:42: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted = gn(aln) fitted /<>/doc/app/evo-model-with-tree.rst:51: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.lf /<>/doc/app/evo-natsel_neutral.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/evo-natsel_neutral.rst:13: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io, evo loader = io.load_aligned(format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") omega_eq_1 = evo.natsel_neutral( "GNC", tree="data/primate_brca1.tree", optimise_motif_probs=False ) result = omega_eq_1(aln) type(result) /<>/doc/app/evo-natsel_neutral.rst:26: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result /<>/doc/app/evo-natsel_neutral.rst:30: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf /<>/doc/app/evo-natsel_sitehet.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/evo-natsel_sitehet.rst:13: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io, evo loader = io.load_aligned(format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") sites_differ = evo.natsel_sitehet( "GNC", tree="data/primate_brca1.tree", optimise_motif_probs=False ) result = sites_differ(aln) result /<>/doc/app/evo-natsel_sitehet.rst:29: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf /<>/doc/app/evo-natsel_sitehet.rst:38: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: bprobs = result.alt.lf.get_bin_probs() bprobs[:, :20] /<>/doc/app/evo-natsel_timehet.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/evo-natsel_timehet.rst:11: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io, evo loader = io.load_aligned(format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") hc_differ = evo.natsel_timehet( "GNC", tree="data/primate_brca1.tree", optimise_motif_probs=False, tip1="Human", tip2="Chimpanzee", ) result = hc_differ(aln) result /<>/doc/app/evo-natsel_timehet.rst:28: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf /<>/doc/app/evo-natsel_zhang.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/evo-natsel_zhang.rst:13: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from numpy import array from cogent3 import make_table from IPython.core.display import HTML header = ['Site Class', 'Proportion', 'Background Edges', 'Foreground Edges'] data = {'Site Class': array(['0', '1', '2a', '2b'], dtype=' 1', '0 < omega0 < 1'], dtype='>/doc/app/evo-natsel_zhang.rst:30: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io, evo loader = io.load_aligned(format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") zhang_test = evo.natsel_zhang( "GNC", tree="data/primate_brca1.tree", optimise_motif_probs=False, tip1="Human", tip2="Chimpanzee", ) result = zhang_test(aln) result /<>/doc/app/evo-natsel_zhang.rst:48: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf /<>/doc/app/evo-natsel_zhang.rst:55: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: bprobs = result.alt.lf.get_bin_probs() bprobs[:, :20] /<>/doc/app/evo-natsel_zhang.rst:63: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tab = evo.tabulate_stats() stats = tab(result.alt) stats /<>/doc/app/evo-natsel_zhang.rst:69: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: stats["edge bin params"][:10] # truncating the table /<>/doc/app/evo-nstat-codon-model.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/evo-nstat-codon-model.rst:13: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io, evo loader = io.load_aligned(format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") /<>/doc/app/evo-nstat-codon-model.rst:22: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: model = evo.model("GNC", tree="data/primate_brca1.tree") result = model(aln) result /<>/doc/app/evo-nstat-codon-model.rst:28: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.lf /<>/doc/app/evo-nstat-codon-model.rst:37: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tree = result.tree fig = tree.get_figure() fig.scale_bar = "top right" fig.show(width=500, height=500) /<>/doc/app/evo-tr-codon-model.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/evo-tr-codon-model.rst:11: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_models available_models("codon") /<>/doc/app/evo-tr-codon-model.rst:22: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io, evo loader = io.load_aligned(format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") model = evo.model( "CNFGTR", tree="data/primate_brca1.tree", sm_args=dict(optimise_motif_probs=True), ) result = model(aln) result /<>/doc/app/evo-tr-codon-model.rst:36: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.lf /<>/doc/app/evo-tr-nuc-model.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/evo-tr-nuc-model.rst:11: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_models available_models("nucleotide") /<>/doc/app/evo-tr-nuc-model.rst:22: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io, evo loader = io.load_aligned(format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") model = evo.model( "GTR", tree="data/primate_brca1.tree", sm_args=dict(optimise_motif_probs=True) ) result = model(aln) result /<>/doc/app/evo-tr-nuc-model.rst:34: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.lf /<>/doc/app/not-completed.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/not-completed.rst:24: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io, sample reader = io.load_aligned(format="fasta") select_seqs = sample.take_named_seqs("Mouse", "Human") aln = reader("data/primate_brca1.fasta") result = select_seqs(aln) result /<>/doc/app/not-completed.rst:34: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result == False result.type result.message /<>/doc/app/not-completed.rst:45: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result = reader("primate_brca1.fasta") result /<>/doc/app/not-completed.rst:54: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: process = reader + select_seqs result = process("data/primate_brca1.fasta") result /<>/doc/app/not-completed.rst:62: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result = process("primate_brca1.fasta") result /<>/doc/app/user_function.rst:25: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app.composable import ALIGNED_TYPE, appify @appify(ALIGNED_TYPE, ALIGNED_TYPE, data_types="Alignment") def up_to(val, index=4): return val[:index] /<>/doc/app/user_function.rst:36: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: up_to /<>/doc/app/user_function.rst:42: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: first4 = up_to(index=4) first4 /<>/doc/app/user_function.rst:49: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=dict(a="GCAAGCGTTTAT", b="GCTTTTGTCAAT"), array_align=False, moltype="dna" ) result = first4(aln) result /<>/doc/app/user_function.rst:66: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app.composable import ( ALIGNED_TYPE, SEQUENCE_TYPE, SERIALISABLE_TYPE, appify, ) @appify((ALIGNED_TYPE, SEQUENCE_TYPE), SERIALISABLE_TYPE) def rename_seqs(aln): """upper case names""" return aln.rename_seqs(lambda x: x.upper()) renamer = rename_seqs() result = renamer(aln) result /<>/doc/app/user_function.rst:89: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app.composable import ( ALIGNED_TYPE, PAIRWISE_DISTANCE_TYPE, appify, ) @appify(ALIGNED_TYPE, PAIRWISE_DISTANCE_TYPE) def get_dists(aln, calc="hamming"): return aln.distance_matrix(calc=calc, show_progress=False) percent_dist = get_dists(calc="percent") result = percent_dist(aln) result /<>/doc/cookbook/DNA_and_RNA_sequences.rst:20: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA my_seq = DNA.make_seq("AGTACACTGGT") my_seq print(my_seq) str(my_seq) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:32: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import RNA rnaseq = RNA.make_seq("ACGUACGUACGUACGU") /<>/doc/cookbook/DNA_and_RNA_sequences.rst:41: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA my_seq = DNA.make_seq("AGTACACTGGT") print(my_seq.to_fasta()) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:51: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import RNA rnaseq = RNA.make_seq("ACGUACGUACGUACGU") rnaseq.to_fasta() /<>/doc/cookbook/DNA_and_RNA_sequences.rst:63: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT", "my_gene", moltype="dna") my_seq type(my_seq) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:74: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT", moltype="dna") my_seq.name = "my_gene" print(my_seq.to_fasta()) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:85: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA my_seq = DNA.make_seq("AGTACACTGGT") print(my_seq.complement()) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:95: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(my_seq.rc()) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:101: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(my_seq.rc()) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:110: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA my_seq = DNA.make_seq("GCTTGGGAAAGTCAAATGGAA", "protein-X") pep = my_seq.get_translation() type(pep) print(pep.to_fasta()) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:122: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA my_seq = DNA.make_seq("ACGTACGTACGTACGT") print(my_seq.to_rna()) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:132: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import RNA rnaseq = RNA.make_seq("ACGUACGUACGUACGU") print(rnaseq.to_dna()) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:142: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA a = DNA.make_seq("AGTACACTGGT") a.can_pair(a.complement()) a.can_pair(a.rc()) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:153: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA my_seq = DNA.make_seq("AGTACACTGGT") extra_seq = DNA.make_seq("CTGAC") long_seq = my_seq + extra_seq long_seq str(long_seq) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:166: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: my_seq[1:6] /<>/doc/cookbook/DNA_and_RNA_sequences.rst:177: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA seq = DNA.make_array_seq("ATGATGATGATG") pos3 = seq[2::3] assert str(pos3) == "GGGG" /<>/doc/cookbook/DNA_and_RNA_sequences.rst:190: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA seq = DNA.make_seq("ATGATGATGATG") indices = [(i, i + 2) for i in range(len(seq))[::3]] pos12 = seq.add_feature("pos12", "pos12", indices) pos12 = pos12.get_slice() assert str(pos12) == "ATATATAT" /<>/doc/cookbook/DNA_and_RNA_sequences.rst:211: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import RNA s = RNA.make_seq("--AUUAUGCUAU-UAu--") print(s.degap()) /<>/doc/cookbook/alignments.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/cookbook/alignments.rst:28: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs, make_unaligned_seqs dna = {"seq1": "ATGACC", "seq2": "ATCGCC"} seqs = make_aligned_seqs(data=dna, moltype="dna") print(type(seqs)) seqs = make_unaligned_seqs(dna, moltype="dna") print(type(seqs)) /<>/doc/cookbook/alignments.rst:41: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs dna = {"seq1": "ATGACC", "seq2": "ATCGCC"} seqs = make_aligned_seqs(data=dna, moltype="dna", array_align=True) print(type(seqs)) print(seqs) /<>/doc/cookbook/alignments.rst:53: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs seqs = load_unaligned_seqs("data/test.paml") print(seqs) /<>/doc/cookbook/alignments.rst:70: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( [("seq1", "ATGAA------"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG")], moltype="dna", ) print(aln) new_seqs = make_aligned_seqs( [("seq0", "ATG-AGT-AGG"), ("seq4", "ATGCC------")], moltype="dna" ) new_aln = aln.add_seqs(new_seqs) print(new_aln) /<>/doc/cookbook/alignments.rst:92: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: new_aln = aln.add_seqs(new_seqs, before_name="seq2") print(new_aln) new_aln = aln.add_seqs(new_seqs, after_name="seq2") print(new_aln) /<>/doc/cookbook/alignments.rst:104: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( [("seq1", "ATGAA------"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG")], moltype="dna", ) ref_aln = make_aligned_seqs( [("seq3", "ATAGGATG"), ("seq0", "ATG-AGCG"), ("seq4", "ATGCTGGG")], moltype="dna", ) new_aln = aln.add_from_ref_aln(ref_aln) print(new_aln) /<>/doc/cookbook/alignments.rst:126: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( [("seq1", "ATGAA---TG-"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG")], moltype="dna", ) new_aln = aln.get_degapped_relative_to("seq1") print(new_aln) /<>/doc/cookbook/alignments.rst:145: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( [("seq1", "ATGAA------"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG")], moltype="dna", array_align=False, ) seq = aln.get_seq("seq1") seq.name type(seq) seq.is_gapped() /<>/doc/cookbook/alignments.rst:161: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = aln.get_gapped_seq("seq1") seq.is_gapped() print(seq) /<>/doc/cookbook/alignments.rst:169: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.names aln.names /<>/doc/cookbook/alignments.rst:179: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs, load_aligned_seqs fn = "data/long_testseqs.fasta" seqs = load_unaligned_seqs(fn, moltype="dna") my_seq = seqs.seqs[0] my_seq[:24] str(my_seq[:24]) type(my_seq) aln = load_aligned_seqs(fn, moltype="dna") aln.seqs[0][:24] print(aln.seqs[0][:24]) /<>/doc/cookbook/alignments.rst:196: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/test.paml", moltype="dna") aln.names new = aln.take_seqs(["Human", "HowlerMon"]) new.names /<>/doc/cookbook/alignments.rst:207: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/test.paml", array_align=False, moltype="dna") seq = aln.get_seq("Human") new = aln.take_seqs(["Human", "HowlerMon"]) id(new.get_seq("Human")) == id(aln.get_seq("Human")) /<>/doc/cookbook/alignments.rst:222: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs from cogent3.core.alignment import Alignment seq = load_unaligned_seqs("data/test.paml") aln = Alignment(seq) fasta_1 = seq fasta_2 = aln assert fasta_1 == fasta_2 /<>/doc/cookbook/alignments.rst:238: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs data = [("a", "ACG---"), ("b", "CCTGGG")] aln = make_aligned_seqs(data=data) dna = aln.to_dna() dna /<>/doc/cookbook/alignments.rst:249: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs data = [("a", "ACG---"), ("b", "CCUGGG")] aln = make_aligned_seqs(data=data) rna = aln.to_rna() rna /<>/doc/cookbook/alignments.rst:260: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs data = [("x", "TYV"), ("y", "TE-")] aln = make_aligned_seqs(data=data) prot = aln.to_protein() prot /<>/doc/cookbook/alignments.rst:277: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta") degapped = aln.degap() print(type(degapped)) /<>/doc/cookbook/alignments.rst:292: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs dna = {"seq1": "ATGACC", "seq2": "ATCGCC"} aln = make_aligned_seqs(data=dna, moltype="dna") aln.write("sample.fasta") /<>/doc/cookbook/alignments.rst:302: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.write("sample", format="fasta") /<>/doc/cookbook/alignments.rst:308: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import remove_files remove_files(["sample", "sample.fasta"], error_on_missing=False) /<>/doc/cookbook/alignments.rst:317: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.core.alignment import Alignment seq = load_aligned_seqs("data/long_testseqs.fasta") aln = Alignment(seq) fasta_align = aln /<>/doc/cookbook/alignments.rst:329: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.core.alignment import Alignment seq = load_aligned_seqs("data/test.paml") aln = Alignment(seq) got = aln.to_phylip() print(got) /<>/doc/cookbook/alignments.rst:342: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.core.alignment import Alignment seq = load_aligned_seqs("data/test.paml") aln = Alignment(seq) string_list = aln.to_dict().values() /<>/doc/cookbook/alignments.rst:359: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs fn = "data/long_testseqs.fasta" aln = load_aligned_seqs(fn, moltype="dna") print(aln[:24]) /<>/doc/cookbook/alignments.rst:369: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: TypeError from cogent3 import load_unaligned_seqs fn = "data/long_testseqs.fasta" seqs = load_unaligned_seqs(fn) print(seqs[:24]) /<>/doc/cookbook/alignments.rst:381: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs seq = load_aligned_seqs("data/test.paml") column_four = aln[3] /<>/doc/cookbook/alignments.rst:391: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta") region = aln[50:70] /<>/doc/cookbook/alignments.rst:401: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta") col = aln[113:115].iter_positions() type(col) list(col) /<>/doc/cookbook/alignments.rst:415: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data={"seq1": "ATGATGATG---", "seq2": "ATGATGATGATG"}, array_align=False ) list(range(len(aln))[2::3]) indices = [(i, i + 1) for i in range(len(aln))[2::3]] indices pos3 = aln.add_feature("pos3", "pos3", indices) pos3 = pos3.get_slice() print(pos3) /<>/doc/cookbook/alignments.rst:434: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data={"seq1": "ATGATGATG---", "seq2": "ATGATGATGATG"}, array_align=True ) pos3 = aln[2::3] print(pos3) /<>/doc/cookbook/alignments.rst:454: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data={"seq1": "ACGTAA---", "seq2": "ACGACA---", "seq3": "ACGCAATGA"}, moltype="dna", ) new = aln.trim_stop_codons() print(new) /<>/doc/cookbook/alignments.rst:467: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( data={ "seq1": "ACGTAA---", "seq2": "ACGAC----", # terminal codon incomplete "seq3": "ACGCAATGA", }, moltype="dna", ) new = aln.trim_stop_codons(allow_partial=True) print(new) /<>/doc/cookbook/alignments.rst:485: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[ ("seq1", "ATGAAGGTG---"), ("seq2", "ATGAAGGTGATG"), ("seq3", "ATGAAGGNGATG"), ], moltype="dna", ) /<>/doc/cookbook/alignments.rst:500: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: nucs = aln.no_degenerates() print(nucs) /<>/doc/cookbook/alignments.rst:507: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: trinucs = aln.no_degenerates(motif_length=3) print(trinucs) /<>/doc/cookbook/alignments.rst:515: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta") pos = aln.variable_positions() just_variable_aln = aln.take_positions(pos) print(just_variable_aln[:10]) /<>/doc/cookbook/alignments.rst:527: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta") pos = aln.variable_positions() just_constant_aln = aln.take_positions(pos, negate=True) print(just_constant_aln[:10]) /<>/doc/cookbook/alignments.rst:541: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta") variable_codons = aln.filtered( lambda x: len(set(map(tuple, x))) > 1, motif_length=3 ) print(just_variable_aln[:9]) /<>/doc/cookbook/alignments.rst:553: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = aln.to_type(array_align=False) variable_codons = aln.filtered(lambda x: len(set("".join(x))) > 1, motif_length=3) print(just_variable_aln[:9]) /<>/doc/cookbook/alignments.rst:567: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta") aln.take_seqs(["Human", "Mouse"]) /<>/doc/cookbook/alignments.rst:576: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.take_seqs(["Human", "Mouse"], negate=True) /<>/doc/cookbook/alignments.rst:585: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[ ("seq1", "ATGAAGGTG---"), ("seq2", "ATGAAGGTGATG"), ("seq3", "ATGAAGGNGATG"), ], moltype="dna", ) def no_N_chars(s): return "N" not in s aln.take_seqs_if(no_N_chars) /<>/doc/cookbook/alignments.rst:605: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.take_seqs_if(no_N_chars, negate=True) /<>/doc/cookbook/alignments.rst:617: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[ ("seq1", "ATGAAGGTG---"), ("seq2", "ATGAAGGTGATG"), ("seq3", "ATGAAGGNGATG"), ], moltype="dna", ) counts = aln.counts() print(counts) counts = aln.counts(motif_length=3) print(counts) counts = aln.counts(include_ambiguity=True) print(counts) /<>/doc/cookbook/alignments.rst:645: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta", moltype="dna") motif_probs = aln.get_motif_probs() print(motif_probs) /<>/doc/cookbook/alignments.rst:655: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, DNA trinuc_alphabet = DNA.alphabet.get_word_alphabet(3) aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta", moltype="dna") motif_probs = aln.get_motif_probs(alphabet=trinuc_alphabet) for m in sorted(motif_probs, key=lambda x: motif_probs[x], reverse=True): print("%s %.3f" % (m, motif_probs[m])) /<>/doc/cookbook/alignments.rst:669: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs(data=[("a", "AACAAC"), ("b", "AAGAAG")], moltype="dna") motif_probs = aln.get_motif_probs() assert motif_probs["T"] == 0.0 motif_probs = aln.get_motif_probs(pseudocount=1e-6) assert 0 < motif_probs["T"] <= 1e-6 /<>/doc/cookbook/alignments.rst:681: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: seqs = [("a", "AACGTAAG"), ("b", "AACGTAAG")] aln = make_aligned_seqs(data=seqs, moltype="dna") dinuc_alphabet = DNA.alphabet.get_word_alphabet(2) motif_probs = aln.get_motif_probs(alphabet=dinuc_alphabet) assert motif_probs["AA"] == 0.25 /<>/doc/cookbook/alignments.rst:691: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: seqs = [("my_seq", "AAAGTAAG")] aln = make_aligned_seqs(data=seqs, moltype="dna") my_seq = aln.get_seq("my_seq") my_seq.count("AA") "AAA".count("AA") "AAAA".count("AA") /<>/doc/cookbook/alignments.rst:702: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq seq = make_seq(moltype="dna", seq="AAAGTAAG") seq di_nucs = [seq[i : i + 2] for i in range(len(seq) - 1)] sum([nn == "AA" for nn in di_nucs]) /<>/doc/cookbook/alignments.rst:717: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta") col = aln[113:115].iter_positions() c1, c2 = list(col) c1, c2 list(filter(lambda x: x == "-", c1)) list(filter(lambda x: x == "-", c2)) /<>/doc/cookbook/alignments.rst:731: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta") for column in aln[113:150].iter_positions(): ungapped = list(filter(lambda x: x == "-", column)) gap_fraction = len(ungapped) * 1.0 / len(column) print(gap_fraction) /<>/doc/cookbook/alignments.rst:746: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[ ("seq1", "ATGAAGG-TG--"), ("seq2", "ATG-AGGTGATG"), ("seq3", "ATGAAG--GATG"), ], moltype="dna", ) seq_to_aln_map = aln.get_gapped_seq("seq1").gap_maps()[0] /<>/doc/cookbook/alignments.rst:762: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq_to_aln_map[3] seq_to_aln_map[8] /<>/doc/cookbook/alignments.rst:771: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln_to_seq_map = aln.get_gapped_seq("seq1").gap_maps()[1] aln_to_seq_map[3] aln_to_seq_map[8] /<>/doc/cookbook/alignments.rst:779: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: KeyError seq_pos = aln_to_seq_map[7] /<>/doc/cookbook/alignments.rst:793: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( data=[ ("seq1", "ATGAA---TG-"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG"), ], moltype="dna", ) print(aln.omit_gap_runs(2)) /<>/doc/cookbook/alignments.rst:807: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( data=[ ("seq1", "ATGAA---TG-"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG"), ], moltype="dna", ) print(aln.omit_gap_pos(0.40)) /<>/doc/cookbook/alignments.rst:821: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( data=[ ("seq1", "ATGAA------"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG"), ], moltype="dna", ) filtered_aln = aln.omit_gap_seqs(0.50) print(filtered_aln) /<>/doc/cookbook/alignments.rst:836: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(filtered_aln.omit_gap_pos()) /<>/doc/cookbook/alphabet.rst:11: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA, PROTEIN print(DNA.alphabet) print(PROTEIN.alphabet) /<>/doc/cookbook/alphabet.rst:20: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: PROTEIN.alphabet.moltype == PROTEIN /<>/doc/cookbook/alphabet.rst:29: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: dinuc_alphabet = DNA.alphabet.get_word_alphabet(2) print(dinuc_alphabet) trinuc_alphabet = DNA.alphabet.get_word_alphabet(3) print(trinuc_alphabet) /<>/doc/cookbook/alphabet.rst:39: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = "TAGT" indices = DNA.alphabet.to_indices(seq) indices /<>/doc/cookbook/alphabet.rst:48: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = DNA.alphabet.from_indices([0, 2, 3, 0]) seq /<>/doc/cookbook/alphabet.rst:55: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = DNA.alphabet.from_ordinals_to_seq([0, 2, 3, 0]) seq /<>/doc/cookbook/annotations.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/cookbook/annotations.rst:21: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.genbank import RichGenbankParser parser = RichGenbankParser(open("data/ST_genome_part.gb")) for accession, seq in parser: print(accession) /<>/doc/cookbook/annotations.rst:29: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: cds = seq.get_annotations_matching("CDS") print(cds) /<>/doc/cookbook/annotations.rst:39: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.core.annotation import Feature def add_annotation(seq, feature, spans): type_ = feature["type"] if type_ != "CDS": return name = feature.get("locus_tag", None) if name and not isinstance(name, str): name = " ".join(name) seq.add_annotation(Feature, type_, name, spans) parser = RichGenbankParser( open("data/ST_genome_part.gb"), add_annotation=add_annotation ) for accession, seq in parser: # just reading one accession,sequence break genes = seq.get_annotations_matching("CDS") print(genes) /<>/doc/cookbook/annotations.rst:63: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA from cogent3.core.annotation import Feature s1 = DNA.make_seq( "AAGAAGAAGACCCCCAAAAAAAAAA" "TTTTTTTTTTAAAAAGGGAACCCT", name="seq1" ) print(s1[10:15]) # this will be exon 1 print(s1[30:40]) # this will be exon 2 print(s1[45:48]) # this will be exon 3 s2 = DNA.make_seq("CGAAACGTTT", name="seq2") s3 = DNA.make_seq("CGAAACGTTT", name="seq3") /<>/doc/cookbook/annotations.rst:83: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA from cogent3.core.annotation import Feature s1 = DNA.make_seq( "AAGAAGAAGACCCCCAAAAAAAAAA" "TTTTTTTTTTAAAAAGGGAACCCT", name="seq1" ) exon1 = s1.add_annotation(Feature, "exon", "A", [(10, 15)]) exon2 = s1.add_annotation(Feature, "exon", "B", [(30, 40)]) /<>/doc/cookbook/annotations.rst:97: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA s1 = DNA.make_seq( "AAGAAGAAGACCCCCAAAAAAAAAA" "TTTTTTTTTTAAAAAGGGAACCCT", name="seq1" ) exon3 = s1.add_feature("exon", "C", [(45, 48)]) /<>/doc/cookbook/annotations.rst:111: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA s2 = DNA.make_seq("CGAAACGTTT", name="seq2") cpgs_series = s2.add_feature("cpgsite", "cpg", [(0, 2), (5, 7)]) s3 = DNA.make_seq("CGAAACGTTT", name="seq3") cpg1 = s3.add_feature("cpgsite", "cpg", [(0, 2)]) cpg2 = s3.add_feature("cpgsite", "cpg", [(5, 7)]) /<>/doc/cookbook/annotations.rst:126: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA s1 = DNA.make_seq( "AAGAAGAAGACCCCCAAAAAAAAAA" "TTTTTTTTTTAAAAAGGGAACCCT", name="seq1" ) exon1 = s1.add_feature("exon", "A", [(10, 15)]) exon2 = s1.add_feature("exon", "B", [(30, 40)]) exon3 = s1.add_feature("exon", "C", [(45, 48)]) cds = s1.get_region_covering_all([exon1, exon2, exon3]) /<>/doc/cookbook/annotations.rst:143: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: cds.get_coordinates() /<>/doc/cookbook/annotations.rst:152: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: not_cds = cds.get_shadow() not_cds /<>/doc/cookbook/annotations.rst:159: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: cds /<>/doc/cookbook/annotations.rst:168: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln1 = make_aligned_seqs( data=[["x", "-AAACCCCCA"], ["y", "TTTT--TTTT"]], array_align=False ) seq_exon = aln1.get_seq("x").add_feature("exon", "A", [(3, 8)]) /<>/doc/cookbook/annotations.rst:182: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.core.annotation import Variable red_data = aln1.add_annotation( Variable, "redline", "align", [((0, 15), 1), ((15, 30), 2), ((30, 45), 3)] ) /<>/doc/cookbook/annotations.rst:195: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA s1 = DNA.make_seq( "AAGAAGAAGACCCCCAAAAAAAAAA" "TTTTTTTTTTAAAAAGGGAACCCT", name="seq1" ) exon1 = s1.add_feature("exon", "A", [(10, 15)]) exon2 = s1.add_feature("exon", "B", [(30, 40)]) s1[exon1] s1[10:15] /<>/doc/cookbook/annotations.rst:209: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: s1[exon2] exon2.get_slice() /<>/doc/cookbook/annotations.rst:217: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA s1 = DNA.make_seq( "AAGAAGAAGACCCCCAAAAAAAAAA" "TTTTTTTTTTAAAAAGGGAACCCT", name="seq1" ) exon1 = s1.add_feature("exon", "A", [(10, 15)]) exon2 = s1.add_feature("exon", "B", [(30, 40)]) exon3 = s1.add_feature("exon", "C", [(45, 48)]) cds = s1.get_region_covering_all([exon1, exon2, exon3]) print(s1[cds]) print(s1[exon1, exon2, exon3]) /<>/doc/cookbook/annotations.rst:233: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(s1) print(s1[exon1, exon2, exon3]) print(s1[exon2]) print(s1[exon3]) print(s1[exon1, exon3, exon2]) /<>/doc/cookbook/annotations.rst:244: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: ValueError s1[1:10, 9:15] s1[exon1, exon1] /<>/doc/cookbook/annotations.rst:252: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(s1.get_region_covering_all([exon3, exon3]).get_slice()) /<>/doc/cookbook/annotations.rst:259: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(s1[exon2]) ex2_start = exon2[0:3] print(s1[ex2_start]) ex2_end = exon2[-3:] print(s1[ex2_end]) /<>/doc/cookbook/annotations.rst:272: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: ValueError aln1[seq_exon] /<>/doc/cookbook/annotations.rst:282: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln2 = make_aligned_seqs( data=[["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False ) seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCC", "x") match_exon = seq.add_feature("exon", "A", [(3, 8)]) aln2.get_seq("x").copy_annotations(seq) copied = list(aln2.get_annotations_from_seq("x", "exon")) copied /<>/doc/cookbook/annotations.rst:295: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln2 = make_aligned_seqs(data=[["x", "-AAAA"], ["y", "TTTTT"]], array_align=False) seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCC", "x") match_exon = seq.add_feature("exon", "A", [(5, 8)]) aln2.get_seq("x").copy_annotations(seq) copied = list(aln2.get_annotations_from_seq("x", "exon")) copied copied[0].get_slice() /<>/doc/cookbook/annotations.rst:307: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: # new test aln2 = make_aligned_seqs( data=[["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False ) seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCC", "x") match_exon = seq.add_feature("exon", "A", [(5, 8)]) aln2.get_seq("y").copy_annotations(seq) copied = list(aln2.get_annotations_from_seq("y", "exon")) copied /<>/doc/cookbook/annotations.rst:321: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln2 = make_aligned_seqs( data=[["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False ) diff_len_seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCCCCCCCCCC", "x") nonmatch = diff_len_seq.add_feature("repeat", "A", [(12, 14)]) aln2.get_seq("y").copy_annotations(diff_len_seq) copied = list(aln2.get_annotations_from_seq("y", "repeat")) copied /<>/doc/cookbook/annotations.rst:337: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln_exon = aln1.get_annotations_from_any_seq("exon") print(aln1[aln_exon]) /<>/doc/cookbook/annotations.rst:345: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: ValueError cpgsite2 = s2.get_annotations_matching("cpgsite") print(s2[cpgsite2]) cpgsite3 = s3.get_annotations_matching("cpgsite") s2[cpgsite3] /<>/doc/cookbook/annotations.rst:358: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: # this test is new dont_exist = s2.get_annotations_matching("dont_exist") dont_exist s2[dont_exist] /<>/doc/cookbook/annotations.rst:370: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln3 = make_aligned_seqs( data=[["x", "C-CCCAAAAA"], ["y", "-T----TTTT"]], array_align=False ) exon = aln3.get_seq("x").add_feature("exon", "ex1", [(0, 4)]) print(exon.get_slice()) aln_exons = list(aln3.get_annotations_from_seq("x", "exon")) print(aln_exons) print(aln3[aln_exons]) /<>/doc/cookbook/annotations.rst:388: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: unified = aln_exons[0].as_one_span() print(aln3[unified]) /<>/doc/cookbook/annotations.rst:398: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: plus = DNA.make_seq("CCCCCAAAAAAAAAATTTTTTTTTTAAAGG") plus_rpt = plus.add_feature("blah", "a", [(5, 15), (25, 28)]) print(plus[plus_rpt]) minus = plus.rc() print(minus) minus_rpt = minus.get_annotations_matching("blah") print(minus[minus_rpt]) /<>/doc/cookbook/annotations.rst:413: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.genbank import RichGenbankParser parser = RichGenbankParser(open("data/ST_genome_part.gb")) seq = [seq for accession, seq in parser][0] no_cds = seq.with_masked_annotations("CDS") print(no_cds[150:400]) /<>/doc/cookbook/annotations.rst:429: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[["x", "C-CCCAAAAAGGGAA"], ["y", "-T----TTTTG-GTT"]], moltype="dna", array_align=False, ) exon = aln.get_seq("x").add_feature("exon", "norwegian", [(0, 4)]) print(aln.with_masked_annotations("exon", mask_char="?")) /<>/doc/cookbook/annotations.rst:443: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: rc = aln.rc() print(rc) print(rc.with_masked_annotations("exon", mask_char="?")) /<>/doc/cookbook/annotations.rst:452: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA s = DNA.make_seq("CCCCAAAAAGGGAA", "x") exon = s.add_feature("exon", "norwegian", [(0, 4)]) rpt = s.add_feature("repeat", "norwegian", [(9, 12)]) rc = s.rc() print(s.with_masked_annotations("exon", shadow=True)) print(rc.with_masked_annotations("exon", shadow=True)) print(s.with_masked_annotations(["exon", "repeat"], shadow=True)) print(rc.with_masked_annotations(["exon", "repeat"], shadow=True)) /<>/doc/cookbook/annotations.rst:468: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA s = DNA.make_seq("ATGACCCTGTAAAAAATGTGTTAACCC", name="a") cds1 = s.add_feature("cds", "cds1", [(0, 12)]) cds2 = s.add_feature("cds", "cds2", [(15, 24)]) all_cds = s.get_annotations_matching("cds") all_cds /<>/doc/cookbook/annotations.rst:483: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.genbank import RichGenbankParser parser = RichGenbankParser(open("data/ST_genome_part.gb")) seq = [seq for accession, seq in parser][0] all_cds = seq.get_annotations_matching("CDS") coding_seqs = seq.get_region_covering_all(all_cds) coding_seqs coding_seqs.get_slice() noncoding_seqs = coding_seqs.get_shadow() noncoding_seqs noncoding_seqs.get_slice() /<>/doc/cookbook/annotations.rst:502: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False ) print(aln) exon = aln.get_seq("x").add_feature("exon", "1", [(3, 8)]) aln_exons = aln.get_annotations_from_seq("x", "exon") aln_exons = aln.get_annotations_from_any_seq("exon") aln_exons /<>/doc/cookbook/annotations.rst:522: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA seq = DNA.make_seq("aaaccggttt" * 10) v = seq.add_feature("exon", "exon", [(20, 35)]) v = seq.add_feature("repeat_unit", "repeat_unit", [(39, 49)]) v = seq.add_feature("repeat_unit", "rep2", [(49, 60)]) /<>/doc/cookbook/annotations.rst:536: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3.util.misc import remove_files remove_files(["annotated_%d.png" % i for i in range(1, 4)], error_on_missing=False) /<>/doc/cookbook/building_alignments.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/cookbook/building_alignments.rst:17: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs, make_tree from cogent3.align.progressive import TreeAlign /<>/doc/cookbook/building_alignments.rst:24: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: seqs = load_unaligned_seqs("data/test2.fasta", moltype="dna") aln, tree = TreeAlign("HKY85", seqs, show_progress=False) aln /<>/doc/cookbook/building_alignments.rst:32: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tree = make_tree( "(((NineBande:0.013,Mouse:0.185):0.023,DogFaced:0.046):0.027,Human:0.034,HowlerMon:0.019)" ) params = {"kappa": 4.0} aln, tree = TreeAlign( "HKY85", seqs, tree=tree, param_vals=params, show_progress=False ) aln /<>/doc/cookbook/building_alignments.rst:48: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs, make_tree from cogent3.align.progressive import TreeAlign seqs = load_unaligned_seqs("data/test2.fasta", moltype="dna") tree = make_tree( "((NineBande:0.058,Mouse:0.595):0.079,DogFaced:0.142,(HowlerMon:0.062,Human:0.103):0.079)" ) params = {"kappa": 4.0, "omega": 1.3} aln, tree = TreeAlign( "MG94HKY", seqs, tree=tree, param_vals=params, show_progress=False ) aln /<>/doc/cookbook/building_alignments.rst:68: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_unaligned_seqs from cogent3.evolve.models import get_model from cogent3.align.progressive import TreeAlign seqs = [ ( "hum", "AAGCAGATCCAGGAAAGCAGCGAGAATGGCAGCCTGGCCGCGCGCCAGGAGAGGCAGGCCCAGGTCAACCTCACT", ), ( "mus", "AAGCAGATCCAGGAGAGCGGCGAGAGCGGCAGCCTGGCCGCGCGGCAGGAGAGGCAGGCCCAAGTCAACCTCACG", ), ("rat", "CTGAACAAGCAGCCACTTTCAAACAAGAAA"), ] unaligned_DNA = make_unaligned_seqs(seqs, moltype="dna") print(unaligned_DNA) /<>/doc/cookbook/building_alignments.rst:88: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(unaligned_DNA.get_translation()) /<>/doc/cookbook/building_alignments.rst:94: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aligned_aa_seqs = [ ("hum", "KQIQESSENGSLAARQERQAQVNLT"), ("mus", "KQIQESGESGSLAARQERQAQVNLT"), ("rat", "LNKQ------PLS---------NKK"), ] aligned_aa = make_aligned_seqs(aligned_aa_seqs, moltype="protein") /<>/doc/cookbook/building_alignments.rst:107: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned_DNA = aligned_aa.replace_seqs(unaligned_DNA, aa_to_codon=True) aligned_DNA /<>/doc/cookbook/building_phylogenies.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/cookbook/building_phylogenies.rst:18: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") tree = aln.quick_tree(calc="TN93", show_progress=False) tree = tree.balanced() # purely for display print(tree.ascii_art()) /<>/doc/cookbook/building_phylogenies.rst:29: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tree = aln.quick_tree(calc="TN93", bootstrap=100, show_progress=False) /<>/doc/cookbook/building_phylogenies.rst:36: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") dists = aln.distance_matrix(calc="TN93") tree = dists.quick_tree(show_progress=False) tree = tree.balanced() # purely for display print(tree.ascii_art()) /<>/doc/cookbook/building_phylogenies.rst:49: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.phylo import nj from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") dists = aln.distance_matrix(calc="TN93") tree = nj.nj(dists, show_progress=False) tree = tree.balanced() # purely for display print(tree.ascii_art()) /<>/doc/cookbook/building_phylogenies.rst:63: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.phylo import nj dists = {("a", "b"): 2.7, ("c", "b"): 2.33, ("c", "a"): 0.73} tree = nj.nj(dists, show_progress=False) print(tree.ascii_art()) /<>/doc/cookbook/building_phylogenies.rst:76: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.deserialise import deserialise_object from cogent3.phylo.least_squares import WLS dists = deserialise_object("data/dists_for_phylo.json") ls = WLS(dists) stat, tree = ls.trex(a=5, k=5, show_progress=False) /<>/doc/cookbook/building_phylogenies.rst:92: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.phylo.maximum_likelihood import ML from cogent3.evolve.models import F81 aln = load_aligned_seqs("data/primate_brca1.fasta") ml = ML(F81(), aln) /<>/doc/cookbook/calc_genetic_distance.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/cookbook/calc_genetic_distance.rst:16: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_distances available_distances() /<>/doc/cookbook/calc_genetic_distance.rst:27: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") dists = aln.distance_matrix(calc="tn93", show_progress=False) dists /<>/doc/cookbook/calc_genetic_distance.rst:38: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, get_distance_calculator aln = load_aligned_seqs("data/primate_brca1.fasta") dist_calc = get_distance_calculator("tn93", alignment=aln) dist_calc /<>/doc/cookbook/calc_genetic_distance.rst:46: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: dist_calc.run(show_progress=False) dists = dist_calc.get_pairwise_distances() dists /<>/doc/cookbook/calc_genetic_distance.rst:54: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: dist_calc.stderr /<>/doc/cookbook/calc_genetic_distance.rst:65: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, get_model from cogent3.evolve import distance aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") d = distance.EstimateDistances(aln, submodel=get_model("F81")) d.run(show_progress=False) dists = d.get_pairwise_distances() dists /<>/doc/cookbook/evo_modelling.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/cookbook/evo_modelling.rst:18: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_models available_models() /<>/doc/cookbook/evo_modelling.rst:27: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model hky = get_model("HKY85") print(hky) /<>/doc/cookbook/evo_modelling.rst:44: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model sub_mod = get_model("GTR", with_rate=True, distribution="gamma") print(sub_mod) /<>/doc/cookbook/evo_modelling.rst:56: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model sub_mod = get_model("CNFGTR", with_rate=True, distribution="gamma") print(sub_mod) /<>/doc/cookbook/evo_modelling.rst:68: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model sub_mod = get_model("JTT92", with_rate=True, distribution="gamma") print(sub_mod) /<>/doc/cookbook/evo_modelling.rst:80: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree from cogent3.evolve.models import get_model sub_mod = get_model("F81") tree = make_tree("(a,b,(c,d))") lf = sub_mod.make_likelihood_function(tree) /<>/doc/cookbook/evo_modelling.rst:94: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree, make_aligned_seqs from cogent3.evolve.models import get_model sub_mod = get_model("F81") tree = make_tree("(a,b,(c,d))") lf = sub_mod.make_likelihood_function(tree) aln = make_aligned_seqs( [("a", "ACGT"), ("b", "AC-T"), ("c", "ACGT"), ("d", "AC-T")] ) lf.set_alignment(aln) /<>/doc/cookbook/evo_modelling.rst:112: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") print(tree.ascii_art()) /<>/doc/cookbook/evo_modelling.rst:120: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = get_model("CNFGTR") lf = sm.make_likelihood_function(tree, digits=2) lf.set_param_rule( "omega", tip_names=["Human", "Orangutan"], outgroup_name="Galago", clade=True, init=0.5, ) /<>/doc/cookbook/evo_modelling.rst:134: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf /<>/doc/cookbook/evo_modelling.rst:145: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") sm = get_model("CNFGTR") lf = sm.make_likelihood_function(tree, digits=2) lf.set_param_rule("omega", is_constant=True) /<>/doc/cookbook/evo_modelling.rst:160: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") sm = get_model("CNFGTR") lf = sm.make_likelihood_function(tree, digits=2) lf.set_param_rule("omega", init=0.1) /<>/doc/cookbook/evo_modelling.rst:175: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") sm = get_model("CNFGTR") lf = sm.make_likelihood_function(tree, digits=2) lf.set_param_rule("omega", init=0.1, lower=1e-9, upper=20.0) /<>/doc/cookbook/evo_modelling.rst:190: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") sm = get_model("F81") lf = sm.make_likelihood_function(tree) lf.set_param_rule("length", upper=1.0) /<>/doc/cookbook/evo_modelling.rst:207: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model sm = get_model("GTR", with_rate=True, distribution="gamma") tree = load_tree("data/primate_brca1.tree") lf = sm.make_likelihood_function(tree, bins=4, digits=2) lf.set_param_rule("bprobs", is_constant=True) /<>/doc/cookbook/evo_modelling.rst:222: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model sm = get_model("GTR", with_rate=True, distribution="gamma") tree = load_tree("data/primate_brca1.tree") lf = sm.make_likelihood_function(tree, bins=4, sites_independent=False, digits=2) lf.set_param_rule("bprobs", is_constant=True) /<>/doc/cookbook/evo_modelling.rst:239: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree, load_aligned_seqs from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) lf.optimise(show_progress=False) /<>/doc/cookbook/evo_modelling.rst:253: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(local=True, max_restarts=5, show_progress=False) /<>/doc/cookbook/evo_modelling.rst:259: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(local=False, global_tolerance=1.0, show_progress=False) /<>/doc/cookbook/evo_modelling.rst:265: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(show_progress=False, max_restarts=5, tolerance=1e-8) /<>/doc/cookbook/evo_modelling.rst:276: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree, load_aligned_seqs from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) try: lf.optimise( show_progress=False, limit_action="raise", max_evaluations=10, return_calculator=True, ) except ArithmeticError as err: print(err) /<>/doc/cookbook/evo_modelling.rst:303: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree, load_aligned_seqs from cogent3.evolve.models import get_model sm = get_model("GTR") tree = load_tree("data/primate_brca1.tree") lf = sm.make_likelihood_function(tree) aln = load_aligned_seqs("data/primate_brca1.fasta") lf.set_alignment(aln) lf.optimise(local=True, show_progress=False) lf /<>/doc/cookbook/evo_modelling.rst:321: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lnL = lf.lnL lnL /<>/doc/cookbook/evo_modelling.rst:326: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: nfp = lf.nfp nfp /<>/doc/cookbook/evo_modelling.rst:338: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.get_aic() /<>/doc/cookbook/evo_modelling.rst:344: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.get_aic(second_order=True) /<>/doc/cookbook/evo_modelling.rst:353: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.get_bic() /<>/doc/cookbook/evo_modelling.rst:367: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: a_g = lf.get_param_value("A/G") a_g /<>/doc/cookbook/evo_modelling.rst:372: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: human = lf.get_param_value("length", "Human") human /<>/doc/cookbook/evo_modelling.rst:380: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: mprobs = lf.get_motif_probs() mprobs /<>/doc/cookbook/evo_modelling.rst:388: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tables = lf.get_statistics(with_motif_probs=True, with_titles=True) tables[0] # just displaying the first /<>/doc/cookbook/evo_modelling.rst:398: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree, load_aligned_seqs from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) lf.set_param_rule( "length", tip_names=["Human", "Chimpanzee"], outgroup_name="Galago", clade=True, is_independent=False, ) lf.set_name("Null Hypothesis") lf.optimise(local=True, show_progress=False) null_lnL = lf.lnL null_nfp = lf.nfp lf /<>/doc/cookbook/evo_modelling.rst:423: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("length", is_independent=True) lf.set_name("Alt Hypothesis") lf.optimise(local=True, show_progress=False) alt_lnL = lf.lnL alt_nfp = lf.nfp lf /<>/doc/cookbook/evo_modelling.rst:434: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.stats import chisqprob LR = 2 * (alt_lnL - null_lnL) # the likelihood ratio statistic df = alt_nfp - null_nfp # the test degrees of freedom p = chisqprob(LR, df) print(f"LR={LR:.4f} ; df={df}; p={df:.4f}") /<>/doc/cookbook/evo_modelling.rst:450: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree, load_aligned_seqs from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) lf.set_param_rule( "length", tip_names=["Human", "Chimpanzee"], outgroup_name="Galago", clade=True, is_independent=False, ) lf.set_name("Null Hypothesis") lf.optimise(local=True, show_progress=False) sim_aln = lf.simulate_alignment() sim_aln[:60] /<>/doc/cookbook/evo_modelling.rst:478: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree, load_aligned_seqs from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("HKY85") lf = sm.make_likelihood_function(tree) lf.set_alignment(aln) lf.optimise(local=True, show_progress=False) kappa_lo, kappa_mle, kappa_hi = lf.get_param_interval("kappa") print(f"lo={kappa_lo:.2f} ; mle={kappa_mle:.2f} ; hi={kappa_hi:.2f}") human_lo, human_mle, human_hi = lf.get_param_interval("length", "Human") print(f"lo={human_lo:.2f} ; mle={human_mle:.2f} ; hi={human_hi:.2f}") /<>/doc/cookbook/evo_modelling.rst:501: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree, load_aligned_seqs from cogent3.evolve.models import get_model aln = make_aligned_seqs(data=dict(a="ACGG", b="ATAG", c="ATGG")) tree = make_tree(tip_names=aln.names) sm = get_model("F81") lf = sm.make_likelihood_function(tree) lf.set_alignment(aln) json = lf.to_json() json[:60] # just truncating the displayed string /<>/doc/cookbook/evo_modelling.rst:516: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.deserialise import deserialise_object newlf = deserialise_object(json) newlf /<>/doc/cookbook/evo_modelling.rst:528: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree, load_aligned_seqs from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) lf.optimise(show_progress=False) /<>/doc/cookbook/evo_modelling.rst:542: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: ancestors = lf.likely_ancestral_seqs() ancestors[:60] /<>/doc/cookbook/evo_modelling.rst:549: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: ancestral_probs = lf.reconstruct_ancestral_seqs() ancestral_probs["root"][:5] /<>/doc/cookbook/genetic_code.rst:4: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code standard_code = get_code(1) standard_code.translate("TTTGCAAAC") /<>/doc/cookbook/genetic_code.rst:16: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq, get_code standard_code = get_code(1) seq = make_seq("ATGCTAACATAAA", moltype="dna") translations = standard_code.sixframes(seq) print(translations) /<>/doc/cookbook/genetic_code.rst:28: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq, get_code standard_code = get_code(1) seq = make_seq("ATGCTAACATAAA", moltype="dna") stops_frame1 = standard_code.get_stop_indices(seq, start=0) stops_frame1 stop_index = stops_frame1[0] seq[stop_index : stop_index + 3] /<>/doc/cookbook/genetic_code.rst:42: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq, get_code standard_code = get_code(1) standard_code["TTT"] /<>/doc/cookbook/genetic_code.rst:51: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: standard_code["A"] /<>/doc/cookbook/genetic_code.rst:58: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code standard_code = get_code(1) standard_code["TTT"] /<>/doc/cookbook/genetic_code.rst:68: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code standard_code = get_code(1) standard_code["A"] /<>/doc/cookbook/genetic_code.rst:78: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: targets = ["A", "C"] codons = [standard_code[aa] for aa in targets] codons flat_list = sum(codons, []) flat_list /<>/doc/cookbook/genetic_code.rst:89: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGTT", moltype="dna") sorted(my_seq.codon_alphabet()) len(my_seq.codon_alphabet()) /<>/doc/cookbook/genetic_code.rst:102: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("ATGCACTGGTAA", name="my_gene", moltype="dna") codons = my_seq.get_in_motif_size(3) print(codons) /<>/doc/cookbook/genetic_code.rst:115: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: AlphabetError pep = my_seq.get_translation() /<>/doc/cookbook/genetic_code.rst:123: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("ATGCACTGGTAA", name="my_gene", moltype="dna") seq = my_seq.trim_stop_codon() pep = seq.get_translation() print(pep.to_fasta()) print(type(pep)) /<>/doc/cookbook/genetic_code.rst:136: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("CAAATGTATTAA", name="my_gene", moltype="dna") pep = my_seq[:-3].get_translation() print(pep.to_fasta()) /<>/doc/cookbook/loading_sequences.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/cookbook/loading_sequences.rst:16: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta", moltype="dna") type(aln) /<>/doc/cookbook/loading_sequences.rst:25: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.info.source /<>/doc/cookbook/loading_sequences.rst:38: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs seqs = load_unaligned_seqs("data/long_testseqs.fasta", moltype="dna") type(seqs) /<>/doc/cookbook/loading_sequences.rst:50: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta", moltype="dna", format="fasta") aln /<>/doc/cookbook/loading_sequences.rst:62: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs protein_seqs = [">seq1", "DEKQL-RG", ">seq2", "DDK--SRG"] proteins_loaded = make_aligned_seqs(protein_seqs) proteins_loaded.moltype print(proteins_loaded) proteins_loaded = make_aligned_seqs(protein_seqs, moltype="protein") print(proteins_loaded) /<>/doc/cookbook/loading_sequences.rst:81: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs seqs = {"seq1": "AATCG-A", "seq2": "AATCGGA"} seqs_loaded = make_aligned_seqs(seqs) /<>/doc/cookbook/loading_sequences.rst:91: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs seqs = [">seq1", "AATCG-A", ">seq2", "AATCGGA"] seqs_loaded = make_aligned_seqs(seqs) print(seqs_loaded) /<>/doc/cookbook/loading_sequences.rst:104: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs DNA_seqs = [ ">sample1 Mus musculus", "AACCTGC--C", ">sample2 Gallus gallus", "AAC-TGCAAC", ] loaded_seqs = make_aligned_seqs( DNA_seqs, moltype="dna", label_to_name=lambda x: x.split()[0] ) loaded_seqs /<>/doc/cookbook/loading_sequences.rst:124: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_unaligned_seqs seqs = {"seq1": "AATCA", "seq2": "AATCGGA"} seqs = make_unaligned_seqs(data=seqs, moltype="dna") seqs /<>/doc/cookbook/loading_sequences.rst:144: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.fasta import MinimalFastaParser f = open("data/long_testseqs.fasta") seqs = [(name, seq) for name, seq in MinimalFastaParser(f)] seqs /<>/doc/cookbook/loading_sequences.rst:157: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.fasta import LabelParser def latin_to_common(latin): return {"Homo sapiens": "human", "Pan troglodtyes": "chimp"}[latin] label_parser = LabelParser( "%(species)s", [[1, "species", latin_to_common]], split_with=":" ) for label in ">abcd:Homo sapiens:misc", ">abcd:Pan troglodtyes:misc": label = label_parser(label) print(label, type(label)) /<>/doc/cookbook/loading_sequences.rst:173: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.fasta import MinimalFastaParser, LabelParser fasta_data = [ ">gi|10047090|ref|NP_055147.1| small muscle protein, X-linked [Homo sapiens]", "MNMSKQPVSNVRAIQANINIPMGAFRPGAGQPPRRKECTPEVEEGVPPTSDEEKKPIPGAKKLPGPAVNL", "SEIQNIKSELKYVPKAEQ", ">gi|10047092|ref|NP_037391.1| neuronal protein [Homo sapiens]", "MANRGPSYGLSREVQEKIEQKYDADLENKLVDWIILQCAEDIEHPPPGRAHFQKWLMDGTVLCKLINSLY", "PPGQEPIPKISESKMAFKQMEQISQFLKAAETYGVRTTDIFQTVDLWEGKDMAAVQRTLMALGSVAVTKD", ] label_to_name = LabelParser( "%(ref)s", [[1, "gi", str], [3, "ref", str], [4, "description", str]], split_with="|", ) for name, seq in MinimalFastaParser(fasta_data, label_to_name=label_to_name): print(name) print(name.info.gi) print(name.info.description) /<>/doc/cookbook/loading_tabular.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/cookbook/loading_tabular.rst:11: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") table /<>/doc/cookbook/loading_tabular.rst:27: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", sep="\t") table /<>/doc/cookbook/loading_tabular.rst:44: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import load_delimited header, rows, title, legend = load_delimited("data/CerebellumDukeDNaseSeq.pk", header=False, sep="\t") rows[:4] /<>/doc/cookbook/loading_tabular.rst:54: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(with_header=False, sep="\t") rows = list(reader("data/CerebellumDukeDNaseSeq.pk")) rows[:4] /<>/doc/cookbook/loading_tabular.rst:70: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", limit=2) table /<>/doc/cookbook/loading_tabular.rst:82: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser( lambda line: float(line[2]) <= 10, with_header=True, sep="\t" ) table = load_table("data/stats.tsv", reader=reader, digits=1) table /<>/doc/cookbook/loading_tabular.rst:94: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: reader = FilteringParser( lambda line: float(line[2]) <= 10, with_header=True, sep="\t", negate=True ) table = load_table("data/stats.tsv", reader=reader, digits=1) table /<>/doc/cookbook/loading_tabular.rst:107: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(columns=["Locus", "Ratio"], with_header=True, sep="\t") table = load_table("data/stats.tsv", reader=reader) table /<>/doc/cookbook/loading_tabular.rst:117: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(columns=[0, -1], with_header=True, sep="\t") table = load_table("data/stats.tsv", reader=reader) table /<>/doc/cookbook/loading_tabular.rst:132: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(with_header=True, sep="\t") data = list(reader("data/stats.tsv")) /<>/doc/cookbook/loading_tabular.rst:141: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: data[:2] /<>/doc/cookbook/loading_tabular.rst:150: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table header = ["A", "B", "C"] rows = [range(3), range(3, 6), range(6, 9), range(9, 12)] table = make_table(header=["A", "B", "C"], data=rows) table /<>/doc/cookbook/loading_tabular.rst:164: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(A=[0, 3, 6], B=[1, 4, 7], C=[2, 5, 8]) table = make_table(data=data) table /<>/doc/cookbook/loading_tabular.rst:175: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(header=["C", "A", "B"], data=data) table /<>/doc/cookbook/loading_tabular.rst:185: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv", index_name="Locus") table["NP_055852"] /<>/doc/cookbook/loading_tabular.rst:190: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table["NP_055852", "Region"] /<>/doc/cookbook/loading_tabular.rst:199: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from pandas import DataFrame from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) df = DataFrame(data=data) table = make_table(data_frame=df) table /<>/doc/cookbook/loading_tabular.rst:213: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table(header=["a", "b"], data=[[0, "a"], [3, "c"]]) table /<>/doc/cookbook/loading_tabular.rst:225: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) table = make_table(data=data) table /<>/doc/cookbook/loading_tabular.rst:236: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table d2D = { "edge.parent": { "NineBande": "root", "edge.1": "root", "DogFaced": "root", "Human": "edge.0", }, "x": { "NineBande": 1.0, "edge.1": 1.0, "DogFaced": 1.0, "Human": 1.0, }, "length": { "NineBande": 4.0, "edge.1": 4.0, "DogFaced": 4.0, "Human": 4.0, }, } table = make_table( data=d2D, ) table /<>/doc/cookbook/loading_tabular.rst:268: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table( header=["abcd", "data"], data=[[range(1, 6), "0"], ["x", 5.0], ["y", None]], missing_data="*", digits=1, ) table /<>/doc/cookbook/loading_tabular.rst:283: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table() table /<>/doc/cookbook/moltypes.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/cookbook/moltypes.rst:17: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_moltypes available_moltypes() /<>/doc/cookbook/moltypes.rst:25: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs seqs = load_aligned_seqs("data/brca1-bats.fasta", moltype="dna") /<>/doc/cookbook/moltypes.rst:34: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_moltype dna = get_moltype("dna") dna /<>/doc/cookbook/moltypes.rst:46: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: dna.ambiguities /<>/doc/cookbook/moltypes.rst:53: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: dna.degenerates /<>/doc/cookbook/moltypes.rst:60: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: dna.complement("AGG") /<>/doc/cookbook/moltypes.rst:69: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = dna.make_seq("AGGCTT", name="seq1") seq /<>/doc/cookbook/moltypes.rst:77: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: rna = get_moltype("rna") rna.is_valid("ACGUACGUACGUACGU") /<>/doc/cookbook/moltypes.rst:87: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.core import moltype as mt DNAgapped = mt.MolType( seq_constructor=mt.DnaSequence, motifset=mt.IUPAC_DNA_chars, ambiguities=mt.IUPAC_DNA_ambiguities, complements=mt.IUPAC_DNA_ambiguities_complements, pairs=mt.DnaStandardPairs, gaps=".", ) seq = DNAgapped.make_seq("ACG.") seq /<>/doc/cookbook/moltypes.rst:104: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA from cogent3.core.sequence import DnaSequence DnaSequence.moltype = DNA /<>/doc/cookbook/protein_sequences.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/cookbook/protein_sequences.rst:14: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import PROTEIN p = PROTEIN.make_seq("THISISAPRQTEIN", "myProtein") type(p) str(p) /<>/doc/cookbook/protein_sequences.rst:25: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.core.genetic_code import DEFAULT as standard_code standard_code.translate("TTTGCAAAC") /<>/doc/cookbook/protein_sequences.rst:36: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs seq = load_aligned_seqs("data/abglobin_aa.phylip", moltype="protein") /<>/doc/cookbook/simple_trees.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/cookbook/simple_trees.rst:14: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.ascii_art()) /<>/doc/cookbook/simple_trees.rst:24: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") tr.write("data/temp.tree") /<>/doc/cookbook/simple_trees.rst:34: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") names = tr.get_node_names() names[:4] /<>/doc/cookbook/simple_trees.rst:42: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: names[4:] names_nodes = tr.get_nodes_dict() names_nodes["Human"] /<>/doc/cookbook/simple_trees.rst:48: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr.get_node_matching_name("Mouse") /<>/doc/cookbook/simple_trees.rst:55: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") hu = tr.get_node_matching_name("Human") tr.name /<>/doc/cookbook/simple_trees.rst:63: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: hu.name /<>/doc/cookbook/simple_trees.rst:70: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") nodes = tr.get_nodes_dict() hu = nodes["Human"] type(hu) /<>/doc/cookbook/simple_trees.rst:79: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: type(tr) /<>/doc/cookbook/simple_trees.rst:88: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") nodes = tr.get_nodes_dict() for n in nodes.items(): print(n) /<>/doc/cookbook/simple_trees.rst:99: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: for n in tr.iter_tips(): print(n) /<>/doc/cookbook/simple_trees.rst:106: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") for n in tr.iter_nontips(): print(n.get_newick()) /<>/doc/cookbook/simple_trees.rst:117: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") edges = tr.get_connecting_edges("edge.1", "Human") for edge in edges: print(edge.name) /<>/doc/cookbook/simple_trees.rst:129: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") nodes = tr.get_nodes_dict() hu = nodes["Human"] mu = nodes["Mouse"] hu.distance(mu) hu.is_tip() /<>/doc/cookbook/simple_trees.rst:143: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") nodes = tr.get_nodes_dict() hu = nodes["Human"] mu = nodes["Mouse"] lca = hu.last_common_ancestor(mu) lca /<>/doc/cookbook/simple_trees.rst:154: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: type(lca) /<>/doc/cookbook/simple_trees.rst:161: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") hu = tr.get_node_matching_name("Human") for a in hu.ancestors(): print(a.name) /<>/doc/cookbook/simple_trees.rst:173: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") node = tr.get_node_matching_name("edge.1") children = list(node.iter_tips()) + list(node.iter_nontips()) for child in children: print(child.name) /<>/doc/cookbook/simple_trees.rst:186: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") dists = tr.get_distances() /<>/doc/cookbook/simple_trees.rst:195: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: human_dists = [names for names in dists if "Human" in names] for dist in human_dists: print(dist, dists[dist]) /<>/doc/cookbook/simple_trees.rst:204: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") tr.max_tip_tip_distance() /<>/doc/cookbook/simple_trees.rst:214: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") hu = tr.get_node_matching_name("Human") tips = hu.tips_within_distance(0.2) for t in tips: print(t) /<>/doc/cookbook/simple_trees.rst:230: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.rooted_at("edge.0").ascii_art()) /<>/doc/cookbook/simple_trees.rst:240: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.root_at_midpoint().ascii_art()) /<>/doc/cookbook/simple_trees.rst:247: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.ascii_art()) /<>/doc/cookbook/simple_trees.rst:254: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.ascii_art()) /<>/doc/cookbook/simple_trees.rst:261: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.rooted_with_tip("Mouse").ascii_art()) /<>/doc/cookbook/simple_trees.rst:271: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") tr.get_newick() /<>/doc/cookbook/simple_trees.rst:278: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr.get_newick(with_distances=True) /<>/doc/cookbook/simple_trees.rst:285: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") xml = tr.get_xml() for line in xml.splitlines(): print(line) /<>/doc/cookbook/simple_trees.rst:299: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.ascii_art()) /<>/doc/cookbook/simple_trees.rst:309: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") for t in tr.preorder(): print(t.get_newick()) /<>/doc/cookbook/simple_trees.rst:320: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") for t in tr.postorder(): print(t.get_newick()) /<>/doc/cookbook/simple_trees.rst:334: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") for tip in tr.iter_nontips(): tip_names = tip.get_tip_names() print(tip_names) sub_tree = tr.get_sub_tree(tip_names) print(sub_tree.ascii_art()) /<>/doc/cookbook/simple_trees.rst:348: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3.util.misc import remove_files remove_files(["data/temp.tree", "data/temp.pdf"], error_on_missing=False) /<>/doc/cookbook/simple_trees.rst:364: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree simple_tree_string = "(B:0.2,(D:0.4)E:0.5)F;" simple_tree = make_tree(simple_tree_string) print(simple_tree.ascii_art()) /<>/doc/cookbook/simple_trees.rst:372: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: simple_tree.prune() print(simple_tree.ascii_art()) /<>/doc/cookbook/simple_trees.rst:377: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(simple_tree) /<>/doc/cookbook/simple_trees.rst:384: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr1 = load_tree("data/test.tree") print(tr1.get_newick()) /<>/doc/cookbook/simple_trees.rst:391: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr2 = tr1.unrooted_deepcopy() print(tr2.get_newick()) /<>/doc/cookbook/simple_trees.rst:401: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tree_string = "(B:0.2,H:0.2,(C:0.3,D:0.4,E:0.1)F:0.5)G;" tr = make_tree(tree_string) print(tr.ascii_art()) /<>/doc/cookbook/simple_trees.rst:409: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.bifurcating().ascii_art()) /<>/doc/cookbook/simple_trees.rst:422: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.ascii_art()) /<>/doc/cookbook/simple_trees.rst:429: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.balanced().ascii_art()) /<>/doc/cookbook/simple_trees.rst:438: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr1 = make_tree("(B:0.2,(C:0.2,D:0.2)F:0.2)G;") tr2 = make_tree("((C:0.1,D:0.1)F:0.1,B:0.1)G;") tr1.same_topology(tr2) /<>/doc/cookbook/simple_trees.rst:452: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = make_tree("(B:0.2,(C:0.3,D:0.4)F:0.5)G;") print(tr.ascii_art()) /<>/doc/cookbook/simple_trees.rst:459: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr.set_tip_distances() for t in tr.preorder(): print(t.name, t.TipDistance) /<>/doc/cookbook/simple_trees.rst:468: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = make_tree("(B:0.2,(C:0.3,D:0.4)F:0.5)G;") print(tr) /<>/doc/cookbook/simple_trees.rst:475: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr.scale_branch_lengths() print(tr) /<>/doc/cookbook/simple_trees.rst:485: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = make_tree("(B:3,(C:2,D:4)F:5)G;") d, tips = tr.tip_to_tip_distances() for i, t in enumerate(tips): print(t.name, d[i]) /<>/doc/cookbook/simple_trees.rst:505: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr1 = make_tree("(B:2,(C:3,D:4)F:5)G;") tr2 = make_tree("(C:2,(B:3,D:4)F:5)G;") tr1.compare_by_tip_distances(tr2) /<>/doc/cookbook/tables.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory cookbook/loading_tabular.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory cookbook/loading_tabular.rst:11: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") table cookbook/loading_tabular.rst:27: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", sep="\t") table cookbook/loading_tabular.rst:44: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import load_delimited header, rows, title, legend = load_delimited("data/CerebellumDukeDNaseSeq.pk", header=False, sep="\t") rows[:4] cookbook/loading_tabular.rst:54: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(with_header=False, sep="\t") rows = list(reader("data/CerebellumDukeDNaseSeq.pk")) rows[:4] cookbook/loading_tabular.rst:70: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", limit=2) table cookbook/loading_tabular.rst:82: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser( lambda line: float(line[2]) <= 10, with_header=True, sep="\t" ) table = load_table("data/stats.tsv", reader=reader, digits=1) table cookbook/loading_tabular.rst:94: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: reader = FilteringParser( lambda line: float(line[2]) <= 10, with_header=True, sep="\t", negate=True ) table = load_table("data/stats.tsv", reader=reader, digits=1) table cookbook/loading_tabular.rst:107: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(columns=["Locus", "Ratio"], with_header=True, sep="\t") table = load_table("data/stats.tsv", reader=reader) table cookbook/loading_tabular.rst:117: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(columns=[0, -1], with_header=True, sep="\t") table = load_table("data/stats.tsv", reader=reader) table cookbook/loading_tabular.rst:132: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(with_header=True, sep="\t") data = list(reader("data/stats.tsv")) cookbook/loading_tabular.rst:141: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: data[:2] cookbook/loading_tabular.rst:150: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table header = ["A", "B", "C"] rows = [range(3), range(3, 6), range(6, 9), range(9, 12)] table = make_table(header=["A", "B", "C"], data=rows) table cookbook/loading_tabular.rst:164: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(A=[0, 3, 6], B=[1, 4, 7], C=[2, 5, 8]) table = make_table(data=data) table cookbook/loading_tabular.rst:175: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(header=["C", "A", "B"], data=data) table cookbook/loading_tabular.rst:185: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv", index_name="Locus") table["NP_055852"] cookbook/loading_tabular.rst:190: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table["NP_055852", "Region"] cookbook/loading_tabular.rst:199: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from pandas import DataFrame from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) df = DataFrame(data=data) table = make_table(data_frame=df) table cookbook/loading_tabular.rst:213: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table(header=["a", "b"], data=[[0, "a"], [3, "c"]]) table cookbook/loading_tabular.rst:225: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) table = make_table(data=data) table cookbook/loading_tabular.rst:236: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table d2D = { "edge.parent": { "NineBande": "root", "edge.1": "root", "DogFaced": "root", "Human": "edge.0", }, "x": { "NineBande": 1.0, "edge.1": 1.0, "DogFaced": 1.0, "Human": 1.0, }, "length": { "NineBande": 4.0, "edge.1": 4.0, "DogFaced": 4.0, "Human": 4.0, }, } table = make_table( data=d2D, ) table cookbook/loading_tabular.rst:268: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table( header=["abcd", "data"], data=[[range(1, 6), "0"], ["x", 5.0], ["y", None]], missing_data="*", digits=1, ) table cookbook/loading_tabular.rst:283: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table() table /<>/doc/cookbook/tables.rst:21: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table() table.columns["a"] = [1, 3, 5] table.columns["b"] = [2, 4, 6] table /<>/doc/cookbook/tables.rst:35: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) table = make_table(data=data, title="Sample title", legend="a legend") table /<>/doc/cookbook/tables.rst:45: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: data = dict(a=[0, 3], b=["a", "c"]) table = make_table(data=data) table.title = "My title" table /<>/doc/cookbook/tables.rst:57: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") for row in table: print(row) break /<>/doc/cookbook/tables.rst:68: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: for row in table: print(row["Locus"]) /<>/doc/cookbook/tables.rst:78: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(a=[0, 3, 5], b=["a", "c", "d"]) table = make_table(data=data) table.shape[0] == 3 /<>/doc/cookbook/tables.rst:91: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.shape[1] == 2 /<>/doc/cookbook/tables.rst:100: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") table.columns /<>/doc/cookbook/tables.rst:107: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["Region"] /<>/doc/cookbook/tables.rst:113: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: for name in table.columns: print(name) /<>/doc/cookbook/tables.rst:121: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table /<>/doc/cookbook/tables.rst:128: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table[:2, "Region":] /<>/doc/cookbook/tables.rst:135: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table[:2, :1] /<>/doc/cookbook/tables.rst:145: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") table.format_column("Ratio", "%.1e") table /<>/doc/cookbook/tables.rst:158: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv", digits=1, space=2) table /<>/doc/cookbook/tables.rst:165: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.space = " " table /<>/doc/cookbook/tables.rst:175: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table h = ["name", "A/C", "A/G", "A/T", "C/A"] rows = [["tardigrade", 0.0425, 0.1424, 0.0226, 0.0391]] wrap_table = make_table(header=h, data=rows, max_width=30) wrap_table /<>/doc/cookbook/tables.rst:184: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: wrap_table = make_table(header=h, data=rows, max_width=30, index_name="name") wrap_table /<>/doc/cookbook/tables.rst:192: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(data=dict(a=list(range(10)), b=list(range(10)))) table.head() /<>/doc/cookbook/tables.rst:199: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.head(2) /<>/doc/cookbook/tables.rst:208: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.tail() /<>/doc/cookbook/tables.rst:214: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.tail(1) /<>/doc/cookbook/tables.rst:221: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.set_repr_policy(random=3) table /<>/doc/cookbook/tables.rst:229: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.set_repr_policy(head=2, tail=3) table /<>/doc/cookbook/tables.rst:241: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") print(table.header) table = table.with_new_header("Ratio", "Stat") print(table.header) /<>/doc/cookbook/tables.rst:251: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table() table /<>/doc/cookbook/tables.rst:258: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["a"] = [1, 3, 5] table.columns["b"] = [2, 4, 6] table /<>/doc/cookbook/tables.rst:269: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table = table.with_new_column( "LargeCon", lambda r_v: r_v[0] == "Con" and r_v[1] > 10.0, columns=["Region", "Ratio"], ) table /<>/doc/cookbook/tables.rst:282: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.array /<>/doc/cookbook/tables.rst:292: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") locus = table.tolist("Locus") locus /<>/doc/cookbook/tables.rst:300: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["Locus"].tolist() /<>/doc/cookbook/tables.rst:309: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") rows = table.tolist(["Region", "Locus"]) rows /<>/doc/cookbook/tables.rst:322: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.to_dict() /<>/doc/cookbook/tables.rst:332: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.columns.to_dict() /<>/doc/cookbook/tables.rst:340: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") df = table.to_dataframe() df /<>/doc/cookbook/tables.rst:348: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: df = table.to_dataframe(categories="Region") /<>/doc/cookbook/tables.rst:357: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(data={"Ts": [31, 58], "Tv": [36, 138], "": ["syn", "nsyn"]}, index_name="") table /<>/doc/cookbook/tables.rst:362: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: contingency = table.to_categorical(["Ts", "Tv"]) contingency /<>/doc/cookbook/tables.rst:367: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: g_test = contingency.G_independence() g_test /<>/doc/cookbook/tables.rst:374: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(data={"Ts": [31, 58], "Tv": [36, 138], "": ["syn", "nsyn"]}) contingency = table.to_categorical(["Ts", "Tv"], index_name="") /<>/doc/cookbook/tables.rst:386: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table1 = load_table("data/stats.tsv") table2 = load_table("data/stats.tsv") table = table1.appended(None, table2) table /<>/doc/cookbook/tables.rst:395: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table1.title = "Data1" table2.title = "Data2" table = table1.appended("Data#", table2, title="") table /<>/doc/cookbook/tables.rst:407: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.summed("Ratio") /<>/doc/cookbook/tables.rst:414: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["Ratio"].sum() /<>/doc/cookbook/tables.rst:423: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table all_numeric = make_table( header=["A", "B", "C"], data=[range(3), range(3, 6), range(6, 9), range(9, 12)] ) all_numeric /<>/doc/cookbook/tables.rst:434: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: all_numeric.summed() /<>/doc/cookbook/tables.rst:440: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: all_numeric.summed(col_sum=False) /<>/doc/cookbook/tables.rst:449: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: mixed = make_table( header=["A", "B", "C"], data=[["*", 1, 2], [3, "*", 5], [6, 7, "*"]] ) mixed /<>/doc/cookbook/tables.rst:458: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: mixed.summed(strict=False) /<>/doc/cookbook/tables.rst:464: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: mixed.summed(col_sum=False, strict=False) /<>/doc/cookbook/tables.rst:473: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") sub_table = table.filtered(lambda x: x < 10.0, columns="Ratio") sub_table /<>/doc/cookbook/tables.rst:481: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: sub_table = table.filtered("Ratio < 10.0") sub_table /<>/doc/cookbook/tables.rst:488: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: sub_table = table.filtered("Ratio < 10.0 and Region == 'NonCon'") sub_table /<>/doc/cookbook/tables.rst:498: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: big_numeric = all_numeric.filtered_by_column(lambda x: sum(x) > 20) big_numeric /<>/doc/cookbook/tables.rst:506: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.sorted(columns="Ratio") /<>/doc/cookbook/tables.rst:514: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.sorted(columns="Ratio", reverse="Ratio") /<>/doc/cookbook/tables.rst:521: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.sorted(columns=["Region", "Ratio"], reverse="Ratio") /<>/doc/cookbook/tables.rst:528: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") raw = table.tolist("Region") raw /<>/doc/cookbook/tables.rst:537: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") raw = table.tolist(["Locus", "Region"]) raw /<>/doc/cookbook/tables.rst:546: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") assert table.distinct_values("Region") == set(["NonCon", "Con"]) /<>/doc/cookbook/tables.rst:554: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") assert table.count("Region == 'NonCon' and Ratio > 1") == 1 /<>/doc/cookbook/tables.rst:564: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table( data=dict(A=["a", "b", "b", "b", "a"], B=["c", "c", "c", "c", "d"]) ) unique = table.count_unique("A") type(unique) /<>/doc/cookbook/tables.rst:574: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: unique /<>/doc/cookbook/tables.rst:580: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: unique = table.count_unique(["A", "B"]) unique /<>/doc/cookbook/tables.rst:585: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: r = unique.to_table() r /<>/doc/cookbook/tables.rst:595: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: rows = [ ["NP_004893", True], ["NP_005079", True], ["NP_005500", False], ["NP_055852", False], ] region_type = make_table(header=["Locus", "LargeCon"], data=rows) stats_table = load_table("data/stats.tsv") new = stats_table.joined(region_type, columns_self="Locus") new /<>/doc/cookbook/tables.rst:615: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table header = ["#OTU ID", "14SK041", "14SK802"] rows = [ [-2920, "332", 294], [-1606, "302", 229], [-393, 141, 125], [-2109, 138, 120], ] table = make_table(header=header, rows=rows) table /<>/doc/cookbook/tables.rst:631: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tp = table.transposed(new_column_name="sample", select_as_header="#OTU ID") tp /<>/doc/cookbook/tables.rst:641: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", format="md") print(table) /<>/doc/cookbook/tables.rst:653: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", format="tex") print(table) /<>/doc/cookbook/tables.rst:665: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") print(table.to_markdown(justify="ccr")) /<>/doc/cookbook/tables.rst:673: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table( "data/stats.tsv", title="Some stats.", legend="Derived from something." ) print(table.to_latex(justify="ccr", label="tab:table1")) /<>/doc/cookbook/tables.rst:683: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table( "data/stats.tsv", title="Some stats.", legend="Derived from something." ) print(table.to_rst(csv_table=True)) /<>/doc/cookbook/tables.rst:693: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table( "data/stats.tsv", title="Some stats.", legend="Derived from something." ) print(table.to_rst()) /<>/doc/cookbook/tables.rst:705: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") print(table.to_string(format="latex")) /<>/doc/cookbook/tables.rst:715: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: rows = [ ["1", 100, 101, 1.123], ["1", 101, 102, 1.123], ["1", 102, 103, 1.123], ["1", 103, 104, 1.123], ["1", 104, 105, 1.123], ["1", 105, 106, 1.123], ["1", 106, 107, 1.123], ["1", 107, 108, 1.123], ["1", 108, 109, 1], ["1", 109, 110, 1], ["1", 110, 111, 1], ["1", 111, 112, 1], ["1", 112, 113, 1], ["1", 113, 114, 1], ["1", 114, 115, 1], ["1", 115, 116, 1], ["1", 116, 117, 1], ["1", 117, 118, 1], ["1", 118, 119, 2], ["1", 119, 120, 2], ["1", 120, 121, 2], ["1", 150, 151, 2], ["1", 151, 152, 2], ["1", 152, 153, 2], ["1", 153, 154, 2], ["1", 154, 155, 2], ["1", 155, 156, 2], ["1", 156, 157, 2], ["1", 157, 158, 2], ["1", 158, 159, 2], ["1", 159, 160, 2], ["1", 160, 161, 2], ] bgraph = make_table(header=["chrom", "start", "end", "value"], rows=rows) /<>/doc/cookbook/tables.rst:754: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: bgraph.head() /<>/doc/cookbook/tables.rst:760: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print( bgraph.to_string( format="bedgraph", name="test track", description="test of bedgraph", color=(255, 0, 0), digits=0, ) ) /<>/doc/cookbook/tables.rst:775: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") straight_html = table.to_html() /<>/doc/cookbook/tables.rst:787: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.format.table import known_formats known_formats /<>/doc/cookbook/tables.rst:796: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.write("stats_tab.tex", justify="ccr", label="tab:table1") /<>/doc/cookbook/tables.rst:805: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.write("stats_tab.txt", sep="\t") /<>/doc/cookbook/tables.rst:812: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import pathlib for name in ("stats_tab.txt", "stats_tab.tex"): p = pathlib.Path(name) if p.exists(): p.unlink() cookbook/union_dict.rst:13: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.union_dict import UnionDict data = UnionDict(a=2, b={"c": 24, "d": [25]}) data.a cookbook/union_dict.rst:20: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: data["a"] cookbook/union_dict.rst:24: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: data.b.d cookbook/union_dict.rst:33: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.union_dict import UnionDict data = UnionDict(a=2, b={"c": 24, "d": [25]}) data.b |= {"d": 25} data.b cookbook/union_dict.rst:43: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: data.b.union({"d": [25]}) cookbook/union_dict.rst:47: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: data.b {"c": 24, "d": [25]} cookbook/union_dict.rst:55: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: KeyError from cogent3.util.union_dict import UnionDict data = UnionDict(a=2, b={"c": 24, "d": [25]}) data["k"] cookbook/union_dict.rst:65: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: AttributeError data.k /<>/doc/cookbook/useful_utilities.rst:16: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: import numpy def DiffOmega(omega): def omega_from_S(S): omega_est = S / (1 - numpy.e ** (-1 * S)) return abs(omega - omega_est) ** 2 return omega_from_S omega = 0.1 f = DiffOmega(omega) /<>/doc/cookbook/useful_utilities.rst:32: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.optimisers import minimise, maximise S = minimise( f, # the function xinit=1.0, # the initial value bounds=(-100, 100), # [lower,upper] bounds for the parameter local=True, # just local optimisation, not Simulated Annealing show_progress=False, ) assert 0.0 <= f(S) < 1e-6 print("S=%.4f" % S) /<>/doc/cookbook/useful_utilities.rst:58: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: TypeError from cogent3.util.misc import iterable my_var = 10 for i in my_var: print("will not work") for i in iterable(my_var): print(i) /<>/doc/cookbook/useful_utilities.rst:75: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import curry def foo(x, y): """Some function""" return x + y bar = curry(foo, 5) print(bar.__doc__) bar(10) /<>/doc/cookbook/useful_utilities.rst:92: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import is_iterable can_iter = [1, 2, 3, 4] cannot_iter = 1.234 is_iterable(can_iter) /<>/doc/cookbook/useful_utilities.rst:100: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: is_iterable(cannot_iter) /<>/doc/cookbook/useful_utilities.rst:109: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import is_char class foo: pass is_char("a") /<>/doc/cookbook/useful_utilities.rst:118: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: is_char("ab") /<>/doc/cookbook/useful_utilities.rst:122: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: is_char(foo()) /<>/doc/cookbook/useful_utilities.rst:131: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import recursive_flatten l = [[[[1, 2], "abcde"], [5, 6]], [7, 8], [9, 10]] /<>/doc/cookbook/useful_utilities.rst:137: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: recursive_flatten(l) /<>/doc/cookbook/useful_utilities.rst:146: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import not_list_tuple not_list_tuple(1) /<>/doc/cookbook/useful_utilities.rst:152: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: not_list_tuple([1]) /<>/doc/cookbook/useful_utilities.rst:156: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: not_list_tuple("ab") /<>/doc/cookbook/useful_utilities.rst:165: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import add_lowercase d = {"A": 5, "B": 6, "C": 7, "foo": 8, 42: "life"} add_lowercase(d) /<>/doc/cookbook/useful_utilities.rst:177: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import DistanceFromMatrix from numpy import array m = array([[1, 2, 3], [4, 5, 6], [7, 8, 9]]) f = DistanceFromMatrix(m) f(0, 0) /<>/doc/cookbook/useful_utilities.rst:186: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: f(1, 2) /<>/doc/cookbook/useful_utilities.rst:195: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import ClassChecker class not_okay(object): pass no = not_okay() class okay(object): pass o = okay() class my_dict(dict): pass md = my_dict() cc = ClassChecker(str, okay, dict) o in cc /<>/doc/cookbook/useful_utilities.rst:216: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: no in cc /<>/doc/cookbook/useful_utilities.rst:220: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: 5 in cc /<>/doc/cookbook/useful_utilities.rst:224: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: {"a": 5} in cc /<>/doc/cookbook/useful_utilities.rst:228: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: "asasas" in cc /<>/doc/cookbook/useful_utilities.rst:232: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: md in cc /<>/doc/cookbook/useful_utilities.rst:241: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import Delegator class ListAndString(list, Delegator): def __init__(self, items, string): Delegator.__init__(self, string) for i in items: self.append(i) ls = ListAndString([1, 2, 3], "ab_cd") len(ls) /<>/doc/cookbook/useful_utilities.rst:254: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls[0] /<>/doc/cookbook/useful_utilities.rst:258: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls.upper() /<>/doc/cookbook/useful_utilities.rst:262: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls.split("_") /<>/doc/cookbook/useful_utilities.rst:271: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import FunctionWrapper f = FunctionWrapper(str) f /<>/doc/cookbook/useful_utilities.rst:278: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: f(123) /<>/doc/cookbook/useful_utilities.rst:289: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import ConstrainedDict d = ConstrainedDict({"a": 1, "b": 2, "c": 3}, constraint="abc") d /<>/doc/cookbook/useful_utilities.rst:296: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: ConstraintError d["d"] = 5 /<>/doc/cookbook/what_codes.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/cookbook/what_codes.rst:10: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_codes available_codes() /<>/doc/cookbook/what_codes.rst:20: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs nt_seqs = load_aligned_seqs("data/brca1-bats.fasta", moltype="dna") nt_seqs[:21] /<>/doc/cookbook/what_codes.rst:29: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aa_seqs = nt_seqs.get_translation(gc=1, incomplete_ok=True) aa_seqs[:20] /<>/doc/cookbook/what_codes.rst:39: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code gc = get_code(4) gc /<>/doc/examples/align_codons_to_protein.rst:8: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_unaligned_seqs, make_aligned_seqs /<>/doc/examples/align_codons_to_protein.rst:14: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: seqs = { "hum": "AAGCAGATCCAGGAAAGCAGCGAGAATGGCAGCCTGGCCGCGCGCCAGGAGAGGCAGGCCCAGGTCAACCTCACT", "mus": "AAGCAGATCCAGGAGAGCGGCGAGAGCGGCAGCCTGGCCGCGCGGCAGGAGAGGCAGGCCCAAGTCAACCTCACG", "rat": "CTGAACAAGCAGCCACTTTCAAACAAGAAA", } unaligned_DNA = make_unaligned_seqs(seqs, moltype="dna") print(unaligned_DNA.to_fasta()) /<>/doc/examples/align_codons_to_protein.rst:26: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: unaligned_aa = unaligned_DNA.get_translation() print(unaligned_aa.to_fasta()) /<>/doc/examples/align_codons_to_protein.rst:33: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned_aa_seqs = { "hum": "KQIQESSENGSLAARQERQAQVNLT", "mus": "KQIQESGESGSLAARQERQAQVNLT", "rat": "LNKQ------PLS---------NKK", } aligned_aa = make_aligned_seqs(aligned_aa_seqs, moltype="protein") aligned_DNA = aligned_aa.replace_seqs(unaligned_DNA) aligned_DNA /<>/doc/examples/calculate_UPGMA_cluster.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/examples/calculate_UPGMA_cluster.rst:15: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.evolve import distance from cogent3.cluster.UPGMA import upgma /<>/doc/examples/calculate_UPGMA_cluster.rst:23: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import HKY85 /<>/doc/examples/calculate_UPGMA_cluster.rst:29: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/test.paml") /<>/doc/examples/calculate_UPGMA_cluster.rst:35: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: d = distance.EstimateDistances(al, submodel=HKY85()) d.run(show_progress=False) /<>/doc/examples/calculate_UPGMA_cluster.rst:42: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: mycluster = upgma(d.get_pairwise_distances()) print(mycluster.ascii_art()) /<>/doc/examples/calculate_UPGMA_cluster.rst:49: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: mycluster.write("test_upgma.tree") /<>/doc/examples/calculate_UPGMA_cluster.rst:55: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import os os.remove("test_upgma.tree") /<>/doc/examples/calculate_neigbourjoining_tree.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/examples/calculate_neigbourjoining_tree.rst:13: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.evolve import distance from cogent3.phylo import nj /<>/doc/examples/calculate_neigbourjoining_tree.rst:21: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model /<>/doc/examples/calculate_neigbourjoining_tree.rst:27: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/long_testseqs.fasta") /<>/doc/examples/calculate_neigbourjoining_tree.rst:33: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: d = distance.EstimateDistances(al, submodel=get_model("HKY85")) d.run(show_progress=False) /<>/doc/examples/calculate_neigbourjoining_tree.rst:40: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: mytree = nj.nj(d.get_pairwise_distances(), show_progress=False) print(mytree.ascii_art()) /<>/doc/examples/calculate_neigbourjoining_tree.rst:47: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: mytree.write("test_nj.tree") /<>/doc/examples/calculate_neigbourjoining_tree.rst:53: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import os os.remove("test_nj.tree") /<>/doc/examples/calculate_pairwise_distances.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/examples/calculate_pairwise_distances.rst:15: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.evolve import distance /<>/doc/examples/calculate_pairwise_distances.rst:22: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import HKY85 /<>/doc/examples/calculate_pairwise_distances.rst:28: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/long_testseqs.fasta") /<>/doc/examples/calculate_pairwise_distances.rst:34: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: d = distance.EstimateDistances(al, submodel=HKY85()) d.run(show_progress=False) d.get_pairwise_distances() /<>/doc/examples/calculate_pairwise_distances.rst:44: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: d.write("dists_for_phylo.phylip", format="phylip") /<>/doc/examples/calculate_pairwise_distances.rst:52: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: import pickle with open("dists_for_phylo.pickle", "wb") as f: pickle.dump(d.get_pairwise_distances(), f) /<>/doc/examples/calculate_pairwise_distances.rst:61: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import os for file_name in "dists_for_phylo.phylip", "dists_for_phylo.pickle": os.remove(file_name) /<>/doc/examples/codon_models.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/examples/codon_models.rst:36: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model /<>/doc/examples/codon_models.rst:42: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tf = get_model("GY94") nf = get_model("MG94GTR") cnf = get_model("CNFGTR") /<>/doc/examples/codon_models.rst:52: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") tree = load_tree("data/primate_brca1.tree") /<>/doc/examples/codon_models.rst:64: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = cnf.make_likelihood_function(tree, digits=2, space=3) lf.set_param_rule("omega", is_constant=True, value=1.0) /<>/doc/examples/codon_models.rst:73: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: optimiser_args = dict( local=True, max_restarts=5, tolerance=1e-8, show_progress=False ) lf.set_alignment(aln) lf.optimise(**optimiser_args) lf /<>/doc/examples/codon_models.rst:92: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: neutral_lnL = lf.get_log_likelihood() neutral_nfp = lf.get_num_free_params() lf.set_param_rule("omega", is_constant=False) lf.optimise(**optimiser_args) non_neutral_lnL = lf.get_log_likelihood() non_neutral_nfp = lf.get_num_free_params() lf /<>/doc/examples/codon_models.rst:104: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.stats import chisqprob LR = 2 * (non_neutral_lnL - neutral_lnL) df = non_neutral_nfp - neutral_nfp print(chisqprob(LR, df)) /<>/doc/examples/codon_models.rst:114: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Chimpanzee", "Human"], outgroup_name="Galago", clade=True ) lf.optimise(**optimiser_args) lf chimp_human_clade_lnL = lf.get_log_likelihood() chimp_human_clade_nfp = lf.get_num_free_params() /<>/doc/examples/codon_models.rst:124: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: LR = 2 * (chimp_human_clade_lnL - non_neutral_lnL) df = chimp_human_clade_nfp - non_neutral_nfp print(chisqprob(LR, df)) /<>/doc/examples/codon_models.rst:137: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = cnf.make_likelihood_function(tree, digits=2, space=3) lf.set_alignment(aln) lf.optimise(**optimiser_args) non_neutral_lnL = lf.get_log_likelihood() non_neutral_nfp = lf.get_num_free_params() /<>/doc/examples/codon_models.rst:149: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: annot_tree = lf.get_annotated_tree() omega_mle = lf.get_param_value("omega") /<>/doc/examples/codon_models.rst:156: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_lf = cnf.make_likelihood_function( annot_tree, bins=["neutral", "adaptive"], digits=2, space=3 ) /<>/doc/examples/codon_models.rst:164: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: epsilon = 1e-6 /<>/doc/examples/codon_models.rst:170: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_lf.set_param_rule("omega", bin="neutral", upper=1, init=omega_mle) rate_lf.set_param_rule( "omega", bin="adaptive", lower=1 + epsilon, upper=100, init=1 + 2 * epsilon ) /<>/doc/examples/codon_models.rst:179: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_lf.set_param_rule("bprobs", init=[1 - epsilon, epsilon]) /<>/doc/examples/codon_models.rst:185: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_lf.set_alignment(aln) rate_lf.optimise(**optimiser_args) rate_lnL = rate_lf.get_log_likelihood() rate_nfp = rate_lf.get_num_free_params() LR = 2 * (rate_lnL - non_neutral_lnL) df = rate_nfp - non_neutral_nfp rate_lf /<>/doc/examples/codon_models.rst:195: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(chisqprob(LR, df)) /<>/doc/examples/codon_models.rst:201: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: pp = rate_lf.get_bin_probs() /<>/doc/examples/codon_models.rst:212: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from numpy import array from cogent3 import make_table from IPython.core.display import HTML header = ['Site Class', 'Proportion', 'Background Edges', 'Foreground Edges'] data = {'Site Class': array(['0', '1', '2a', '2b'], dtype=' 1', '0 < omega0 < 1'], dtype='>/doc/examples/codon_models.rst:231: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_lf = cnf.make_likelihood_function(tree, bins=["0", "1"], digits=2, space=3) rate_lf.set_param_rule("omega", bin="0", upper=1.0 - epsilon, init=1 - epsilon) rate_lf.set_param_rule("omega", bins="1", is_constant=True, value=1.0) rate_lf.set_alignment(aln) rate_lf.optimise(**optimiser_args) tables = rate_lf.get_statistics(with_titles=True) for table in tables: if "bin" in table.title: print(table) /<>/doc/examples/codon_models.rst:245: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: globals = [t for t in tables if "global" in t.title][0] globals = dict(zip(globals.header, globals.tolist()[0])) bin_params = [t for t in tables if "bin" in t.title][0] rate_class_omegas = dict(bin_params.tolist(["bin", "omega"])) rate_class_probs = dict(bin_params.tolist(["bin", "bprobs"])) lengths = [t for t in tables if "edge" in t.title][0] lengths = dict(lengths.tolist(["edge", "length"])) /<>/doc/examples/codon_models.rst:257: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_branch_lf = cnf.make_likelihood_function( tree, bins=["0", "1", "2a", "2b"], digits=2, space=3 ) /<>/doc/examples/codon_models.rst:265: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: for branch, length in lengths.items(): rate_branch_lf.set_param_rule("length", edge=branch, init=length) /<>/doc/examples/codon_models.rst:272: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: for param, mle in globals.items(): rate_branch_lf.set_param_rule(param, init=mle) /<>/doc/examples/codon_models.rst:279: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_branch_lf.set_param_rule( "omega", bins=["0", "2a"], upper=1.0, init=rate_class_omegas["0"] ) rate_branch_lf.set_param_rule( "omega", bins=["1", "2b"], is_constant=True, value=1.0 ) rate_branch_lf.set_param_rule( "omega", bins=["2a", "2b"], edges=["Chimpanzee", "Human"], init=99, lower=1.0, upper=100.0, is_constant=False, ) /<>/doc/examples/codon_models.rst:299: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_branch_lf.set_param_rule( "bprobs", init=[ rate_class_probs["0"] - epsilon, rate_class_probs["1"] - epsilon, epsilon, epsilon, ], ) /<>/doc/examples/codon_models.rst:313: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_branch_lf.set_alignment(aln) /<>/doc/examples/coevolution.rst:10: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs from cogent3.core.alignment import ArrayAlignment from cogent3.evolve.coevolution import validate_alignment aln = make_aligned_seqs( {"1": "GAA", "2": "CTA", "3": "CTC", "4": "-TC"}, moltype="protein", array_align=True, ) validate_alignment(aln) /<>/doc/examples/coevolution.rst:25: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs from cogent3.core.alignment import ArrayAlignment aln = make_aligned_seqs( {"1": "AAA", "2": "CTA", "3": "CTC", "4": "-TC"}, moltype="protein", array_align=True, ) /<>/doc/examples/coevolution.rst:38: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.coevolution import coevolve_pair_functions, coevolve_pair coevolve_pair(coevolve_pair_functions["mi"], aln, pos1=1, pos2=2) /<>/doc/examples/coevolution.rst:46: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.coevolution import coevolve_pair_functions, coevolve_pair coevolve_pair(coevolve_pair_functions["sca"], aln, pos1=1, pos2=2, cutoff=0.5) /<>/doc/examples/coevolution.rst:54: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.coevolution import ( coevolve_position_functions, coevolve_position, ) coevolve_position(coevolve_position_functions["mi"], aln, position=1) /<>/doc/examples/coevolution.rst:65: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.coevolution import ( coevolve_alignment_functions, coevolve_alignment, ) coevolve_alignment(coevolve_alignment_functions["mi"], aln) /<>/doc/examples/coevolution.rst:76: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(coevolve_pair_functions.keys()) /<>/doc/examples/coevolution.rst:82: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.coevolution import ( coevolve_alignment_functions, coevolve_alignments, ) aln1 = make_aligned_seqs( { "human+protein1": "AAA", "pig+protein1": "CTA", "chicken+protein1": "CTC", "echidna+weird_db_identifier": "-TC", }, moltype="protein", array_align=True, ) aln2 = make_aligned_seqs( { "pig+protein2": "AAAY", "chicken+protein2": "CTAY", "echidna+protein2": "CTCF", "human+protein2": "-TCF", }, moltype="protein", array_align=True, ) coevolve_alignments(coevolve_alignment_functions["mi"], aln1, aln2) /<>/doc/examples/complete_seq_features.rst:8: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA from cogent3.core.annotation import Feature s = DNA.make_seq("AAGAAGAAGACCCCCAAAAAAAAAATTTTTTTTTTAAAAAAAAAAAAA", name="Orig") exon1 = s.add_annotation(Feature, "exon", "fred", [(10, 15)]) exon2 = s.add_annotation(Feature, "exon", "trev", [(30, 40)]) /<>/doc/examples/complete_seq_features.rst:19: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: s[exon1] exon1.get_slice() /<>/doc/examples/complete_seq_features.rst:26: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: exons = s.get_annotations_matching("exon") print(exons) /<>/doc/examples/complete_seq_features.rst:33: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: dont_exist = s.get_annotations_matching("dont_exist") dont_exist s[dont_exist] /<>/doc/examples/complete_seq_features.rst:41: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(s.get_region_covering_all(exons)) print(s.get_region_covering_all(exons).get_shadow()) /<>/doc/examples/complete_seq_features.rst:48: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: s.get_region_covering_all(exons).get_slice() /<>/doc/examples/complete_seq_features.rst:54: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: s[exon1, exon2] /<>/doc/examples/complete_seq_features.rst:60: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: ValueError print(s.get_region_covering_all(exons + exons)) s[exon1, exon1, exon1, exon1, exon1] /<>/doc/examples/complete_seq_features.rst:68: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: ValueError s[15:20, 5:16] /<>/doc/examples/complete_seq_features.rst:75: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: exon1[0:3].get_slice() /<>/doc/examples/complete_seq_features.rst:81: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: c = s[exon1[4:]] + s print(len(c)) for feat in c.annotations: print(feat) /<>/doc/examples/complete_seq_features.rst:90: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: ValueError print(c[exon1]) /<>/doc/examples/complete_seq_features.rst:97: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: len(s.annotations) region = s.get_region_covering_all(exons) len(s.annotations) region.attach() len(s.annotations) region.detach() len(s.annotations) /<>/doc/examples/complete_seq_features.rst:109: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: plus = DNA.make_seq("AAGGGGAAAACCCCCAAAAAAAAAATTTTTTTTTTAAA", name="plus") plus_cds = plus.add_annotation(Feature, "CDS", "gene", [(2, 6), (10, 15), (25, 35)]) print(plus_cds.get_slice()) minus = plus.rc() minus_cds = minus.get_annotations_matching("CDS")[0] print(minus_cds.get_slice()) /<>/doc/examples/complete_seq_features.rst:120: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( [["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False ) print(aln) exon = aln.get_seq("x").add_annotation(Feature, "exon", "fred", [(3, 8)]) aln_exons = aln.get_annotations_from_seq("x", "exon") aln_exons = aln.get_annotations_from_any_seq("exon") /<>/doc/examples/complete_seq_features.rst:134: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(exon) print(aln_exons[0]) print(aln_exons[0].get_slice()) aln_exons[0].attach() len(aln.annotations) /<>/doc/examples/complete_seq_features.rst:144: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: exons = aln.get_projected_annotations("y", "exon") print(exons) print(aln.get_seq("y")[exons[0].map.without_gaps()]) /<>/doc/examples/complete_seq_features.rst:152: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( [["x", "-AAAAAAAAA"], ["y", "TTTT--CCCC"]], array_align=False ) s = DNA.make_seq("AAAAAAAAA", name="x") exon = s.add_annotation(Feature, "exon", "fred", [(3, 8)]) exon = aln.get_seq("x").copy_annotations(s) aln_exons = list(aln.get_annotations_from_seq("x", "exon")) print(aln_exons) /<>/doc/examples/complete_seq_features.rst:165: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: exon = aln.get_seq("y").copy_annotations(s) aln_exons = list(aln.get_annotations_from_seq("y", "exon")) print(aln_exons) print(aln[aln_exons]) /<>/doc/examples/complete_seq_features.rst:174: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs([["x", "-AAAA"], ["y", "TTTTT"]], array_align=False) seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCC", "x") exon = seq.add_feature("exon", "A", [(5, 8)]) aln.get_seq("x").copy_annotations(seq) copied = list(aln.get_annotations_from_seq("x", "exon")) copied copied[0].get_slice() /<>/doc/examples/complete_seq_features.rst:186: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( [["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False ) seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCC", "x") match_exon = seq.add_feature("exon", "A", [(5, 8)]) aln.get_seq("y").copy_annotations(seq) copied = list(aln.get_annotations_from_seq("y", "exon")) copied /<>/doc/examples/complete_seq_features.rst:199: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( [["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False ) diff_len_seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCCCCCCCCCC", "x") nonmatch = diff_len_seq.add_feature("repeat", "A", [(12, 14)]) aln.get_seq("y").copy_annotations(diff_len_seq) copied = list(aln.get_annotations_from_seq("y", "repeat")) copied /<>/doc/examples/complete_seq_features.rst:212: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( [["x", "-AAAAAAAAA"], ["y", "------TTTT"]], array_align=False ) exon = aln.get_seq("x").add_feature("exon", "fred", [(3, 8)]) aln_exons = list(aln.get_annotations_from_seq("x", "exon")) print(aln_exons) print(aln_exons[0].get_slice()) aln = make_aligned_seqs( [["x", "-AAAAAAAAA"], ["y", "TTTT--T---"]], array_align=False ) exon = aln.get_seq("x").add_feature("exon", "fred", [(3, 8)]) aln_exons = list(aln.get_annotations_from_seq("x", "exon")) print(aln_exons[0].get_slice()) /<>/doc/examples/complete_seq_features.rst:230: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( [["x", "C-CCCAAAAA"], ["y", "-T----TTTT"]], moltype="dna", array_align=False ) print(aln) exon = aln.get_seq("x").add_feature("exon", "ex1", [(0, 4)]) print(exon) print(exon.get_slice()) aln_exons = list(aln.get_annotations_from_seq("x", "exon")) print(aln_exons) print(aln_exons[0].get_slice()) /<>/doc/examples/complete_seq_features.rst:245: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(aln_exons[0].as_one_span().get_slice()) /<>/doc/examples/complete_seq_features.rst:251: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln_rc = aln.rc() rc_exons = list(aln_rc.get_annotations_from_any_seq("exon")) print(aln_rc[rc_exons]) # not using as_one_span, so gap removed from x print(aln_rc[rc_exons[0].as_one_span()]) /<>/doc/examples/complete_seq_features.rst:260: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: all_exons = aln.get_region_covering_all(aln_exons) coords = all_exons.get_coordinates() assert coords == [(0, 1), (2, 5)] /<>/doc/examples/complete_seq_features.rst:270: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( [["x", "C-CCCAAAAAGGGAA"], ["y", "-T----TTTTG-GTT"]], array_align=False ) print(aln) exon = aln.get_seq("x").add_feature("exon", "norwegian", [(0, 4)]) print(exon.get_slice()) repeat = aln.get_seq("x").add_feature("repeat", "blue", [(9, 12)]) print(repeat.get_slice()) repeat = aln.get_seq("y").add_feature("repeat", "frog", [(5, 7)]) print(repeat.get_slice()) /<>/doc/examples/complete_seq_features.rst:285: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(aln.get_seq("x").with_masked_annotations("exon", mask_char="?")) print(aln.get_seq("x").with_masked_annotations("exon", mask_char="?", shadow=True)) print(aln.get_seq("x").with_masked_annotations(["exon", "repeat"], mask_char="?")) print( aln.get_seq("x").with_masked_annotations( ["exon", "repeat"], mask_char="?", shadow=True ) ) print(aln.get_seq("y").with_masked_annotations("exon", mask_char="?")) print(aln.get_seq("y").with_masked_annotations("repeat", mask_char="?")) print( aln.get_seq("y").with_masked_annotations("repeat", mask_char="?", shadow=True) ) /<>/doc/examples/complete_seq_features.rst:303: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(aln.with_masked_annotations("exon", mask_char="?")) print(aln.with_masked_annotations("exon", mask_char="?", shadow=True)) print(aln.with_masked_annotations("repeat", mask_char="?")) print(aln.with_masked_annotations("repeat", mask_char="?", shadow=True)) print(aln.with_masked_annotations(["repeat", "exon"], mask_char="?")) print(aln.with_masked_annotations(["repeat", "exon"], shadow=True)) /<>/doc/examples/complete_seq_features.rst:314: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: data = [["human", "CGAAACGTTT"], ["mouse", "CTAAACGTCG"]] as_series = make_aligned_seqs(data, array_align=False) as_items = make_aligned_seqs(data, array_align=False) /<>/doc/examples/complete_seq_features.rst:322: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: as_series.get_seq("human").add_feature("cpgsite", "cpg", [(0, 2), (5, 7)]) as_series.get_seq("mouse").add_feature("cpgsite", "cpg", [(5, 7), (8, 10)]) /<>/doc/examples/complete_seq_features.rst:329: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: as_items.get_seq("human").add_feature("cpgsite", "cpg", [(0, 2)]) as_items.get_seq("human").add_feature("cpgsite", "cpg", [(5, 7)]) as_items.get_seq("mouse").add_feature("cpgsite", "cpg", [(5, 7)]) as_items.get_seq("mouse").add_feature("cpgsite", "cpg", [(8, 10)]) /<>/doc/examples/complete_seq_features.rst:338: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: serial = as_series.with_masked_annotations(["cpgsite"]) print(serial) itemwise = as_items.with_masked_annotations(["cpgsite"]) print(itemwise) /<>/doc/examples/complete_seq_features.rst:347: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(plus.with_masked_annotations("CDS")) print(minus.with_masked_annotations("CDS")) /<>/doc/examples/empirical_protein_models.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/examples/empirical_protein_models.rst:13: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, make_tree from cogent3.evolve.substitution_model import EmpiricalProteinMatrix from cogent3.parse.paml_matrix import PamlMatrixParser /<>/doc/examples/empirical_protein_models.rst:21: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: treestring = "(((rabbit,rat),human),goat-cow,marsupial);" t = make_tree(treestring) /<>/doc/examples/empirical_protein_models.rst:28: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/abglobin_aa.phylip", moltype="protein") /<>/doc/examples/empirical_protein_models.rst:34: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: matrix_file = open("data/dayhoff.dat") /<>/doc/examples/empirical_protein_models.rst:40: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: empirical_matrix, empirical_frequencies = PamlMatrixParser(matrix_file) /<>/doc/examples/empirical_protein_models.rst:46: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = EmpiricalProteinMatrix(empirical_matrix, empirical_frequencies) /<>/doc/examples/empirical_protein_models.rst:52: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = sm.make_likelihood_function(t) lf.set_alignment(al) lf.optimise(show_progress=False) lf /<>/doc/examples/hmm_par_heterogeneity.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/examples/hmm_par_heterogeneity.rst:21: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.substitution_model import TimeReversibleNucleotide, predicate from cogent3 import load_aligned_seqs, load_tree from cogent3.maths.stats import chisqprob /<>/doc/examples/hmm_par_heterogeneity.rst:29: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs("data/long_testseqs.fasta") tree = load_tree("data/test.tree") /<>/doc/examples/hmm_par_heterogeneity.rst:39: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: MotifChange = predicate.MotifChange treat_gap = dict(recode_gaps=True, model_gaps=False) kappa = (~MotifChange("R", "Y")).aliased("kappa") model = TimeReversibleNucleotide(predicates=[kappa], **treat_gap) /<>/doc/examples/hmm_par_heterogeneity.rst:48: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf_one = model.make_likelihood_function(tree, digits=2, space=3) lf_one.set_alignment(aln) lf_one.optimise(show_progress=False) lnL_one = lf_one.get_log_likelihood() df_one = lf_one.get_num_free_params() lf_one /<>/doc/examples/hmm_par_heterogeneity.rst:62: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: bin_submod = TimeReversibleNucleotide( predicates=[kappa], ordered_param="rate", distribution="gamma", **treat_gap ) lf_bins = bin_submod.make_likelihood_function( tree, bins=2, sites_independent=True, digits=2, space=3 ) lf_bins.set_param_rule("bprobs", is_constant=True) lf_bins.set_alignment(aln) lf_bins.optimise(local=True, show_progress=False) lnL_bins = lf_bins.get_log_likelihood() df_bins = lf_bins.get_num_free_params() assert df_bins == 9 lf_bins /<>/doc/examples/hmm_par_heterogeneity.rst:83: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf_patches = bin_submod.make_likelihood_function( tree, bins=2, sites_independent=False, digits=2, space=3 ) lf_patches.set_param_rule("bprobs", is_constant=True) lf_patches.set_alignment(aln) lf_patches.optimise(local=True, show_progress=False) lnL_patches = lf_patches.get_log_likelihood() df_patches = lf_patches.get_num_free_params() lf_patches /<>/doc/examples/hmm_par_heterogeneity.rst:97: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: LR = lambda alt, null: 2 * (alt - null) /<>/doc/examples/hmm_par_heterogeneity.rst:103: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lr = LR(lnL_bins, lnL_one) lr /<>/doc/examples/hmm_par_heterogeneity.rst:108: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print("%.4f" % chisqprob(lr, df_patches - df_bins)) /<>/doc/examples/hmm_par_heterogeneity.rst:114: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: bprobs = lf_patches.get_param_value("bprobs") print("%.1f : %.1f" % tuple(bprobs)) /<>/doc/examples/hmm_par_heterogeneity.rst:121: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: pp = lf_patches.get_bin_probs() /<>/doc/examples/hmm_par_heterogeneity.rst:127: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(pp["bin0"][20]) /<>/doc/examples/hmm_par_heterogeneity.rst:140: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from numpy import array single_kappa = lf_one.get_param_value("kappa") /<>/doc/examples/hmm_par_heterogeneity.rst:148: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: kappa_bin_submod = TimeReversibleNucleotide(predicates=[kappa], **treat_gap) lf_kappa = kappa_bin_submod.make_likelihood_function( tree, bins=["slow", "fast"], sites_independent=False, digits=1, space=3 ) /<>/doc/examples/hmm_par_heterogeneity.rst:157: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: epsilon = 1e-6 lf_kappa.set_param_rule( kappa, init=single_kappa - epsilon, upper=single_kappa, bin="slow" ) lf_kappa.set_param_rule( kappa, init=single_kappa + epsilon, lower=single_kappa, bin="fast" ) /<>/doc/examples/hmm_par_heterogeneity.rst:169: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf_kappa.set_param_rule("bprobs", init=array([1.0 - epsilon, 0.0 + epsilon])) lf_kappa.set_alignment(aln) lf_kappa.optimise(local=True, show_progress=False) lf_kappa /<>/doc/examples/manipulating_tree_nodes.rst:8: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.core.tree import PhyloNode from cogent3 import load_tree, make_tree from cogent3.parse.tree import DndParser /<>/doc/examples/manipulating_tree_nodes.rst:24: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: simple_tree_string = "(B:0.2,(C:0.3,D:0.4)E:0.5)F;" complex_tree_string = "(((363564 AB294167.1 Alkalibacterium putridalgicola:0.0028006,55874 AB083411.1 Marinilactibacillus psychrotolerans:0.0022089):0.40998,(15050 Y10772.1 Facklamia hominis:0.32304,(132509 AY707780.1 Aerococcus viridans:0.58815,((143063 AY879307.1 Abiotrophia defectiva:0.5807,83619 AB042060.1 Bacillus schlegelii:0.23569):0.03586,169722 AB275483.1 Fibrobacter succinogenes:0.38272):0.06516):0.03492):0.14265):0.63594,(3589 M62687.1 Fibrobacter intestinalis:0.65866,314063 CP001146.1 Dictyoglomus thermophilum:0.38791):0.32147,276579 EU652053.1 Thermus scotoductus:0.57336);" simple_tree = make_tree(simple_tree_string) complex_tree = DndParser(complex_tree_string, PhyloNode) /<>/doc/examples/manipulating_tree_nodes.rst:35: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(simple_tree.ascii_art()) /<>/doc/examples/manipulating_tree_nodes.rst:41: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: A_node = PhyloNode(name="A", Length=0.1) /<>/doc/examples/manipulating_tree_nodes.rst:47: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(simple_tree.children) /<>/doc/examples/manipulating_tree_nodes.rst:53: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: simple_tree.children[1].remove("C") /<>/doc/examples/manipulating_tree_nodes.rst:59: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: simple_tree.children[1].insert(0, A_node) /<>/doc/examples/manipulating_tree_nodes.rst:65: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(simple_tree.ascii_art()) /<>/doc/examples/manipulating_tree_nodes.rst:71: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: simple_tree.children[1].remove("A") print(simple_tree.ascii_art()) /<>/doc/examples/manipulating_tree_nodes.rst:78: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: simple_tree.prune() print(simple_tree.ascii_art()) /<>/doc/examples/manipulating_tree_nodes.rst:90: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: for n in complex_tree.iter_tips(): n.name = n.name.split()[2] + " " + n.name.split()[3] /<>/doc/examples/manipulating_tree_nodes.rst:97: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(complex_tree.ascii_art(show_internal=False)) /<>/doc/examples/manipulating_tree_nodes.rst:105: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tips = complex_tree.tips() /<>/doc/examples/manipulating_tree_nodes.rst:111: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tips_to_delete = [] AEROCOCCUS_INDEX = 3 for n in tips: if tips[AEROCOCCUS_INDEX].distance(n) > 1.8: tips_to_delete.append(n) /<>/doc/examples/manipulating_tree_nodes.rst:121: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: for n in tips_to_delete: n.parent.remove(n) complex_tree.prune() /<>/doc/examples/manipulating_tree_nodes.rst:129: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(complex_tree.ascii_art(show_internal=False)) /<>/doc/examples/neutral_test.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/examples/neutral_test.rst:13: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model from cogent3.maths import stats /<>/doc/examples/neutral_test.rst:21: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/long_testseqs.fasta") t = load_tree("data/test.tree") /<>/doc/examples/neutral_test.rst:28: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = get_model("MG94GTR") /<>/doc/examples/neutral_test.rst:34: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = sm.make_likelihood_function(t, digits=2, space=2) /<>/doc/examples/neutral_test.rst:40: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_alignment(al) /<>/doc/examples/neutral_test.rst:46: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(global_tolerance=1.0, show_progress=False) /<>/doc/examples/neutral_test.rst:52: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf /<>/doc/examples/neutral_test.rst:58: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: null_lnL = lf.get_log_likelihood() null_nfp = lf.get_num_free_params() /<>/doc/examples/neutral_test.rst:65: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("omega", is_independent=True) /<>/doc/examples/neutral_test.rst:71: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(local=True, show_progress=False) /<>/doc/examples/neutral_test.rst:77: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf /<>/doc/examples/neutral_test.rst:83: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: at = lf.get_annotated_tree() /<>/doc/examples/neutral_test.rst:89: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: LR = 2 * (lf.get_log_likelihood() - null_lnL) df = lf.get_num_free_params() - null_nfp P = stats.chisqprob(LR, df) /<>/doc/examples/neutral_test.rst:97: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(f"Likelihood ratio statistic = {LR}") print(f"degrees-of-freedom = {df}") print(f"probability = {P}") /<>/doc/examples/parametric_bootstrap.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/examples/parametric_bootstrap.rst:17: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve import bootstrap from cogent3.evolve.models import HKY85 from cogent3.maths import stats /<>/doc/examples/parametric_bootstrap.rst:28: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: def create_alt_function(): t = load_tree("data/test.tree") sm = HKY85() return sm.make_likelihood_function(t) /<>/doc/examples/parametric_bootstrap.rst:37: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: def create_null_function(): lf = create_alt_function() # set the local clock for humans & howler monkey lf.set_local_clock("Human", "HowlerMon") return lf /<>/doc/examples/parametric_bootstrap.rst:47: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs("data/long_testseqs.fasta") /<>/doc/examples/parametric_bootstrap.rst:53: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: estimateP = bootstrap.EstimateProbability( create_null_function(), create_alt_function(), aln ) /<>/doc/examples/parametric_bootstrap.rst:61: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: estimateP.set_num_replicates(5) /<>/doc/examples/parametric_bootstrap.rst:67: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: estimateP.run(show_progress=False) /<>/doc/examples/parametric_bootstrap.rst:73: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: p = estimateP.get_estimated_prob() /<>/doc/examples/parametric_bootstrap.rst:79: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print("%.2f, %.2f" % estimateP.get_observed_lnL()) /<>/doc/examples/period_estimation.rst:26: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import numpy numpy.random.seed(11) /<>/doc/examples/period_estimation.rst:33: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: import numpy t = numpy.arange(0, 10, 0.1) n = numpy.random.randn(len(t)) nse = numpy.convolve(n, numpy.exp(-t / 0.05)) * 0.1 nse = nse[: len(t)] sig = numpy.sin(2 * numpy.pi * t) + nse /<>/doc/examples/period_estimation.rst:48: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import dft pwr, period = dft(sig) print(period) print(pwr) /<>/doc/examples/period_estimation.rst:58: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: pwr = abs(pwr) max_pwr, max_period = sorted(zip(pwr, period))[-1] print(max_pwr, max_period) /<>/doc/examples/period_estimation.rst:69: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import auto_corr pwr, period = auto_corr(sig) print(period) print(pwr) /<>/doc/examples/period_estimation.rst:79: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: max_pwr, max_period = sorted(zip(pwr, period))[-1] print(max_pwr, max_period) /<>/doc/examples/period_estimation.rst:89: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: s = ( "ATCGTTGGGACCGGTTCAAGTTTTGGAACTCGCAAGGGGTGAATGGTCTTCGTCTAACGCTGG" "GGAACCCTGAATCGTTGTAACGCTGGGGTCTTTAACCGTTCTAATTTAACGCTGGGGGGTTCT" "AATTTTTAACCGCGGAATTGCGTC" ) /<>/doc/examples/period_estimation.rst:99: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.stats.period import SeqToSymbols seq_to_symbols = SeqToSymbols(["AA", "TT", "AT"]) symbols = seq_to_symbols(s) len(symbols) == len(s) symbols /<>/doc/examples/period_estimation.rst:110: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import ipdft powers, periods = ipdft(symbols) powers /<>/doc/examples/period_estimation.rst:117: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: periods /<>/doc/examples/period_estimation.rst:123: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import auto_corr, hybrid powers, periods = auto_corr(symbols) powers /<>/doc/examples/period_estimation.rst:130: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: periods /<>/doc/examples/period_estimation.rst:134: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: powers, periods = hybrid(symbols) powers /<>/doc/examples/period_estimation.rst:139: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: periods /<>/doc/examples/period_estimation.rst:151: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import goertzel pwr = goertzel(sig, 10) print(pwr) /<>/doc/examples/period_estimation.rst:165: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: powers, periods = auto_corr(symbols) llim = 2 period5 = 5 - llim periods[period5] /<>/doc/examples/period_estimation.rst:172: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: powers[period5] /<>/doc/examples/period_estimation.rst:178: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import goertzel period = 4 power = goertzel(symbols, period) ipdft_powers, periods = ipdft(symbols) ipdft_power = abs(ipdft_powers[period - llim]) round(power, 6) == round(ipdft_power, 6) power /<>/doc/examples/period_estimation.rst:191: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: power = hybrid(symbols, period=period) power /<>/doc/examples/period_estimation.rst:204: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import Goertzel goertzel_calc = Goertzel(len(sig), period=10) /<>/doc/examples/period_estimation.rst:212: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.stats.period import blockwise_bootstrap obs_stat, p = blockwise_bootstrap( sig, calc=goertzel_calc, block_size=10, num_reps=1000 ) print(obs_stat) print(p) /<>/doc/examples/period_estimation.rst:230: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import Hybrid hybrid_calculator = Hybrid(len(s), period=4) /<>/doc/examples/period_estimation.rst:240: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.stats.period import SeqToSymbols seq_to_symbols = SeqToSymbols(["AA", "TT", "AT"], length=len(s)) /<>/doc/examples/period_estimation.rst:248: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.stats.period import blockwise_bootstrap stat, p = blockwise_bootstrap( s, calc=hybrid_calculator, block_size=10, num_reps=1000, seq_to_symbols=seq_to_symbols, ) print(stat) p < 0.1 /<>/doc/examples/phylo_by_ls.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/examples/phylo_by_ls.rst:15: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import pickle from cogent3 import load_aligned_seqs from cogent3.evolve import distance from cogent3.evolve.models import HKY85 from cogent3.evolve.fast_distance import DistanceMatrix al = load_aligned_seqs("data/long_testseqs.fasta") d = distance.EstimateDistances(al, submodel=HKY85()) d.run(show_progress=False) with open("dists_for_phylo.pickle", "wb") as f: pickle.dump(d.get_pairwise_distances(), f) /<>/doc/examples/phylo_by_ls.rst:31: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: import pickle from cogent3.phylo import least_squares /<>/doc/examples/phylo_by_ls.rst:38: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: with open("dists_for_phylo.pickle", "rb") as f: dists = pickle.load(f) /<>/doc/examples/phylo_by_ls.rst:47: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls = least_squares.WLS(dists) /<>/doc/examples/phylo_by_ls.rst:53: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls_distance_matrix = least_squares.WLS(DistanceMatrix(dists)) ls_pairwise_matrix = least_squares.WLS(dists.to_dict()) /<>/doc/examples/phylo_by_ls.rst:65: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: score, tree = ls.trex(a=5, k=1, show_progress=False) assert score < 1e-4 /<>/doc/examples/phylo_by_ls.rst:77: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: trees = ls.trex(a=5, k=5, return_all=True, show_progress=False) /<>/doc/examples/phylo_by_ls.rst:83: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(len(trees)) /<>/doc/examples/phylo_by_ls.rst:89: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: wls_stats = [tree[0] for tree in trees] /<>/doc/examples/phylo_by_ls.rst:101: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: t1 = trees[0][1].balanced() t2 = trees[1][1].balanced() print(t1.ascii_art()) /<>/doc/examples/phylo_by_ls.rst:107: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(t2.ascii_art()) /<>/doc/examples/phylo_by_ls.rst:118: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree query_tree = make_tree( "((Human:.2,DogFaced:.2):.3,(NineBande:.1, Mouse:.5):.2,HowlerMon:.1)" ) /<>/doc/examples/phylo_by_ls.rst:128: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls.evaluate_tree(query_tree) /<>/doc/examples/phylo_by_ls.rst:134: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: wls, t = ls.evaluate_topology(query_tree) assert "%.4f" % wls == "0.0084" /<>/doc/examples/phylo_by_ls.rst:146: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import os os.remove("dists_for_phylo.pickle") /<>/doc/examples/rate_heterogeneity.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/examples/rate_heterogeneity.rst:15: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.substitution_model import TimeReversibleNucleotide from cogent3 import load_tree /<>/doc/examples/rate_heterogeneity.rst:22: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: model = TimeReversibleNucleotide(equal_motif_probs=True) tree = load_tree("data/test.tree") lf = model.make_likelihood_function(tree) lf.set_param_rule("length", value=0.6, is_constant=True) aln1 = lf.simulate_alignment(sequence_length=10000) lf.set_param_rule("length", value=0.2, is_constant=True) aln2 = lf.simulate_alignment(sequence_length=10000) aln3 = aln1 + aln2 /<>/doc/examples/rate_heterogeneity.rst:35: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: model = TimeReversibleNucleotide( equal_motif_probs=True, ordered_param="rate", distribution="free" ) lf = model.make_likelihood_function(tree, bins=2, digits=2, space=3) lf.set_alignment(aln3) lf.optimise(local=True, max_restarts=2, show_progress=False) /<>/doc/examples/rate_heterogeneity.rst:46: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: bprobs = [t for t in lf.get_statistics() if "bin" in t.title][0] bprobs /<>/doc/examples/rate_heterogeneity.rst:53: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: model = TimeReversibleNucleotide( equal_motif_probs=True, ordered_param="rate", distribution="gamma" ) lf = model.make_likelihood_function(tree, bins=4) lf.set_param_rule("bprobs", is_constant=True) lf.set_alignment(aln3) lf.optimise(local=True, max_restarts=2, show_progress=False) /<>/doc/examples/relative_rate.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/examples/relative_rate.rst:13: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model from cogent3.maths import stats /<>/doc/examples/relative_rate.rst:21: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs("data/long_testseqs.fasta") t = load_tree(filename="data/test.tree") /<>/doc/examples/relative_rate.rst:28: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = get_model("HKY85") /<>/doc/examples/relative_rate.rst:34: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = sm.make_likelihood_function(t, digits=2, space=3) /<>/doc/examples/relative_rate.rst:40: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_local_clock("Human", "HowlerMon") /<>/doc/examples/relative_rate.rst:46: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_alignment(aln) /<>/doc/examples/relative_rate.rst:52: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(show_progress=False) /<>/doc/examples/relative_rate.rst:58: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_name("clock") lf /<>/doc/examples/relative_rate.rst:65: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: null_lnL = lf.get_log_likelihood() null_nfp = lf.get_num_free_params() /<>/doc/examples/relative_rate.rst:72: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("length", is_independent=True) /<>/doc/examples/relative_rate.rst:78: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(show_progress=False) /<>/doc/examples/relative_rate.rst:84: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_name("non clock") lf /<>/doc/examples/relative_rate.rst:91: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: LR = 2 * (lf.get_log_likelihood() - null_lnL) df = lf.get_num_free_params() - null_nfp P = stats.chisqprob(LR, df) /<>/doc/examples/relative_rate.rst:99: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print("Likelihood ratio statistic = ", LR) print("degrees-of-freedom = ", df) print("probability = ", P) /<>/doc/examples/scope_model_params_on_trees.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/examples/scope_model_params_on_trees.rst:17: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import MG94HKY aln = load_aligned_seqs("data/long_testseqs.fasta") tree = load_tree("data/test.tree") /<>/doc/examples/scope_model_params_on_trees.rst:27: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = MG94HKY() lf = sm.make_likelihood_function(tree, digits=2, space=3) lf.set_alignment(aln) /<>/doc/examples/scope_model_params_on_trees.rst:35: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tree.ascii_art()) /<>/doc/examples/scope_model_params_on_trees.rst:53: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["DogFaced", "Mouse"], outgroup_name="Human", init=2.0, clade=True, ) lf /<>/doc/examples/scope_model_params_on_trees.rst:73: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("omega", init=1.0) lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", init=2.0, stem=True, clade=False, ) lf /<>/doc/examples/scope_model_params_on_trees.rst:91: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: lf.set_param_rule("omega", init=1.0) /<>/doc/examples/scope_model_params_on_trees.rst:96: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", init=2.0, stem=True, clade=True, ) lf /<>/doc/examples/scope_model_params_on_trees.rst:160: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: lf.set_param_rule("omega", init=1.0) /<>/doc/examples/scope_model_params_on_trees.rst:165: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", clade=True, value=1.0, is_constant=True, ) lf.optimise(local=True, show_progress=False) lf /<>/doc/examples/scope_model_params_on_trees.rst:180: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", clade=True, is_constant=False, ) lf.optimise(local=True, show_progress=False) lf /<>/doc/examples/scope_model_params_on_trees.rst:194: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", clade=True, is_independent=True, ) lf.optimise(local=True, show_progress=False) lf /<>/doc/examples/scope_model_params_on_trees.rst:208: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("omega", is_independent=True) lf.optimise(local=True, show_progress=False) lf /<>/doc/examples/seq_features.rst:14: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA s = DNA.make_seq("aagaagaagacccccaaaaaaaaaattttttttttaaaaaaaaaaaaa", name="Orig") exon1 = s.add_feature("exon", "exon1", [(10, 15)]) exon2 = s.add_feature("exon", "exon2", [(30, 40)]) /<>/doc/examples/seq_features.rst:26: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.core.annotation import Feature s2 = DNA.make_seq("aagaagaagacccccaaaaaaaaaattttttttttaaaaaaaaaaaaa", name="Orig2") exon3 = s2.add_annotation(Feature, "exon", "exon1", [(35, 40)]) /<>/doc/examples/seq_features.rst:35: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: s[exon1] /<>/doc/examples/seq_features.rst:41: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: exons = s.get_annotations_matching("exon") print(exons) /<>/doc/examples/seq_features.rst:48: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(s.get_region_covering_all(exons)) s.get_region_covering_all(exons).get_slice() /<>/doc/examples/seq_features.rst:55: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(s.get_region_covering_all(exons).get_shadow().get_slice()) /<>/doc/examples/seq_features.rst:63: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: exon1[0:3].get_slice() /<>/doc/examples/simple.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/examples/simple.rst:13: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model from cogent3 import load_aligned_seqs, make_tree model = get_model("HKY85") aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta") tree = make_tree(tip_names=aln.names) lf = model.make_likelihood_function(tree) lf.set_alignment(aln) lf.optimise(show_progress=False) lf /<>/doc/examples/simulate_alignment.rst:8: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: import sys from cogent3 import make_tree from cogent3.evolve.models import get_model /<>/doc/examples/simulate_alignment.rst:16: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: t = make_tree("(a:0.4,b:0.3,(c:0.15,d:0.2)edge.0:0.1);") /<>/doc/examples/simulate_alignment.rst:22: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = get_model("F81") lf = sm.make_likelihood_function(t) lf.set_constant_lengths() lf.set_motif_probs(dict(A=0.1, C=0.2, G=0.3, T=0.4)) lf /<>/doc/examples/simulate_alignment.rst:32: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: simulated = lf.simulate_alignment(sequence_length=1000) simulated /<>/doc/examples/testing_multi_loci.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/examples/testing_multi_loci.rst:13: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, make_tree, make_table from cogent3.evolve.models import HKY85 from cogent3.recalculation.scope import EACH, ALL from cogent3.maths.stats import chisqprob aln = load_aligned_seqs("data/long_testseqs.fasta") half = len(aln) // 2 aln1 = aln[:half] aln2 = aln[half:] /<>/doc/examples/testing_multi_loci.rst:27: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: loci_names = ["1st-half", "2nd-half"] loci = [aln1, aln2] tree = make_tree(tip_names=aln.names) mod = HKY85() /<>/doc/examples/testing_multi_loci.rst:36: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = mod.make_likelihood_function(tree, loci=loci_names, digits=2, space=3) lf.set_param_rule("length", is_independent=False) lf.set_param_rule("kappa", loci=ALL) lf.set_alignment(loci) lf.optimise(show_progress=False) lf /<>/doc/examples/testing_multi_loci.rst:45: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: all_lnL = lf.lnL all_nfp = lf.nfp lf.set_param_rule("kappa", loci=EACH) lf.optimise(show_progress=False) lf /<>/doc/examples/testing_multi_loci.rst:53: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: each_lnL = lf.lnL each_nfp = lf.nfp LR = 2 * (each_lnL - all_lnL) df = each_nfp - all_nfp /<>/doc/examples/testing_multi_loci.rst:62: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: make_table( header=["LR", "df", "p"], rows=[[LR, df, chisqprob(LR, df)]], digits=2, space=3, ) /<>/doc/index.rst:8: WARNING: Unknown directive type "dropdown". .. dropdown:: Click to see an animation showing testing a hypothesis involving a non-stationary nucleotide process. .. raw:: html /<>/doc/index.rst:16: WARNING: Unknown directive type "dropdown". .. dropdown:: Click to see an animation showing defining and using sequence annotations. .. raw:: html /<>/doc/index.rst:22: WARNING: Unknown directive type "panels". .. panels:: :header: bg-primary :footer: text-right --- ``cogent3`` apps ^^^^^^^^^^^^^^^^ ``cogent3`` comes with pre-defined "apps" that simplify otherwise complex tasks. They provide capabilities that can be used by themselves, or added together to define a pipeline. They also simplify parallel execution of pipelines. +++++++++++ .. link-button:: app/index :type: ref :text: … :classes: stretched-link --- Cookbook ^^^^^^^^ The cookbook presents short code recipes targeted at specific problems. +++++++++++ .. link-button:: cookbook/index :type: ref :text: … :classes: stretched-link --- Tutorials ^^^^^^^^^ The tutorials present code for solving more extensive problems. +++++++++++ .. link-button:: examples/index :type: ref :text: … :classes: stretched-link --- API ^^^ The API for major ``cogent3`` objects +++++++++++ .. link-button:: api/index :type: ref :text: … :classes: stretched-link looking for now-outdated files... none found pickling environment... done checking consistency... /<>/doc/data_file_links.rst: WARNING: document isn't included in any toctree /<>/doc/general.rst: WARNING: document isn't included in any toctree /<>/doc/install.rst: WARNING: document isn't included in any toctree /<>/doc/licenses.rst: WARNING: document isn't included in any toctree /<>/doc/pycogent.rst: WARNING: document isn't included in any toctree done preparing documents... done writing output... [ 0%] api/__init__/cogent3.__init__.available_apps writing output... [ 1%] api/__init__/cogent3.__init__.available_codes writing output... [ 2%] api/__init__/cogent3.__init__.available_models writing output... [ 3%] api/__init__/cogent3.__init__.available_moltypes writing output... [ 4%] api/__init__/cogent3.__init__.get_code writing output... [ 5%] api/__init__/cogent3.__init__.get_model writing output... [ 6%] api/__init__/cogent3.__init__.get_moltype writing output... [ 7%] api/__init__/cogent3.__init__.load_aligned_seqs writing output... [ 8%] api/__init__/cogent3.__init__.load_delimited writing output... [ 9%] api/__init__/cogent3.__init__.load_table writing output... [ 10%] api/__init__/cogent3.__init__.load_tree writing output... [ 10%] api/__init__/cogent3.__init__.load_unaligned_seqs writing output... [ 11%] api/__init__/cogent3.__init__.make_aligned_seqs writing output... [ 12%] api/__init__/cogent3.__init__.make_seq writing output... [ 13%] api/__init__/cogent3.__init__.make_table writing output... [ 14%] api/__init__/cogent3.__init__.make_tree writing output... [ 15%] api/__init__/cogent3.__init__.make_unaligned_seqs writing output... [ 16%] api/alignment/alignment writing output... [ 17%] api/alignment/classes/cogent3.core.alignment.Alignment writing output... [ 18%] api/alignment/classes/cogent3.core.alignment.ArrayAlignment writing output... [ 19%] api/alignment/classes/cogent3.core.alignment.SequenceCollection writing output... [ 20%] api/alphabet/alphabet writing output... [ 20%] api/alphabet/classes/cogent3.core.alphabet.Alphabet writing output... [ 21%] api/genetic_code/classes/cogent3.core.genetic_code.GeneticCode writing output... [ 22%] api/genetic_code/genetic_code writing output... [ 23%] api/index writing output... [ 24%] api/moltype/classes/cogent3.core.moltype.MolType writing output... [ 25%] api/moltype/moltype writing output... [ 26%] api/sequence/classes/cogent3.core.sequence.DnaSequence writing output... [ 27%] api/sequence/classes/cogent3.core.sequence.ProteinSequence writing output... [ 28%] api/sequence/classes/cogent3.core.sequence.RnaSequence writing output... [ 29%] api/sequence/sequence writing output... [ 30%] api/table/classes/cogent3.parse.table.FilteringParser writing output... [ 30%] api/table/classes/cogent3.util.table.Columns writing output... [ 31%] api/table/classes/cogent3.util.table.Table writing output... [ 32%] api/table/table writing output... [ 33%] api/tree/classes/cogent3.core.tree.PhyloNode writing output... [ 34%] api/tree/tree writing output... [ 35%] app/align-codon writing output... [ 36%] app/align-nucleotide writing output... [ 37%] app/align-protein writing output... [ 38%] app/app-overview writing output... [ 39%] app/available-apps writing output... [ 40%] app/dstore writing output... [ 40%] app/evo-ancestral-states writing output... [ 41%] app/evo-dt-nuc-model writing output... [ 42%] app/evo-extract-model-stats writing output... [ 43%] app/evo-hypothesis writing output... [ 44%] app/evo-model writing output... [ 45%] app/evo-model-timehet writing output... [ 46%] app/evo-model-with-tree writing output... [ 47%] app/evo-natsel_neutral writing output... [ 48%] app/evo-natsel_sitehet writing output... [ 49%] app/evo-natsel_timehet writing output... [ 50%] app/evo-natsel_zhang writing output... [ 50%] app/evo-nstat-codon-model writing output... [ 51%] app/evo-tr-codon-model writing output... [ 52%] app/evo-tr-nuc-model writing output... [ 53%] app/index writing output... [ 54%] app/not-completed writing output... [ 55%] app/user_function writing output... [ 56%] app/warning writing output... [ 57%] cookbook/DNA_and_RNA_sequences writing output... [ 58%] cookbook/alignments writing output... [ 59%] cookbook/alphabet writing output... [ 60%] cookbook/annotations writing output... [ 60%] cookbook/building_alignments writing output... [ 61%] cookbook/building_phylogenies writing output... [ 62%] cookbook/calc_genetic_distance writing output... [ 63%] cookbook/evo_modelling writing output... [ 64%] cookbook/genetic_code writing output... [ 65%] cookbook/index writing output... [ 66%] cookbook/loading_sequences writing output... [ 67%] cookbook/loading_tabular writing output... [ 68%] cookbook/manipulating_biological_data writing output... [ 69%] cookbook/moltypes writing output... [ 70%] cookbook/protein_sequences writing output... [ 70%] cookbook/simple_trees writing output... [ 71%] cookbook/tables writing output... [ 72%] cookbook/useful_utilities writing output... [ 73%] cookbook/what_codes writing output... [ 74%] data_file_links writing output... [ 75%] examples/align_codons_to_protein writing output... [ 76%] examples/calculate_UPGMA_cluster writing output... [ 77%] examples/calculate_neigbourjoining_tree writing output... [ 78%] examples/calculate_pairwise_distances writing output... [ 79%] examples/codon_models writing output... [ 80%] examples/coevolution writing output... [ 80%] examples/complete_seq_features writing output... [ 81%] examples/empirical_protein_models writing output... [ 82%] examples/hmm_par_heterogeneity writing output... [ 83%] examples/index writing output... [ 84%] examples/manipulating_tree_nodes writing output... [ 85%] examples/neutral_test writing output... [ 86%] examples/parallel writing output... [ 87%] examples/parametric_bootstrap writing output... [ 88%] examples/period_estimation writing output... [ 89%] examples/phylo_by_ls writing output... [ 90%] examples/rate_heterogeneity writing output... [ 90%] examples/relative_rate writing output... [ 91%] examples/scope_model_params_on_trees writing output... [ 92%] examples/seq_features writing output... [ 93%] examples/simple writing output... [ 94%] examples/simulate_alignment writing output... [ 95%] examples/testing_multi_loci writing output... [ 96%] general writing output... [ 97%] index writing output... [ 98%] install writing output... [ 99%] licenses writing output... [100%] pycogent generating indices... genindex done writing additional pages... search done copying downloadable files... [ 4%] data/abglobin_aa.phylip copying downloadable files... [ 8%] data/dists_for_phylo.json copying downloadable files... [ 12%] data/long_testseqs.fasta copying downloadable files... [ 16%] data/primate_brca1.fasta copying downloadable files... [ 20%] data/primate_brca1.tree copying downloadable files... [ 24%] data/primate_cdx2_promoter.fasta copying downloadable files... [ 28%] data/test.paml copying downloadable files... [ 32%] data/test.tree copying downloadable files... [ 36%] data/test2.fasta copying downloadable files... [ 40%] data/trna_profile.fasta copying downloadable files... [ 44%] data/refseqs.fasta copying downloadable files... [ 48%] data/refseqs_protein.fasta copying downloadable files... [ 52%] data/inseqs.fasta copying downloadable files... [ 56%] data/inseqs_protein.fasta copying downloadable files... [ 60%] data/SCA1-cds.fasta copying downloadable files... [ 64%] data/tp53.json copying downloadable files... [ 68%] data/brca1-bats.fasta copying downloadable files... [ 72%] data/brca1.fasta copying downloadable files... [ 76%] data/GN-tree.json copying downloadable files... [ 80%] data/tree-with-support.json copying downloadable files... [ 84%] data/F9-demo.fa copying downloadable files... [ 88%] data/BRCA1-demo.fasta copying downloadable files... [ 92%] data/tbp.jaspar copying downloadable files... [ 96%] data/stats.tsv copying downloadable files... [100%] data/CerebellumDukeDNaseSeq.pk copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 858 warnings. The HTML pages are in _build/html. Build finished. The HTML pages are in _build/html. rm -rf draw/ make[2]: Leaving directory '/<>/doc' # remove superfluous files and dirs find doc/_build -name "*.doctree*" -delete rm -f doc/_build/html/_sources/COGENT_LICENSE.txt rm -f doc/_build/html/_static/jquery.js rm -f doc/_build/html/_static/underscore.js rm -rf doc/_build/html/_images/math/ make[1]: Leaving directory '/<>' dh_auto_test -a -O--buildsystem=pybuild I: pybuild pybuild:300: cp -r /<>/tests/data /<>/.pybuild/cpython3_3.10_cogent3/build I: pybuild base:239: cd /<>/.pybuild/cpython3_3.10_cogent3/build; python3.10 -m pytest -k 'not test_pickleable_member_roundtrip and not test_pickleable_roundtrip' ============================= test session starts ============================== platform linux -- Python 3.10.4, pytest-6.2.5, py-1.10.0, pluggy-0.13.0 rootdir: /<>, configfile: pyproject.toml collected 2605 items / 5 deselected / 2600 selected tests/test_phylo.py ................ [ 0%] tests/test_recalculation.py . [ 0%] tests/test_align/test_align.py ............................. [ 1%] tests/test_app/test_align.py ....................... [ 2%] tests/test_app/test_app_mpi.py s [ 2%] tests/test_app/test_composable.py ...................... [ 3%] tests/test_app/test_data_store.py .............ss.............s......... [ 5%] ........... [ 5%] tests/test_app/test_dist.py ...... [ 5%] tests/test_app/test_evo.py ....................................... [ 7%] tests/test_app/test_init.py ... [ 7%] tests/test_app/test_io.py ............................. [ 8%] tests/test_app/test_result.py ........................... [ 9%] tests/test_app/test_sample.py ................ [ 10%] tests/test_app/test_translate.py ...... [ 10%] tests/test_app/test_tree.py ..... [ 10%] tests/test_cluster/test_UPGMA.py ....... [ 10%] tests/test_core/test_alignment.py ...................................... [ 12%] ........................................................................ [ 14%] ........................................................................ [ 17%] ........................................................................ [ 20%] ........................................................................ [ 23%] ............................................................. [ 25%] tests/test_core/test_alphabet.py ............................ [ 26%] tests/test_core/test_annotation.py ......... [ 27%] tests/test_core/test_core_standalone.py ................................ [ 28%] ......................... [ 29%] tests/test_core/test_features.py ............................. [ 30%] tests/test_core/test_genetic_code.py ................... [ 31%] tests/test_core/test_info.py ............ [ 31%] tests/test_core/test_location.py ................................... [ 32%] tests/test_core/test_maps.py .... [ 33%] tests/test_core/test_moltype.py ........................................ [ 34%] ......................... [ 35%] tests/test_core/test_profile.py ................................ [ 36%] tests/test_core/test_seq_aln_integration.py .............. [ 37%] tests/test_core/test_sequence.py ....................................... [ 38%] ........................................................................ [ 41%] ........................................................................ [ 44%] ............................. [ 45%] tests/test_core/test_tree.py ........................................... [ 47%] ........................................................................ [ 49%] ....................... [ 50%] tests/test_data/test_molecular_weight.py . [ 50%] tests/test_draw/test_dendrogram.py ......... [ 51%] tests/test_draw/test_dotplot.py ........... [ 51%] tests/test_draw/test_draw_integration.py ...................... [ 52%] tests/test_draw/test_logo.py ..... [ 52%] tests/test_draw/test_shapes.py ... [ 52%] tests/test_evolve/test_best_likelihood.py ....... [ 53%] tests/test_evolve/test_bootstrap.py .. [ 53%] tests/test_evolve/test_coevolution.py .................................. [ 54%] ........................................................................ [ 57%] .............. [ 57%] tests/test_evolve/test_distance.py ..................................... [ 59%] ..... [ 59%] tests/test_evolve/test_likelihood_function.py .......................... [ 60%] ......................................... [ 61%] tests/test_evolve/test_models.py ........... [ 62%] tests/test_evolve/test_motifchange.py ............. [ 62%] tests/test_evolve/test_newq.py ............. [ 63%] tests/test_evolve/test_ns_substitution_model.py .............. [ 63%] tests/test_evolve/test_parameter_controller.py .......... [ 64%] tests/test_evolve/test_scale_rules.py .... [ 64%] tests/test_evolve/test_substitution_model.py ...................... [ 65%] tests/test_format/test_bedgraph.py ........ [ 65%] tests/test_format/test_clustal.py ... [ 65%] tests/test_format/test_fasta.py . [ 65%] tests/test_maths/test_distance_transform.py ............................ [ 66%] ..... [ 66%] tests/test_maths/test_geometry.py .......... [ 67%] tests/test_maths/test_matrix_exponential_integration.py .... [ 67%] tests/test_maths/test_matrix_logarithm.py ... [ 67%] tests/test_maths/test_measure.py ....... [ 67%] tests/test_maths/test_optimisers.py ...... [ 68%] tests/test_maths/test_period.py ....... [ 68%] tests/test_maths/test_util.py ....... [ 68%] tests/test_maths/test_stats/test_contingency.py .................... [ 69%] tests/test_maths/test_stats/test_distribution.py ....................... [ 70%] .............. [ 70%] tests/test_maths/test_stats/test_information_criteria.py ... [ 70%] tests/test_maths/test_stats/test_jackknife.py .... [ 71%] tests/test_maths/test_stats/test_ks.py ...... [ 71%] tests/test_maths/test_stats/test_number.py ...................... [ 72%] tests/test_maths/test_stats/test_period.py .......... [ 72%] tests/test_maths/test_stats/test_special.py ....................... [ 73%] tests/test_maths/test_stats/test_test.py ............................... [ 74%] ........................................................................ [ 77%] [ 77%] tests/test_parse/test_blast.py .............. [ 77%] tests/test_parse/test_blast_xml.py ............... [ 78%] tests/test_parse/test_cigar.py ..... [ 78%] tests/test_parse/test_clustal.py ......... [ 79%] tests/test_parse/test_dialign.py ... [ 79%] tests/test_parse/test_ebi.py ........................................... [ 80%] ............ [ 81%] tests/test_parse/test_fasta.py ..................... [ 82%] tests/test_parse/test_gbseq.py . [ 82%] tests/test_parse/test_genbank.py ................ [ 82%] tests/test_parse/test_gff.py ...... [ 83%] tests/test_parse/test_greengenes.py .... [ 83%] tests/test_parse/test_locuslink.py ............. [ 83%] tests/test_parse/test_ncbi_taxonomy.py .................. [ 84%] tests/test_parse/test_nexus.py ............... [ 84%] tests/test_parse/test_pamlmatrix.py . [ 84%] tests/test_parse/test_phylip.py ... [ 85%] tests/test_parse/test_psl.py ... [ 85%] tests/test_parse/test_pwm_parsers.py .. [ 85%] tests/test_parse/test_rdb.py .................. [ 85%] tests/test_parse/test_record.py ........................................ [ 87%] .. [ 87%] tests/test_parse/test_record_finder.py ................. [ 88%] tests/test_parse/test_tinyseq.py . [ 88%] tests/test_parse/test_tree.py ............... [ 88%] tests/test_parse/test_unigene.py .... [ 89%] tests/test_util/test_deserialise.py .......................... [ 90%] tests/test_util/test_dictarray.py ............................... [ 91%] tests/test_util/test_misc.py ........................................... [ 92%] ................................................... [ 94%] tests/test_util/test_parallel.py ..s. [ 94%] tests/test_util/test_recode_alignment.py ............... [ 95%] tests/test_util/test_table.py .......................................... [ 97%] .......................................................... [ 99%] tests/test_util/test_transform.py ..... [ 99%] tests/test_util/test_union_dict.py ........... [100%] =============================== warnings summary =============================== cogent3/evolve/coevolution.py:50 cogent3/evolve/coevolution.py:50 /<>/.pybuild/cpython3_3.10_cogent3/build/cogent3/evolve/coevolution.py:50: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here. Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations from numpy import ( .pybuild/cpython3_3.10_cogent3/build/tests/test_app/test_data_store.py::TinyDBDataStoreTests::test_db_creation /<>/.pybuild/cpython3_3.10_cogent3/build/cogent3/app/data_store.py:946: UserWarning: 'tmp7i9m61xx/data.tinydb' is locked to 12103, current pid is 12103. warn(f"'{self.source}' is locked to {locked_id}, current pid is {pid}.") .pybuild/cpython3_3.10_cogent3/build/tests/test_app/test_data_store.py::TinyDBDataStoreTests::test_db_creation2 /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/<>/.pybuild/cpython3_3.10_cogent3/build/cogent3/app/data_store.py", line 681, in __del__ self.close() File "/<>/.pybuild/cpython3_3.10_cogent3/build/cogent3/app/data_store.py", line 695, in close self.unlock() File "/<>/.pybuild/cpython3_3.10_cogent3/build/cogent3/app/data_store.py", line 721, in unlock got = self.db.get(query) File "/<>/.pybuild/cpython3_3.10_cogent3/build/cogent3/app/data_store.py", line 668, in db self._db = TinyDB(self.source, storage=storage) File "/usr/lib/python3/dist-packages/tinydb/database.py", line 159, in __init__ self._storage = storage(*args, **kwargs) File "/usr/lib/python3/dist-packages/tinydb/middlewares.py", line 63, in __call__ self.storage = self._storage_cls(*args, **kwargs) File "/usr/lib/python3/dist-packages/tinydb/storages.py", line 99, in __init__ touch(path, create_dirs=create_dirs) # Create file if not exists File "/usr/lib/python3/dist-packages/tinydb/storages.py", line 34, in touch with open(fname, 'a'): FileNotFoundError: [Errno 2] No such file or directory: 'tmpbgpx79ai/subdir/data.tinydb' warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) .pybuild/cpython3_3.10_cogent3/build/tests/test_app/test_evo.py::TestModel::test_hyp_init /<>/.pybuild/cpython3_3.10_cogent3/build/cogent3/app/evo.py:316: UserWarning: init_alt is specified, ignoring sequential warnings.warn("init_alt is specified, ignoring sequential") .pybuild/cpython3_3.10_cogent3/build/tests/test_app/test_evo.py::TestHypothesisResult::test_alt_hyp_fail_error /<>/.pybuild/cpython3_3.10_cogent3/build/cogent3/core/sequence.py:1117: UserWarning: Dropped remainder "GA" from end of sequence warnings.warn( .pybuild/cpython3_3.10_cogent3/build/tests/test_app/test_evo.py::TestBootstrap::test_bstrap /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/<>/.pybuild/cpython3_3.10_cogent3/build/cogent3/app/data_store.py", line 681, in __del__ self.close() File "/<>/.pybuild/cpython3_3.10_cogent3/build/cogent3/app/data_store.py", line 695, in close self.unlock() File "/<>/.pybuild/cpython3_3.10_cogent3/build/cogent3/app/data_store.py", line 721, in unlock got = self.db.get(query) File "/<>/.pybuild/cpython3_3.10_cogent3/build/cogent3/app/data_store.py", line 668, in db self._db = TinyDB(self.source, storage=storage) File "/usr/lib/python3/dist-packages/tinydb/database.py", line 159, in __init__ self._storage = storage(*args, **kwargs) File "/usr/lib/python3/dist-packages/tinydb/middlewares.py", line 63, in __call__ self.storage = self._storage_cls(*args, **kwargs) File "/usr/lib/python3/dist-packages/tinydb/storages.py", line 99, in __init__ touch(path, create_dirs=create_dirs) # Create file if not exists File "/usr/lib/python3/dist-packages/tinydb/storages.py", line 34, in touch with open(fname, 'a'): FileNotFoundError: [Errno 2] No such file or directory: 'tmpdabx4gy3/delme.tinydb' warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) .pybuild/cpython3_3.10_cogent3/build/tests/test_app/test_io.py::TestIo::test_load_db_failure_json_file /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/<>/.pybuild/cpython3_3.10_cogent3/build/cogent3/app/data_store.py", line 681, in __del__ self.close() File "/<>/.pybuild/cpython3_3.10_cogent3/build/cogent3/app/data_store.py", line 695, in close self.unlock() File "/<>/.pybuild/cpython3_3.10_cogent3/build/cogent3/app/data_store.py", line 721, in unlock got = self.db.get(query) File "/<>/.pybuild/cpython3_3.10_cogent3/build/cogent3/app/data_store.py", line 668, in db self._db = TinyDB(self.source, storage=storage) File "/usr/lib/python3/dist-packages/tinydb/database.py", line 159, in __init__ self._storage = storage(*args, **kwargs) File "/usr/lib/python3/dist-packages/tinydb/middlewares.py", line 63, in __call__ self.storage = self._storage_cls(*args, **kwargs) File "/usr/lib/python3/dist-packages/tinydb/storages.py", line 99, in __init__ touch(path, create_dirs=create_dirs) # Create file if not exists File "/usr/lib/python3/dist-packages/tinydb/storages.py", line 34, in touch with open(fname, 'a'): FileNotFoundError: [Errno 2] No such file or directory: '/<>/.pybuild/cpython3_3.10_cogent3/build/tests/tmpl79s4d2v/delme.tinydb' warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) .pybuild/cpython3_3.10_cogent3/build/tests/test_core/test_alignment.py::SequenceCollectionTests::test_get_identical_sets .pybuild/cpython3_3.10_cogent3/build/tests/test_core/test_alignment.py::AlignmentTests::test_get_identical_sets /<>/.pybuild/cpython3_3.10_cogent3/build/cogent3/core/alignment.py:890: UserWarning: in get_identical_sets, mask_degen has no effect as moltype 'text' has no degenerate characters warnings.warn( .pybuild/cpython3_3.10_cogent3/build/tests/test_core/test_alignment.py::ArrayAlignmentTests::test_get_identical_sets /<>/.pybuild/cpython3_3.10_cogent3/build/cogent3/core/alignment.py:4240: UserWarning: in get_identical_sets, mask_degen has no effect as moltype 'text' has no degenerate characters warnings.warn( .pybuild/cpython3_3.10_cogent3/build/tests/test_core/test_alignment.py::AlignmentTests::test_init_aln /usr/lib/python3/dist-packages/numpy/lib/type_check.py:340: VisibleDeprecationWarning: Creating an ndarray from nested sequences exceeding the maximum number of dimensions of 32 is deprecated. If you mean to do this, you must specify 'dtype=object' when creating the ndarray. type_ = asarray(x).dtype.type .pybuild/cpython3_3.10_cogent3/build/tests/test_core/test_alignment.py::AlignmentTests::test_init_aln /usr/lib/python3/dist-packages/numpy/testing/_private/utils.py:380: VisibleDeprecationWarning: Creating an ndarray from nested sequences exceeding the maximum number of dimensions of 32 is deprecated. If you mean to do this, you must specify 'dtype=object' when creating the ndarray. isdesnat = isnat(desired) .pybuild/cpython3_3.10_cogent3/build/tests/test_core/test_alignment.py::AlignmentTests::test_init_aln /usr/lib/python3/dist-packages/numpy/testing/_private/utils.py:110: VisibleDeprecationWarning: Creating an ndarray from nested sequences exceeding the maximum number of dimensions of 32 is deprecated. If you mean to do this, you must specify 'dtype=object' when creating the ndarray. st = isnan(x) .pybuild/cpython3_3.10_cogent3/build/tests/test_evolve/test_likelihood_function.py::LikelihoodFunctionTests::test_make_discrete_markov /<>/.pybuild/cpython3_3.10_cogent3/build/tests/test_evolve/test_likelihood_function.py:785: UserWarning: Ignoring tree edge lengths lf = dm.make_likelihood_function(t) .pybuild/cpython3_3.10_cogent3/build/tests/test_evolve/test_newq.py::NewQ::test_cond_pos_differ .pybuild/cpython3_3.10_cogent3/build/tests/test_evolve/test_newq.py::NewQ::test_get_motif_probs .pybuild/cpython3_3.10_cogent3/build/tests/test_evolve/test_newq.py::NewQ::test_get_statistics .pybuild/cpython3_3.10_cogent3/build/tests/test_evolve/test_newq.py::NewQ::test_newQ_is_nuc_process .pybuild/cpython3_3.10_cogent3/build/tests/test_evolve/test_newq.py::NewQ::test_results_different .pybuild/cpython3_3.10_cogent3/build/tests/test_evolve/test_newq.py::NewQ::test_sim_alignment /<>/.pybuild/cpython3_3.10_cogent3/build/cogent3/evolve/substitution_model.py:721: UserWarning: Motif probs overspecified _ContinuousSubstitutionModel.__init__(self, alphabet, **kw) .pybuild/cpython3_3.10_cogent3/build/tests/test_evolve/test_ns_substitution_model.py::NonStatMarkov::test_general_vs_constructed_general /<>/.pybuild/cpython3_3.10_cogent3/build/cogent3/maths/optimisers.py:192: UserWarning: Unused arg for local alignment: results warnings.warn("Unused arg for local alignment: " + k) .pybuild/cpython3_3.10_cogent3/build/tests/test_evolve/test_ns_substitution_model.py::NonStatMarkov::test_general_vs_constructed_general /<>/.pybuild/cpython3_3.10_cogent3/build/tests/test_evolve/test_ns_substitution_model.py:125: UserWarning: FORCED EXIT from optimiser after 25 evaluations nuc_lf.optimise(**optargs) .pybuild/cpython3_3.10_cogent3/build/tests/test_maths/test_stats/test_test.py::TestsTests::test_median .pybuild/cpython3_3.10_cogent3/build/tests/test_maths/test_stats/test_test.py::TestsTests::test_median .pybuild/cpython3_3.10_cogent3/build/tests/test_maths/test_stats/test_test.py::TestsTests::test_median .pybuild/cpython3_3.10_cogent3/build/tests/test_maths/test_stats/test_test.py::TestsTests::test_median /<>/.pybuild/cpython3_3.10_cogent3/build/cogent3/maths/stats/test.py:161: DeprecationWarning: function median is discontinued, support will be stopped in version 2021.11 discontinued("function", "median", "2021.11") .pybuild/cpython3_3.10_cogent3/build/tests/test_maths/test_stats/test_test.py::StatTests::test_t_two_sample_switch /usr/lib/python3/dist-packages/numpy/core/_methods.py:262: RuntimeWarning: Degrees of freedom <= 0 for slice ret = _var(a, axis=axis, dtype=dtype, out=out, ddof=ddof, .pybuild/cpython3_3.10_cogent3/build/tests/test_util/test_misc.py::UtilsTests::test_get_setting_from_environ /<>/.pybuild/cpython3_3.10_cogent3/build/cogent3/util/misc.py:1268: UserWarning: could not cast name=blah to type , skipping warnings.warn( .pybuild/cpython3_3.10_cogent3/build/tests/test_util/test_table.py::TableTests::test_cast_str_to_numerical /<>/.pybuild/cpython3_3.10_cogent3/build/tests/test_util/test_table.py:1772: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information. Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations for d_type in [numpy.int, numpy.complex, numpy.float64]: .pybuild/cpython3_3.10_cogent3/build/tests/test_util/test_table.py::TableTests::test_cast_str_to_numerical /<>/.pybuild/cpython3_3.10_cogent3/build/tests/test_util/test_table.py:1772: DeprecationWarning: `np.complex` is a deprecated alias for the builtin `complex`. To silence this warning, use `complex` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.complex128` here. Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations for d_type in [numpy.int, numpy.complex, numpy.float64]: .pybuild/cpython3_3.10_cogent3/build/tests/test_util/test_table.py::TableTests::test_cast_str_to_numerical /<>/.pybuild/cpython3_3.10_cogent3/build/tests/test_util/test_table.py:1773: ComplexWarning: Casting complex values to real discards the imaginary part d = d.astype(d_type) .pybuild/cpython3_3.10_cogent3/build/tests/test_util/test_table.py::TableTests::test_cast_str_to_numerical /<>/.pybuild/cpython3_3.10_cogent3/build/tests/test_util/test_table.py:1782: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here. Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations self.assertIsInstance(r[0], numpy.float) .pybuild/cpython3_3.10_cogent3/build/tests/test_util/test_table.py::TableTests::test_cast_str_to_numerical /<>/.pybuild/cpython3_3.10_cogent3/build/tests/test_util/test_table.py:1785: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here. Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations self.assertIsInstance(r[0], numpy.float) -- Docs: https://docs.pytest.org/en/stable/warnings.html ==== 2595 passed, 5 skipped, 5 deselected, 34 warnings in 501.40s (0:08:21) ==== create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild dh_auto_install -a -O--buildsystem=pybuild W: pybuild validate:127: Couldn't get list of valid classifiers to check against I: pybuild plugin_flit:66: Installing package /<>/src/cogent3 -> /<>/debian/python3-cogent3/usr/lib/python3.10/dist-packages/cogent3 I: pybuild plugin_flit:79: Writing dist-info /<>/debian/python3-cogent3/usr/lib/python3.10/dist-packages dh_install -a -O--buildsystem=pybuild debian/rules override_dh_installdocs make[1]: Entering directory '/<>' dh_installdocs rm -rf debian/python-cogent/usr/share/doc/python-cogent/html/_sources find debian -name doctrees -type d | xargs rm -rf make[1]: Leaving directory '/<>' dh_installchangelogs -a -O--buildsystem=pybuild debian/rules override_dh_python3 make[1]: Entering directory '/<>' dh_python3 --shebang=/usr/bin/python3 make[1]: Leaving directory '/<>' dh_installsystemduser -a -O--buildsystem=pybuild dh_lintian -a -O--buildsystem=pybuild dh_perl -a -O--buildsystem=pybuild dh_usrlocal -a -O--buildsystem=pybuild dh_link -a -O--buildsystem=pybuild dh_strip_nondeterminism -a -O--buildsystem=pybuild debian/rules override_dh_compress make[1]: Entering directory '/<>' dh_compress --exclude=.js --exclude=.fasta --exclude=.txt --exclude=.pdb make[1]: Leaving directory '/<>' dh_fixperms -a -O--buildsystem=pybuild dh_missing -a -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild debian/rules override_dh_shlibdeps make[1]: Entering directory '/<>' dh_shlibdeps dh_numpy3 make[1]: Leaving directory '/<>' dh_installdeb -a -O--buildsystem=pybuild dh_gencontrol -a -O--buildsystem=pybuild dpkg-gencontrol: warning: Depends field of package python3-cogent3: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums -a -O--buildsystem=pybuild dh_builddeb -a -O--buildsystem=pybuild INFO: pkgstriptranslations version 149 pkgstriptranslations: processing python3-cogent3 (in debian/python3-cogent3); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/python3-cogent3/DEBIAN/control, package python3-cogent3, directory debian/python3-cogent3 pkgstripfiles: Truncating usr/share/doc/python3-cogent3/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package python3-cogent3 ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python3-cogent3' in '../python3-cogent3_2021.10.12a1+dfsg-1_armhf.deb'. dpkg-genbuildinfo --build=any -O../python-cogent_2021.10.12a1+dfsg-1_armhf.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../python-cogent_2021.10.12a1+dfsg-1_armhf.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2022-04-09T09:20:57Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ python-cogent_2021.10.12a1+dfsg-1_armhf.changes: ------------------------------------------------ Format: 1.8 Date: Thu, 04 Nov 2021 09:29:04 +0100 Source: python-cogent Binary: python3-cogent3 Built-For-Profiles: noudeb Architecture: armhf Version: 2021.10.12a1+dfsg-1 Distribution: jammy-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: python3-cogent3 - framework for genomic biology Changes: python-cogent (2021.10.12a1+dfsg-1) unstable; urgency=medium . * New upstream version * Upstream switched to filt build system Checksums-Sha1: 9d397195eefac83aed96904c27cca8b90c1db2c3 11703 python-cogent_2021.10.12a1+dfsg-1_armhf.buildinfo 3f47d7aeddc051af84feb7de3940c8c6a82d3775 1277572 python3-cogent3_2021.10.12a1+dfsg-1_armhf.deb Checksums-Sha256: ec8374f710582f9bf92e9b959f85aab9a1b38ee5aa78dd6faff3cb93bce7c8e2 11703 python-cogent_2021.10.12a1+dfsg-1_armhf.buildinfo 0c91de0e5ca57830b67fde3e47a00a08ef89494976cde30004a3206ae2851232 1277572 python3-cogent3_2021.10.12a1+dfsg-1_armhf.deb Files: 7a9117886b029c60b4798f2dcf7fbe6b 11703 python optional python-cogent_2021.10.12a1+dfsg-1_armhf.buildinfo 1aeff663bf143b4ec8c285a8f81706b0 1277572 python optional python3-cogent3_2021.10.12a1+dfsg-1_armhf.deb /<>/python-cogent_2021.10.12a1+dfsg-1_armhf.changes.new could not be renamed to /<>/python-cogent_2021.10.12a1+dfsg-1_armhf.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: python-cogent Binary: python3-cogent3 Architecture: armhf Version: 2021.10.12a1+dfsg-1 Checksums-Md5: 1aeff663bf143b4ec8c285a8f81706b0 1277572 python3-cogent3_2021.10.12a1+dfsg-1_armhf.deb Checksums-Sha1: 3f47d7aeddc051af84feb7de3940c8c6a82d3775 1277572 python3-cogent3_2021.10.12a1+dfsg-1_armhf.deb Checksums-Sha256: 0c91de0e5ca57830b67fde3e47a00a08ef89494976cde30004a3206ae2851232 1277572 python3-cogent3_2021.10.12a1+dfsg-1_armhf.deb Build-Origin: Ubuntu Build-Architecture: armhf Build-Date: Sat, 09 Apr 2022 09:20:56 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-2), automake (= 1:1.16.5-1.3), autopoint (= 0.21-4ubuntu4), autotools-dev (= 20220109.1), base-files (= 12ubuntu3), base-passwd (= 3.5.52build1), bash (= 5.1-6ubuntu1), binutils (= 2.38-3ubuntu1), binutils-arm-linux-gnueabihf (= 2.38-3ubuntu1), binutils-common (= 2.38-3ubuntu1), blt (= 2.5.3+dfsg-4.1build2), bsdextrautils (= 2.37.2-4ubuntu3), bsdutils (= 1:2.37.2-4ubuntu3), build-essential (= 12.9ubuntu3), bzip2 (= 1.0.8-5build1), ca-certificates (= 20211016), coreutils (= 8.32-4.1ubuntu1), cpp (= 4:11.2.0-1ubuntu1), cpp-11 (= 11.2.0-19ubuntu1), cython3 (= 0.29.28-1ubuntu3), dash (= 0.5.11+git20210903+057cd650a4ed-3build1), debconf (= 1.5.79ubuntu1), debhelper (= 13.6ubuntu1), debianutils (= 5.5-1ubuntu2), debugedit (= 1:5.0-4build1), dh-autoreconf (= 20), dh-python (= 5.20220403), dh-strip-nondeterminism (= 1.13.0-1), diffutils (= 1:3.8-0ubuntu2), docutils-common (= 0.17.1+dfsg-2), dpkg (= 1.21.1ubuntu2), dpkg-dev (= 1.21.1ubuntu2), dwz (= 0.14-1build2), file (= 1:5.41-3), findutils (= 4.8.0-1ubuntu3), flit (= 3.6.0-1), fontconfig-config (= 2.13.1-4.2ubuntu5), fonts-dejavu-core (= 2.37-2build1), fonts-lyx (= 2.3.6-1), g++ (= 4:11.2.0-1ubuntu1), g++-11 (= 11.2.0-19ubuntu1), gcc (= 4:11.2.0-1ubuntu1), gcc-11 (= 11.2.0-19ubuntu1), gcc-11-base (= 11.2.0-19ubuntu1), gcc-12-base (= 12-20220319-1ubuntu1), gettext (= 0.21-4ubuntu4), gettext-base (= 0.21-4ubuntu4), grep (= 3.7-1build1), groff-base (= 1.22.4-8build1), gzip (= 1.10-4ubuntu4), hostname (= 3.23ubuntu2), init-system-helpers (= 1.62), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.3.1-1), libarchive-zip-perl (= 1.68-1), libasan6 (= 11.2.0-19ubuntu1), libatomic1 (= 12-20220319-1ubuntu1), libattr1 (= 1:2.5.1-1build1), libaudit-common (= 1:3.0.7-1build1), libaudit1 (= 1:3.0.7-1build1), libbinutils (= 2.38-3ubuntu1), libblas3 (= 3.10.0-2ubuntu1), libblkid1 (= 2.37.2-4ubuntu3), libbrotli1 (= 1.0.9-2build6), libbsd0 (= 0.11.5-1), libbz2-1.0 (= 1.0.8-5build1), libc-bin (= 2.35-0ubuntu3), libc-dev-bin (= 2.35-0ubuntu3), libc6 (= 2.35-0ubuntu3), libc6-dev (= 2.35-0ubuntu3), libcap-ng0 (= 0.7.9-2.2build3), libcap2 (= 1:2.44-1build3), libcc1-0 (= 12-20220319-1ubuntu1), libcmark-gfm-extensions0.29.0.gfm.3 (= 0.29.0.gfm.3-3), libcmark-gfm0.29.0.gfm.3 (= 0.29.0.gfm.3-3), libcom-err2 (= 1.46.5-2ubuntu1), libcrypt-dev (= 1:4.4.27-1), libcrypt1 (= 1:4.4.27-1), libctf-nobfd0 (= 2.38-3ubuntu1), libctf0 (= 2.38-3ubuntu1), libdb5.3 (= 5.3.28+dfsg1-0.8ubuntu3), libdebconfclient0 (= 0.261ubuntu1), libdebhelper-perl (= 13.6ubuntu1), libdeflate0 (= 1.10-2), libdpkg-perl (= 1.21.1ubuntu2), libdw1 (= 0.186-1build1), libedit2 (= 3.1-20210910-1build1), libelf1 (= 0.186-1build1), libexpat1 (= 2.4.7-1), libexpat1-dev (= 2.4.7-1), libffi8 (= 3.4.2-4), libfile-stripnondeterminism-perl (= 1.13.0-1), libfontconfig1 (= 2.13.1-4.2ubuntu5), libfreetype6 (= 2.11.1+dfsg-1build1), libfribidi0 (= 1.0.8-2ubuntu3), libgcc-11-dev (= 11.2.0-19ubuntu1), libgcc-s1 (= 12-20220319-1ubuntu1), libgcrypt20 (= 1.9.4-3ubuntu3), libgdbm-compat4 (= 1.23-1), libgdbm6 (= 1.23-1), libgfortran5 (= 12-20220319-1ubuntu1), libglib2.0-0 (= 2.72.0-1), libgmp10 (= 2:6.2.1+dfsg-3ubuntu1), libgomp1 (= 12-20220319-1ubuntu1), libgpg-error0 (= 1.43-3), libgraphite2-3 (= 1.3.14-1build2), libgssapi-krb5-2 (= 1.19.2-2), libharfbuzz0b (= 2.7.4-1ubuntu3), libicu70 (= 70.1-2), libimagequant0 (= 2.17.0-1), libisl23 (= 0.24-2build1), libjbig0 (= 2.1-3.1build3), libjpeg-turbo8 (= 2.1.2-0ubuntu1), libjpeg8 (= 8c-2ubuntu10), libjs-jquery (= 3.6.0+dfsg+~3.5.13-1), libjs-jquery-ui (= 1.13.1+dfsg-1), libjs-sphinxdoc (= 4.3.2-1), libjs-underscore (= 1.13.2~dfsg-2), libk5crypto3 (= 1.19.2-2), libkeyutils1 (= 1.6.1-2ubuntu3), libkrb5-3 (= 1.19.2-2), libkrb5support0 (= 1.19.2-2), liblapack3 (= 3.10.0-2ubuntu1), liblbfgsb0 (= 3.0+dfsg.3-10), liblcms2-2 (= 2.12~rc1-2build2), libllvm11 (= 1:11.1.0-6), liblz4-1 (= 1.9.3-2build2), liblzma5 (= 5.2.5-2ubuntu1), libmagic-mgc (= 1:5.41-3), libmagic1 (= 1:5.41-3), libmd0 (= 1.0.4-1build1), libmount1 (= 2.37.2-4ubuntu3), libmpc3 (= 1.2.1-2build1), libmpdec3 (= 2.5.1-2build2), libmpfr6 (= 4.1.0-3build3), libncursesw6 (= 6.3-2), libnorm1 (= 1.5.9+dfsg-2), libnsl-dev (= 1.3.0-2build2), libnsl2 (= 1.3.0-2build2), libopenjp2-7 (= 2.4.0-6), libpam-modules (= 1.4.0-11ubuntu2), libpam-modules-bin (= 1.4.0-11ubuntu2), libpam-runtime (= 1.4.0-11ubuntu2), libpam0g (= 1.4.0-11ubuntu2), libpcre2-8-0 (= 10.39-3build1), libpcre3 (= 2:8.39-13build5), libperl5.34 (= 5.34.0-3ubuntu1), libpfm4 (= 4.11.1+git32-gd0b85fb-1), libpgm-5.3-0 (= 5.3.128~dfsg-2), libpipeline1 (= 1.5.5-1), libpng16-16 (= 1.6.37-3build5), libpython3-all-dev (= 3.10.4-0ubuntu2), libpython3-dev (= 3.10.4-0ubuntu2), libpython3-stdlib (= 3.10.4-0ubuntu2), libpython3.10 (= 3.10.4-3), libpython3.10-dev (= 3.10.4-3), libpython3.10-minimal (= 3.10.4-3), libpython3.10-stdlib (= 3.10.4-3), libqhull-r8.0 (= 2020.2-4), libraqm0 (= 0.7.0-4ubuntu1), libreadline8 (= 8.1.2-1), libseccomp2 (= 2.5.3-2ubuntu2), libselinux1 (= 3.3-1build2), libsigsegv2 (= 2.13-1ubuntu3), libsmartcols1 (= 2.37.2-4ubuntu3), libsodium23 (= 1.0.18-1build2), libsqlite3-0 (= 3.37.2-2), libssl3 (= 3.0.2-0ubuntu1), libstdc++-11-dev (= 11.2.0-19ubuntu1), libstdc++6 (= 12-20220319-1ubuntu1), libsub-override-perl (= 0.09-2), libsystemd0 (= 249.11-0ubuntu3), libtbb12 (= 2021.5.0-7ubuntu2), libtbbmalloc2 (= 2021.5.0-7ubuntu2), libtcl8.6 (= 8.6.12+dfsg-1build1), libtiff5 (= 4.3.0-6), libtinfo6 (= 6.3-2), libtirpc-common (= 1.3.2-2build1), libtirpc-dev (= 1.3.2-2build1), libtirpc3 (= 1.3.2-2build1), libtk8.6 (= 8.6.12-1build1), libtool (= 2.4.6-15build2), libubsan1 (= 12-20220319-1ubuntu1), libuchardet0 (= 0.0.7-1build2), libudev1 (= 249.11-0ubuntu3), libunistring2 (= 1.0-1), libuuid1 (= 2.37.2-4ubuntu3), libwebp7 (= 1.2.2-2), libwebpdemux2 (= 1.2.2-2), libwebpmux3 (= 1.2.2-2), libx11-6 (= 2:1.7.5-1), libx11-data (= 2:1.7.5-1), libxau6 (= 1:1.0.9-1build5), libxcb1 (= 1.14-3ubuntu3), libxdmcp6 (= 1:1.1.3-0ubuntu5), libxext6 (= 2:1.3.4-1build1), libxft2 (= 2.3.3-0ubuntu5), libxml2 (= 2.9.13+dfsg-1build1), libxrender1 (= 1:0.9.10-1build4), libxslt1.1 (= 1.1.34-4build2), libxss1 (= 1:1.2.3-1build2), libzmq5 (= 4.3.4-2), libzstd1 (= 1.4.8+dfsg-3build1), linux-libc-dev (= 5.15.0-25.25), llvm-11 (= 1:11.1.0-6), llvm-11-linker-tools (= 1:11.1.0-6), llvm-11-runtime (= 1:11.1.0-6), login (= 1:4.8.1-2ubuntu2), lsb-base (= 11.1.0ubuntu4), lto-disabled-list (= 24), m4 (= 1.4.18-5ubuntu2), make (= 4.3-4.1build1), man-db (= 2.10.2-1), mawk (= 1.3.4.20200120-3), media-types (= 7.0.0), ncurses-base (= 6.3-2), ncurses-bin (= 6.3-2), openssl (= 3.0.2-0ubuntu1), pandoc (= 2.9.2.1-3ubuntu2), pandoc-data (= 2.9.2.1-3ubuntu2), patch (= 2.7.6-7build2), perl (= 5.34.0-3ubuntu1), perl-base (= 5.34.0-3ubuntu1), perl-modules-5.34 (= 5.34.0-3ubuntu1), po-debconf (= 1.0.21+nmu1), python-babel-localedata (= 2.8.0+dfsg.1-7), python-matplotlib-data (= 3.5.1-2build1), python3 (= 3.10.4-0ubuntu2), python3-alabaster (= 0.7.12-1), python3-all (= 3.10.4-0ubuntu2), python3-all-dev (= 3.10.4-0ubuntu2), python3-appdirs (= 1.4.4-2), python3-attr (= 21.2.0-1), python3-babel (= 2.8.0+dfsg.1-7), python3-bleach (= 4.1.0-1), python3-brotli (= 1.0.9-2build6), python3-certifi (= 2020.6.20-1), python3-cffi-backend (= 1.15.0-1build2), python3-chardet (= 4.0.0-1), python3-cycler (= 0.11.0-1), python3-dateutil (= 2.8.1-6), python3-decorator (= 4.4.2-0ubuntu1), python3-defusedxml (= 0.7.1-1), python3-dev (= 3.10.4-0ubuntu2), python3-distutils (= 3.10.4-0ubuntu1), python3-docutils (= 0.17.1+dfsg-2), python3-entrypoints (= 0.4-1), python3-fonttools (= 4.29.1-2build1), python3-fs (= 2.4.12-1), python3-html5lib (= 1.1-3), python3-idna (= 3.3-1), python3-imagesize (= 1.3.0-1), python3-importlib-metadata (= 4.6.4-1), python3-iniconfig (= 1.1.1-2), python3-ipython-genutils (= 0.2.0-5), python3-jinja2 (= 3.0.3-1), python3-jsonschema (= 3.2.0-0ubuntu2), python3-jupyter-client (= 7.1.2-1), python3-jupyter-core (= 4.9.1-1), python3-jupyterlab-pygments (= 0.1.2-8), python3-kiwisolver (= 1.3.2-1build1), python3-lib2to3 (= 3.10.4-0ubuntu1), python3-llvmlite (= 0.38.0-1), python3-lxml (= 4.8.0-1build1), python3-lz4 (= 3.1.3+dfsg-1build3), python3-markupsafe (= 2.0.1-2build1), python3-matplotlib (= 3.5.1-2build1), python3-minimal (= 3.10.4-0ubuntu2), python3-more-itertools (= 8.10.0-2), python3-mpmath (= 1.2.1-2), python3-nbclient (= 0.5.6-2), python3-nbconvert (= 6.4.0-1), python3-nbformat (= 5.1.3-1), python3-nbsphinx (= 0.8.7+ds-1), python3-nest-asyncio (= 1.5.4-1), python3-numba (= 0.55.1-0ubuntu2), python3-numpy (= 1:1.21.5-1build2), python3-numpydoc (= 1.2-1), python3-packaging (= 21.3-1), python3-pandas (= 1.3.5+dfsg-3), python3-pandas-lib (= 1.3.5+dfsg-3), python3-pandocfilters (= 1.5.0-1), python3-pil (= 9.0.1-1build1), python3-pil.imagetk (= 9.0.1-1build1), python3-pkg-resources (= 59.6.0-1.2), python3-pluggy (= 0.13.0-7.1), python3-py (= 1.10.0-1), python3-pygments (= 2.11.2+dfsg-2), python3-pyparsing (= 2.4.7-1), python3-pyrsistent (= 0.18.1-1build1), python3-pytest (= 6.2.5-1ubuntu2), python3-requests (= 2.25.1+dfsg-2), python3-roman (= 3.3-1), python3-scipy (= 1.8.0-1exp2ubuntu1), python3-scitrack (= 2021.5.3-2), python3-setuptools (= 59.6.0-1.2), python3-six (= 1.16.0-3), python3-snowballstemmer (= 2.2.0-1build1), python3-sphinx (= 4.3.2-1), python3-sphinx-bootstrap-theme (= 0.8.1-1), python3-sphinx-gallery (= 0.10.1-1), python3-sympy (= 1.9-1), python3-testpath (= 0.5.0+dfsg-1), python3-tinydb (= 3.15.2-2), python3-tk (= 3.10.4-0ubuntu1), python3-toml (= 0.10.2-1), python3-tomli (= 1.2.2-2), python3-tomli-w (= 1.0.0-1), python3-tornado (= 6.1.0-3build1), python3-tqdm (= 4.57.0-2), python3-traitlets (= 5.1.1-1), python3-tz (= 2022.1-1), python3-ufolib2 (= 0.13.1+dfsg1-1), python3-unicodedata2 (= 14.0.0+ds-8), python3-urllib3 (= 1.26.5-1~exp1), python3-webencodings (= 0.5.1-4), python3-zipp (= 1.0.0-3), python3-zmq (= 22.3.0-1build1), python3.10 (= 3.10.4-3), python3.10-dev (= 3.10.4-3), python3.10-minimal (= 3.10.4-3), readline-common (= 8.1.2-1), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.8-1ubuntu2), sensible-utils (= 0.0.17), sgml-base (= 1.30), sphinx-common (= 4.3.2-1), sysvinit-utils (= 3.01-1ubuntu1), tar (= 1.34+dfsg-1build3), tk8.6-blt2.5 (= 2.5.3+dfsg-4.1build2), tzdata (= 2022a-0ubuntu1), ucf (= 3.0043), unicode-data (= 14.0.0-1.1), util-linux (= 2.37.2-4ubuntu3), x11-common (= 1:7.7+23ubuntu2), xml-core (= 0.18+nmu1), xz-utils (= 5.2.5-2ubuntu1), zlib1g (= 1:1.2.11.dfsg-2ubuntu9), zlib1g-dev (= 1:1.2.11.dfsg-2ubuntu9) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1636014544" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ python3-cogent3_2021.10.12a1+dfsg-1_armhf.deb --------------------------------------------- new Debian package, version 2.0. size 1277572 bytes: control archive=10266 bytes. 1252 bytes, 27 lines control 31563 bytes, 333 lines md5sums 1042 bytes, 43 lines * postinst #!/bin/sh 421 bytes, 12 lines * prerm #!/bin/sh Package: python3-cogent3 Source: python-cogent Version: 2021.10.12a1+dfsg-1 Architecture: armhf Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 3769 Depends: python3-chardet, python3-numba, python3-numpy (>= 1:1.20.0), python3-numpy-abi9, python3-scitrack, python3-tinydb, python3-tqdm, python3:any, python3-matplotlib, python3-pandas, python3-plotly Recommends: ncbi-blast+-legacy, dialign Suggests: python-cogent-doc Breaks: python-cogent Replaces: python-cogent Provides: python-cogent Section: python Priority: optional Homepage: https://github.com/cogent3/cogent3 Description: framework for genomic biology PyCogent is a software library for genomic biology. It is a fully integrated and thoroughly tested framework for: * controlling third-party applications, * devising workflows; querying databases, * conducting novel probabilistic analyses of biological sequence evolution, and * generating publication quality graphics. It is distinguished by many unique built-in capabilities (such as true codon alignment) and the frequent addition of entirely new methods for the analysis of genomic data. drwxr-xr-x root/root 0 2021-11-04 08:29 ./ drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/ drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/lib/ drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/lib/python3/ drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/lib/python3/dist-packages/ drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/lib/python3/dist-packages/cogent3-2021.10.12a1.dist-info/ -rw-r--r-- root/root 4 2021-11-04 08:29 ./usr/lib/python3/dist-packages/cogent3-2021.10.12a1.dist-info/INSTALLER -rw-r--r-- root/root 9731 2021-11-04 08:29 ./usr/lib/python3/dist-packages/cogent3-2021.10.12a1.dist-info/METADATA -rw-r--r-- root/root 24650 2021-11-04 08:29 ./usr/lib/python3/dist-packages/cogent3-2021.10.12a1.dist-info/RECORD -rw-r--r-- root/root 0 2021-11-04 08:29 ./usr/lib/python3/dist-packages/cogent3-2021.10.12a1.dist-info/REQUESTED drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/lib/python3/dist-packages/cogent3/ -rw-r--r-- root/root 16836 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/__init__.py drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/lib/python3/dist-packages/cogent3/align/ -rw-r--r-- root/root 661 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/align/__init__.py -rw-r--r-- root/root 3410 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/align/align.py -rw-r--r-- root/root 1326 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/align/compare_numba.py -rw-r--r-- root/root 6144 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/align/dp_calculation.py -rw-r--r-- root/root 3815 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/align/indel_model.py -rw-r--r-- root/root 8125 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/align/indel_positions.py -rw-r--r-- root/root 39280 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/align/pairwise.py -rw-r--r-- root/root 11257 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/align/pairwise_pogs_numba.py -rw-r--r-- root/root 9062 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/align/pairwise_seqs_numba.py -rw-r--r-- root/root 3984 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/align/progressive.py -rw-r--r-- root/root 1459 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/align/pycompare.py -rw-r--r-- root/root 2895 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/align/traceback.py drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/lib/python3/dist-packages/cogent3/app/ -rw-r--r-- root/root 1981 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/app/__init__.py -rw-r--r-- root/root 17756 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/app/align.py -rw-r--r-- root/root 24517 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/app/composable.py -rw-r--r-- root/root 33809 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/app/data_store.py -rw-r--r-- root/root 4775 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/app/dist.py -rw-r--r-- root/root 38280 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/app/evo.py -rw-r--r-- root/root 18992 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/app/io.py -rw-r--r-- root/root 19734 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/app/result.py -rw-r--r-- root/root 26368 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/app/sample.py -rw-r--r-- root/root 9338 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/app/translate.py -rw-r--r-- root/root 5291 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/app/tree.py drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/lib/python3/dist-packages/cogent3/cluster/ -rw-r--r-- root/root 6008 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/cluster/UPGMA.py -rw-r--r-- root/root 404 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/cluster/__init__.py drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/lib/python3/dist-packages/cogent3/core/ -rw-r--r-- root/root 583 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/core/__init__.py -rw-r--r-- root/root 167743 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/core/alignment.py -rw-r--r-- root/root 33394 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/core/alphabet.py -rw-r--r-- root/root 17325 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/core/annotation.py -rw-r--r-- root/root 17402 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/core/genetic_code.py -rw-r--r-- root/root 5860 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/core/info.py -rw-r--r-- root/root 35171 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/core/location.py -rw-r--r-- root/root 47652 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/core/moltype.py -rw-r--r-- root/root 18311 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/core/profile.py -rw-r--r-- root/root 69678 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/core/sequence.py -rw-r--r-- root/root 89939 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/core/tree.py drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/lib/python3/dist-packages/cogent3/data/ -rw-r--r-- root/root 345 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/data/__init__.py -rw-r--r-- root/root 3312 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/data/energy_params.py -rw-r--r-- root/root 1842 2021-11-04 08:29 ./usr/lib/python3/dist-packages/cogent3/data/molecular_weight.py drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/lib/python3/dist-packages/cogent3/draw/ -rw-r--r-- root/root 424 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/draw/__init__.py -rw-r--r-- root/root 31034 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/draw/dendrogram.py -rw-r--r-- root/root 9687 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/draw/dotplot.py -rw-r--r-- root/root 26639 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/draw/drawable.py -rw-r--r-- root/root 49216 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/draw/letter.py -rw-r--r-- root/root 4282 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/draw/logo.py drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/lib/python3/dist-packages/cogent3/evolve/ -rw-r--r-- root/root 744 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/evolve/__init__.py -rw-r--r-- root/root 4797 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/evolve/best_likelihood.py -rw-r--r-- root/root 7168 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/evolve/bootstrap.py -rwxr-xr-x root/root 95138 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/evolve/coevolution.py -rw-r--r-- root/root 3496 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/evolve/discrete_markov.py -rw-r--r-- root/root 13337 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/evolve/distance.py -rw-r--r-- root/root 25378 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/evolve/fast_distance.py -rw-r--r-- root/root 9978 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/evolve/likelihood_calculation.py -rw-r--r-- root/root 42389 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/evolve/likelihood_function.py -rw-r--r-- root/root 10919 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/evolve/likelihood_tree.py -rw-r--r-- root/root 1501 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/evolve/likelihood_tree_numba.py -rw-r--r-- root/root 64281 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/evolve/models.py -rw-r--r-- root/root 10854 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/evolve/motif_prob_model.py -rw-r--r-- root/root 7075 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/evolve/ns_substitution_model.py -rw-r--r-- root/root 848 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/evolve/pairwise_distance_numba.py -rw-r--r-- root/root 20493 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/evolve/parameter_controller.py -rw-r--r-- root/root 9239 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/evolve/predicate.py -rw-r--r-- root/root 5039 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/evolve/simulate.py -rw-r--r-- root/root 3346 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/evolve/solved_models.py -rw-r--r-- root/root 1669 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/evolve/solved_models_numba.py -rw-r--r-- root/root 2393 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/evolve/substitution_calculation.py -rw-r--r-- root/root 37583 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/evolve/substitution_model.py drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/lib/python3/dist-packages/cogent3/format/ -rw-r--r-- root/root 731 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/format/__init__.py -rw-r--r-- root/root 1908 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/format/alignment.py -rw-r--r-- root/root 5122 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/format/bedgraph.py -rw-r--r-- root/root 2203 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/format/clustal.py -rw-r--r-- root/root 1727 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/format/fasta.py -rw-r--r-- root/root 1619 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/format/gde.py -rw-r--r-- root/root 1346 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/format/nexus.py -rw-r--r-- root/root 1695 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/format/paml.py -rw-r--r-- root/root 2222 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/format/phylip.py -rw-r--r-- root/root 31886 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/format/table.py -rw-r--r-- root/root 3226 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/format/util.py drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/lib/python3/dist-packages/cogent3/maths/ -rw-r--r-- root/root 704 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/maths/__init__.py -rw-r--r-- root/root 52511 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/maths/distance_transform.py -rw-r--r-- root/root 6772 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/maths/geometry.py -rw-r--r-- root/root 7224 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/maths/markov.py -rw-r--r-- root/root 3467 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/maths/matrix_exponential_integration.py -rw-r--r-- root/root 4751 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/maths/matrix_exponentiation.py -rw-r--r-- root/root 3907 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/maths/matrix_logarithm.py -rw-r--r-- root/root 4115 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/maths/measure.py -rw-r--r-- root/root 6592 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/maths/optimisers.py -rw-r--r-- root/root 8779 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/maths/period.py -rw-r--r-- root/root 1484 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/maths/period_numba.py -rw-r--r-- root/root 3579 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/maths/scipy_optimisers.py -rw-r--r-- root/root 16787 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/maths/scipy_optimize.py -rw-r--r-- root/root 9367 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/maths/simannealingoptimiser.py -rw-r--r-- root/root 4149 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/maths/solve.py drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/lib/python3/dist-packages/cogent3/maths/stats/ -rw-r--r-- root/root 722 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/maths/stats/__init__.py -rw-r--r-- root/root 13505 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/maths/stats/contingency.py -rw-r--r-- root/root 15404 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/maths/stats/distribution.py -rw-r--r-- root/root 1107 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/maths/stats/information_criteria.py -rw-r--r-- root/root 6214 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/maths/stats/jackknife.py -rw-r--r-- root/root 3719 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/maths/stats/kendall.py -rw-r--r-- root/root 3826 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/maths/stats/ks.py -rw-r--r-- root/root 11922 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/maths/stats/number.py -rw-r--r-- root/root 7103 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/maths/stats/period.py -rw-r--r-- root/root 33133 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/maths/stats/special.py -rw-r--r-- root/root 63916 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/maths/stats/test.py -rw-r--r-- root/root 8182 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/maths/util.py drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/lib/python3/dist-packages/cogent3/parse/ -rw-r--r-- root/root 957 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/parse/__init__.py -rw-r--r-- root/root 11645 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/parse/blast.py -rw-r--r-- root/root 10002 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/parse/blast_xml.py -rw-r--r-- root/root 5063 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/parse/cigar.py -rw-r--r-- root/root 1129 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/parse/cisbp.py -rw-r--r-- root/root 3458 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/parse/clustal.py -rw-r--r-- root/root 1591 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/parse/cogent3_json.py -rw-r--r-- root/root 2164 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/parse/dialign.py -rw-r--r-- root/root 58796 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/parse/ebi.py -rw-r--r-- root/root 9958 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/parse/fasta.py -rw-r--r-- root/root 4447 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/parse/gbseq.py -rw-r--r-- root/root 1740 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/parse/gcg.py -rw-r--r-- root/root 22497 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/parse/genbank.py -rw-r--r-- root/root 3704 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/parse/gff.py -rw-r--r-- root/root 2846 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/parse/greengenes.py -rw-r--r-- root/root 1256 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/parse/jaspar.py -rw-r--r-- root/root 10510 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/parse/locuslink.py -rw-r--r-- root/root 9261 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/parse/ncbi_taxonomy.py -rw-r--r-- root/root 7157 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/parse/newick.py -rw-r--r-- root/root 7284 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/parse/nexus.py -rw-r--r-- root/root 1064 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/parse/paml.py -rw-r--r-- root/root 1517 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/parse/paml_matrix.py -rw-r--r-- root/root 3945 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/parse/phylip.py -rw-r--r-- root/root 2059 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/parse/psl.py -rw-r--r-- root/root 5320 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/parse/rdb.py -rw-r--r-- root/root 20525 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/parse/record.py -rw-r--r-- root/root 6823 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/parse/record_finder.py -rw-r--r-- root/root 3165 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/parse/sequence.py -rw-r--r-- root/root 5432 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/parse/table.py -rw-r--r-- root/root 2485 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/parse/tinyseq.py -rw-r--r-- root/root 6350 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/parse/tree.py -rw-r--r-- root/root 2660 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/parse/tree_xml.py -rw-r--r-- root/root 4256 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/parse/unigene.py drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/lib/python3/dist-packages/cogent3/phylo/ -rw-r--r-- root/root 412 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/phylo/__init__.py -rw-r--r-- root/root 10622 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/phylo/consensus.py -rw-r--r-- root/root 3358 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/phylo/least_squares.py -rw-r--r-- root/root 2547 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/phylo/maximum_likelihood.py -rw-r--r-- root/root 9797 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/phylo/nj.py -rw-r--r-- root/root 5414 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/phylo/tree_collection.py -rw-r--r-- root/root 9845 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/phylo/tree_space.py -rw-r--r-- root/root 2868 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/phylo/util.py drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/lib/python3/dist-packages/cogent3/recalculation/ -rw-r--r-- root/root 357 2021-11-04 08:29 ./usr/lib/python3/dist-packages/cogent3/recalculation/__init__.py -rw-r--r-- root/root 22874 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/recalculation/calculation.py -rw-r--r-- root/root 22077 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/recalculation/definition.py -rw-r--r-- root/root 30598 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/recalculation/scope.py -rw-r--r-- root/root 2949 2021-11-04 08:29 ./usr/lib/python3/dist-packages/cogent3/recalculation/setting.py drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/lib/python3/dist-packages/cogent3/util/ -rw-r--r-- root/root 685 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/util/__init__.py -rw-r--r-- root/root 1520 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/util/checkpointing.py -rw-r--r-- root/root 10180 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/util/deserialise.py -rw-r--r-- root/root 19893 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/util/dict_array.py -rw-r--r-- root/root 40023 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/util/misc.py -rw-r--r-- root/root 5576 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/util/parallel.py -rw-r--r-- root/root 6774 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/util/progress_display.py -rwxr-xr-x root/root 16572 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/util/recode_alignment.py -rw-r--r-- root/root 69970 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/util/table.py -rw-r--r-- root/root 3678 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/util/transform.py -rw-r--r-- root/root 3421 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/util/union_dict.py -rw-r--r-- root/root 1914 2021-10-12 00:17 ./usr/lib/python3/dist-packages/cogent3/util/warning.py drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/share/ drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/share/doc/ drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/share/doc/python3-cogent3/ -rw-r--r-- root/root 2587 2021-11-04 08:29 ./usr/share/doc/python3-cogent3/README.Debian -rw-r--r-- root/root 364 2021-11-04 08:29 ./usr/share/doc/python3-cogent3/README.test -rw-r--r-- root/root 1102 2021-11-04 08:29 ./usr/share/doc/python3-cogent3/changelog.Debian.gz -rw-r--r-- root/root 1987 2021-11-04 08:29 ./usr/share/doc/python3-cogent3/copyright -rw-r--r-- root/root 478 2021-11-04 08:29 ./usr/share/doc/python3-cogent3/run-unit-test drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/share/doc/python3-cogent3/tests/ -rw-r--r-- root/root 585 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/__init__.py -rw-r--r-- root/root 1916 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/benchmark.py.gz -rw-r--r-- root/root 1450 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/benchmark_aligning.py drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/share/doc/python3-cogent3/tests/data/ -rw-r--r-- root/root 99549 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/1A1X.pdb -rw-r--r-- root/root 83673 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/1LJO.pdb -rw-r--r-- root/root 163053 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/2E12.pdb -rw-r--r-- root/root 2102 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/ENSG00000198712.fa -rw-r--r-- root/root 12006 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/F6AVWTA01.sff.gz -rw-r--r-- root/root 146765 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/Homo_sapiens_codon_usage.pri.gz -rw-r--r-- root/root 682 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/M0926_1.02.txt -rw-r--r-- root/root 5905 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/annotated_seq.gb.gz -rw-r--r-- root/root 854 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/bowtie_output.map -rw-r--r-- root/root 168104 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/brca1.fasta -rw-r--r-- root/root 1323 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/brca1_5.250.paml -rw-r--r-- root/root 352 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/brca1_5.paml -rw-r--r-- root/root 47 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/brca1_5.tree -rw-r--r-- root/root 104 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/c_elegans_WS199_dna_shortened.fasta -rw-r--r-- root/root 1296 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/c_elegans_WS199_shortened_gff.gff3 -rw-r--r-- root/root 1312 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/fastq.txt -rw-r--r-- root/root 1357 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/formattest.aln.gz -rw-r--r-- root/root 3122 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/formattest.fasta -rw-r--r-- root/root 790 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/formattest.fasta.bz2 -rw-r--r-- root/root 719 2021-11-04 08:29 ./usr/share/doc/python3-cogent3/tests/data/formattest.fasta.gz -rw-r--r-- root/root 3105 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/formattest.gde -rw-r--r-- root/root 3499 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/formattest.msf -rw-r--r-- root/root 3103 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/formattest.paml -rw-r--r-- root/root 3528 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/formattest.phylip -rw-r--r-- root/root 514 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/gff2_test.gff -rw-r--r-- root/root 1321 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/interleaved.phylip.gz -rw-r--r-- root/root 12921 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/long_testseqs.fasta -rw-r--r-- root/root 157 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/long_testseqs.tree -rw-r--r-- root/root 579 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/murphy.tree -rw-r--r-- root/root 2813 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/nexus_aa.nxs -rw-r--r-- root/root 478 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/nexus_comments.nex -rw-r--r-- root/root 2387 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/nexus_dna.nex.gz -rw-r--r-- root/root 401 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/nexus_mixed.nex -rw-r--r-- root/root 20093 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/primate_brca1.fasta -rw-r--r-- root/root 69 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/primate_brca1.tree -rw-r--r-- root/root 29415 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/primates_brca1.fasta -rw-r--r-- root/root 101 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/primates_brca1.tree -rw-r--r-- root/root 244 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/sample.jaspar -rw-r--r-- root/root 251 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/sample.tsv -rw-r--r-- root/root 1272 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/scitrack.log.gz -rw-r--r-- root/root 9918 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/site-het-param-rules.json -rw-r--r-- root/root 767 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/test.psl -rw-r--r-- root/root 2216 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/data/test.sff drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/share/doc/python3-cogent3/tests/test_align/ -rw-r--r-- root/root 339 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_align/__init__.py -rw-r--r-- root/root 2757 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_align/test_align.py.gz drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/share/doc/python3-cogent3/tests/test_app/ -rw-r--r-- root/root 4678 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_app/test_align.py.gz -rw-r--r-- root/root 1761 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_app/test_app_mpi.py -rw-r--r-- root/root 3784 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_app/test_composable.py.gz -rw-r--r-- root/root 5506 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_app/test_data_store.py.gz -rw-r--r-- root/root 1888 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_app/test_dist.py.gz -rw-r--r-- root/root 5352 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_app/test_evo.py.gz -rw-r--r-- root/root 1230 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_app/test_init.py.gz -rw-r--r-- root/root 4061 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_app/test_io.py.gz -rw-r--r-- root/root 2427 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_app/test_result.py.gz -rw-r--r-- root/root 3789 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_app/test_sample.py.gz -rw-r--r-- root/root 1594 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_app/test_translate.py.gz -rw-r--r-- root/root 2055 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_app/test_tree.py.gz drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/share/doc/python3-cogent3/tests/test_cluster/ -rw-r--r-- root/root 360 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_cluster/__init__.py -rw-r--r-- root/root 1669 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_cluster/test_UPGMA.py.gz drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/share/doc/python3-cogent3/tests/test_core/ -rw-r--r-- root/root 724 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_core/__init__.py -rw-r--r-- root/root 25747 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_core/test_alignment.py.gz -rw-r--r-- root/root 2938 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_core/test_alphabet.py.gz -rw-r--r-- root/root 2418 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_core/test_annotation.py.gz -rw-r--r-- root/root 6562 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_core/test_core_standalone.py.gz -rw-r--r-- root/root 6269 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_core/test_features.py.gz -rw-r--r-- root/root 3771 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_core/test_genetic_code.py.gz -rw-r--r-- root/root 1728 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_core/test_info.py.gz -rw-r--r-- root/root 4162 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_core/test_location.py.gz -rw-r--r-- root/root 1559 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_core/test_maps.py.gz -rw-r--r-- root/root 7821 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_core/test_moltype.py.gz -rw-r--r-- root/root 3720 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_core/test_profile.py.gz -rw-r--r-- root/root 2729 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_core/test_seq_aln_integration.py.gz -rw-r--r-- root/root 9907 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_core/test_sequence.py.gz -rw-r--r-- root/root 17063 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_core/test_tree.py.gz drwxr-xr-x root/root 0 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_data/ -rw-r--r-- root/root 311 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_data/__init__.py -rw-r--r-- root/root 1794 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_data/test_molecular_weight.py drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/share/doc/python3-cogent3/tests/test_draw/ -rw-r--r-- root/root 404 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_draw/__init__.py -rw-r--r-- root/root 2064 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_draw/test_dendrogram.py.gz -rw-r--r-- root/root 1664 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_draw/test_dotplot.py.gz -rw-r--r-- root/root 3263 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_draw/test_draw_integration.py.gz -rw-r--r-- root/root 3078 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_draw/test_logo.py -rw-r--r-- root/root 1500 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_draw/test_shapes.py drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/share/doc/python3-cogent3/tests/test_evolve/ -rw-r--r-- root/root 604 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_evolve/__init__.py -rw-r--r-- root/root 1366 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_evolve/test_best_likelihood.py.gz -rw-r--r-- root/root 1692 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_evolve/test_bootstrap.py.gz -rw-r--r-- root/root 166617 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_evolve/test_coevolution.py.gz -rw-r--r-- root/root 5975 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_evolve/test_distance.py.gz -rw-r--r-- root/root 13428 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_evolve/test_likelihood_function.py.gz -rw-r--r-- root/root 1525 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_evolve/test_models.py.gz -rw-r--r-- root/root 1293 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_evolve/test_motifchange.py.gz -rw-r--r-- root/root 3776 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_evolve/test_newq.py.gz -rw-r--r-- root/root 15027 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_evolve/test_ns_substitution_model.py.gz -rw-r--r-- root/root 2295 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_evolve/test_parameter_controller.py.gz -rw-r--r-- root/root 2153 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_evolve/test_scale_rules.py.gz -rw-r--r-- root/root 2652 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_evolve/test_simulation.py -rw-r--r-- root/root 2685 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_evolve/test_substitution_model.py.gz drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/share/doc/python3-cogent3/tests/test_format/ -rw-r--r-- root/root 424 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_format/__init__.py -rw-r--r-- root/root 1053 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_format/test_bedgraph.py.gz -rw-r--r-- root/root 2753 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_format/test_clustal.py -rw-r--r-- root/root 2420 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_format/test_fasta.py drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/share/doc/python3-cogent3/tests/test_maths/ -rw-r--r-- root/root 562 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_maths/__init__.py -rw-r--r-- root/root 4048 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_maths/test_distance_transform.py.gz -rw-r--r-- root/root 1839 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_maths/test_geometry.py.gz -rw-r--r-- root/root 1575 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_maths/test_matrix_exponential_integration.py.gz -rw-r--r-- root/root 1363 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_maths/test_matrix_logarithm.py.gz -rw-r--r-- root/root 1949 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_maths/test_measure.py.gz -rw-r--r-- root/root 3467 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_maths/test_optimisers.py -rw-r--r-- root/root 2950 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_maths/test_period.py.gz drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/share/doc/python3-cogent3/tests/test_maths/test_stats/ -rw-r--r-- root/root 401 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_maths/test_stats/__init__.py -rw-r--r-- root/root 2234 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_maths/test_stats/test_contingency.py.gz -rw-r--r-- root/root 11030 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_maths/test_stats/test_distribution.py.gz -rw-r--r-- root/root 1081 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_maths/test_stats/test_information_criteria.py -rw-r--r-- root/root 1796 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_maths/test_stats/test_jackknife.py.gz -rw-r--r-- root/root 1515 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_maths/test_stats/test_ks.py.gz -rw-r--r-- root/root 2896 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_maths/test_stats/test_number.py.gz -rw-r--r-- root/root 1517 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_maths/test_stats/test_period.py.gz -rw-r--r-- root/root 4461 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_maths/test_stats/test_special.py.gz -rw-r--r-- root/root 17207 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_maths/test_stats/test_test.py.gz -rw-r--r-- root/root 1659 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_maths/test_util.py.gz drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/share/doc/python3-cogent3/tests/test_parse/ -rw-r--r-- root/root 865 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_parse/__init__.py -rw-r--r-- root/root 3105 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_parse/test_blast.py.gz -rw-r--r-- root/root 3260 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_parse/test_blast_xml.py.gz -rw-r--r-- root/root 3309 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_parse/test_cigar.py -rw-r--r-- root/root 1610 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_parse/test_clustal.py.gz -rw-r--r-- root/root 1729 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_parse/test_dialign.py.gz -rw-r--r-- root/root 8828 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_parse/test_ebi.py.gz -rw-r--r-- root/root 4413 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_parse/test_fasta.py.gz -rw-r--r-- root/root 1913 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_parse/test_gbseq.py.gz -rw-r--r-- root/root 6129 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_parse/test_genbank.py.gz -rw-r--r-- root/root 1490 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_parse/test_gff.py.gz -rw-r--r-- root/root 2161 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_parse/test_greengenes.py.gz -rw-r--r-- root/root 3798 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_parse/test_locuslink.py.gz -rw-r--r-- root/root 3443 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_parse/test_ncbi_taxonomy.py.gz -rw-r--r-- root/root 4093 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_parse/test_nexus.py.gz -rw-r--r-- root/root 2497 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_parse/test_pamlmatrix.py -rw-r--r-- root/root 4173 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_parse/test_phylip.py.gz -rw-r--r-- root/root 1756 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_parse/test_psl.py -rw-r--r-- root/root 1823 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_parse/test_pwm_parsers.py -rw-r--r-- root/root 2808 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_parse/test_rdb.py.gz -rw-r--r-- root/root 4584 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_parse/test_record.py.gz -rw-r--r-- root/root 1768 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_parse/test_record_finder.py.gz -rw-r--r-- root/root 1765 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_parse/test_tinyseq.py -rw-r--r-- root/root 2125 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_parse/test_tree.py.gz -rw-r--r-- root/root 2202 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_parse/test_unigene.py.gz -rw-r--r-- root/root 4099 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_phylo.py.gz -rw-r--r-- root/root 2313 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_recalculation.py.gz drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/share/doc/python3-cogent3/tests/test_util/ -rw-r--r-- root/root 554 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_util/__init__.py -rw-r--r-- root/root 3597 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_util/test_deserialise.py.gz -rw-r--r-- root/root 4013 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_util/test_dictarray.py.gz -rw-r--r-- root/root 10360 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_util/test_misc.py.gz -rw-r--r-- root/root 2781 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_util/test_parallel.py -rw-r--r-- root/root 2654 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_util/test_recode_alignment.py.gz -rw-r--r-- root/root 14380 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_util/test_table.py.gz -rw-r--r-- root/root 1918 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_util/test_transform.py.gz -rw-r--r-- root/root 1176 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/test_util/test_union_dict.py.gz -rw-r--r-- root/root 3333 2021-10-12 00:17 ./usr/share/doc/python3-cogent3/tests/timetrial.py drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/share/lintian/ drwxr-xr-x root/root 0 2021-11-04 08:29 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 75 2021-11-04 08:29 ./usr/share/lintian/overrides/python3-cogent3 +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build Type: any Build-Space: 36684 Build-Time: 585 Distribution: jammy-proposed Host Architecture: armhf Install-Time: 115 Job: python-cogent_2021.10.12a1+dfsg-1.dsc Machine Architecture: arm64 Package: python-cogent Package-Time: 702 Source-Version: 2021.10.12a1+dfsg-1 Space: 36684 Status: successful Version: 2021.10.12a1+dfsg-1 -------------------------------------------------------------------------------- Finished at 2022-04-09T09:20:57Z Build needed 00:11:42, 36684k disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=jammy --arch=armhf PACKAGEBUILD-22372247 Scanning for processes to kill in build PACKAGEBUILD-22372247