https://launchpad.net/ubuntu/+source/pyensembl/2.3.9-2/+build/27848328 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos03-amd64-040 5.4.0-172-generic #190-Ubuntu SMP Fri Feb 2 23:24:22 UTC 2024 x86_64 Buildd toolchain package versions: launchpad-buildd_236~650~ubuntu20.04.1 python3-lpbuildd_236~650~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.11 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1.1. Syncing the system clock with the buildd NTP service... 29 Feb 05:34:40 ntpdate[1863]: adjust time server 10.211.37.1 offset -0.002589 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27848328 --image-type chroot /home/buildd/filecache-default/1fe94ca8758119221c8de2550665a1bb335bd6a9 Creating target for build PACKAGEBUILD-27848328 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27848328 Starting target for build PACKAGEBUILD-27848328 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27848328 'deb http://ftpmaster.internal/ubuntu noble main universe' 'deb http://ftpmaster.internal/ubuntu noble-security main universe' 'deb http://ftpmaster.internal/ubuntu noble-updates main universe' 'deb http://ftpmaster.internal/ubuntu noble-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-27848328 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27848328 Updating target for build PACKAGEBUILD-27848328 Get:1 http://ftpmaster.internal/ubuntu noble InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu noble-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu noble-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 Packages [1430 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main Translation-en [519 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe amd64 Packages [15.1 MB] Get:8 http://ftpmaster.internal/ubuntu noble/universe Translation-en [6032 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 Packages [200 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [66.1 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 Packages [758 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [284 kB] Fetched 25.0 MB in 5s (5452 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: libperl5.36 libunistring2 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libapt-pkg6.0* usrmerge* The following NEW packages will be installed: cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-13-x86-64-linux-gnu gcc-14-base gcc-x86-64-linux-gnu libapt-pkg6.0t64 libperl5.38 libunistring5 perl-modules-5.38 The following packages will be upgraded: apt apt-utils base-files base-passwd bash bash-completion binutils binutils-common binutils-x86-64-linux-gnu bsdextrautils bsdutils bzip2 ca-certificates coreutils cpp cpp-13 dash debconf debconf-i18n debianutils diffutils dpkg dpkg-dev fakeroot g++ g++-13 gcc gcc-13 gcc-13-base gpg gpg-agent gpgconf gpgv grep gzip hostname init init-system-helpers krb5-locales libacl1 libapparmor1 libargon2-1 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdb5.3 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libfakeroot libfdisk1 libffi8 libgcc-13-dev libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgnutls30 libgomp1 libgpg-error-l10n libgpg-error0 libgprofng0 libgssapi-krb5-2 libhwasan0 libidn2-0 libip4tc2 libitm1 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblsan0 liblzma5 libmd0 libmount1 libncursesw6 libnsl-dev libnsl2 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libpng16-16 libproc2-0 libquadmath0 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libsqlite3-0 libssl3 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtext-charwidth-perl libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libtirpc3 libtsan2 libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev login lto-disabled-list mawk mount ncurses-base ncurses-bin openssl optipng passwd perl perl-base pinentry-curses procps psmisc readline-common sed sensible-utils systemd systemd-dev systemd-sysv sysvinit-utils tar tzdata ubuntu-keyring util-linux uuid-runtime xz-utils zlib1g 161 upgraded, 11 newly installed, 2 to remove and 0 not upgraded. Need to get 118 MB of archives. After this operation, 77.7 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble/main amd64 libnsl-dev amd64 1.3.0-3 [71.2 kB] Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 libcrypt-dev amd64 1:4.4.36-4 [128 kB] Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 libc6-dev amd64 2.39-0ubuntu2 [2126 kB] Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 libc-dev-bin amd64 2.39-0ubuntu2 [20.4 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 libtirpc-common all 1.3.4+ds-1build1 [8566 B] Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 libtirpc-dev amd64 1.3.4+ds-1build1 [222 kB] Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 libgssapi-krb5-2 amd64 1.20.1-5build1 [142 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main amd64 libkrb5-3 amd64 1.20.1-5build1 [346 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 libk5crypto3 amd64 1.20.1-5build1 [81.3 kB] Get:10 http://ftpmaster.internal/ubuntu noble/main amd64 libkrb5support0 amd64 1.20.1-5build1 [33.2 kB] Get:11 http://ftpmaster.internal/ubuntu noble/main amd64 libkeyutils1 amd64 1.6.3-3 [9386 B] Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 libssl3 amd64 3.0.10-1ubuntu4 [1909 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 libtirpc3 amd64 1.3.4+ds-1build1 [95.7 kB] Get:14 http://ftpmaster.internal/ubuntu noble/main amd64 libnsl2 amd64 1.3.0-3 [41.3 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 libcrypt1 amd64 1:4.4.36-4 [95.3 kB] Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 linux-libc-dev amd64 6.8.0-11.11 [1595 kB] Get:17 http://ftpmaster.internal/ubuntu noble/main amd64 libc6 amd64 2.39-0ubuntu2 [3262 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 libc-bin amd64 2.39-0ubuntu2 [682 kB] Get:19 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gcc-14-base amd64 14-20240221-2ubuntu1 [46.7 kB] Get:20 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libgcc-s1 amd64 14-20240221-2ubuntu1 [78.1 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 base-files amd64 13ubuntu7 [74.2 kB] Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 debianutils amd64 5.16 [93.9 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 bash amd64 5.2.21-2ubuntu2 [794 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main amd64 bsdutils amd64 1:2.39.3-6ubuntu2 [94.6 kB] Get:25 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 coreutils amd64 9.4-3ubuntu2 [1412 kB] Get:26 http://ftpmaster.internal/ubuntu noble/main amd64 bzip2 amd64 1.0.8-5ubuntu1 [34.6 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 libbz2-1.0 amd64 1.0.8-5ubuntu1 [34.4 kB] Get:28 http://ftpmaster.internal/ubuntu noble/main amd64 libgpg-error-l10n all 1.47-3build1 [8024 B] Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 libgpg-error0 amd64 1.47-3build1 [70.0 kB] Get:30 http://ftpmaster.internal/ubuntu noble/main amd64 libgcrypt20 amd64 1.10.3-2 [532 kB] Get:31 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 liblzma5 amd64 5.6.0-0.1 [157 kB] Get:32 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libstdc++6 amd64 14-20240221-2ubuntu1 [795 kB] Get:33 http://ftpmaster.internal/ubuntu noble/main amd64 libacl1 amd64 2.3.2-1 [16.7 kB] Get:34 http://ftpmaster.internal/ubuntu noble/main amd64 libapparmor1 amd64 4.0.0~alpha4-0ubuntu1 [49.0 kB] Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libaudit-common all 1:3.1.2-2.1 [5674 B] Get:36 http://ftpmaster.internal/ubuntu noble/main amd64 libcap-ng0 amd64 0.8.4-2 [15.0 kB] Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libaudit1 amd64 1:3.1.2-2.1 [46.8 kB] Get:38 http://ftpmaster.internal/ubuntu noble/main amd64 libblkid1 amd64 2.39.3-6ubuntu2 [122 kB] Get:39 http://ftpmaster.internal/ubuntu noble/main amd64 libcap2 amd64 1:2.66-5ubuntu1 [29.9 kB] Get:40 http://ftpmaster.internal/ubuntu noble/main amd64 libzstd1 amd64 1.5.5+dfsg2-2 [297 kB] Get:41 http://ftpmaster.internal/ubuntu noble/main amd64 libkmod2 amd64 30+20230601-2ubuntu1 [51.4 kB] Get:42 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-8-0 amd64 10.42-4ubuntu1 [228 kB] Get:43 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libselinux1 amd64 3.5-2build2 [79.2 kB] Get:44 http://ftpmaster.internal/ubuntu noble/main amd64 libmount1 amd64 2.39.3-6ubuntu2 [134 kB] Get:45 http://ftpmaster.internal/ubuntu noble/main amd64 perl-modules-5.38 all 5.38.2-3 [3110 kB] Get:46 http://ftpmaster.internal/ubuntu noble/main amd64 libperl5.38 amd64 5.38.2-3 [4871 kB] Get:47 http://ftpmaster.internal/ubuntu noble/main amd64 perl amd64 5.38.2-3 [231 kB] Get:48 http://ftpmaster.internal/ubuntu noble/main amd64 perl-base amd64 5.38.2-3 [1823 kB] Get:49 http://ftpmaster.internal/ubuntu noble/main amd64 liblocale-gettext-perl amd64 1.07-6build1 [15.5 kB] Get:50 http://ftpmaster.internal/ubuntu noble/main amd64 libtext-iconv-perl amd64 1.7-8build1 [13.4 kB] Get:51 http://ftpmaster.internal/ubuntu noble/main amd64 libtext-charwidth-perl amd64 0.04-11build1 [9266 B] Get:52 http://ftpmaster.internal/ubuntu noble/main amd64 libdb5.3 amd64 5.3.28+dfsg2-4 [736 kB] Get:53 http://ftpmaster.internal/ubuntu noble/main amd64 libgdbm6 amd64 1.23-5 [33.3 kB] Get:54 http://ftpmaster.internal/ubuntu noble/main amd64 libgdbm-compat4 amd64 1.23-5 [6498 B] Get:55 http://ftpmaster.internal/ubuntu noble/main amd64 zlib1g amd64 1:1.3.dfsg-3ubuntu1 [63.3 kB] Get:56 http://ftpmaster.internal/ubuntu noble/main amd64 debconf-i18n all 1.5.86 [205 kB] Get:57 http://ftpmaster.internal/ubuntu noble/main amd64 debconf all 1.5.86 [124 kB] Get:58 http://ftpmaster.internal/ubuntu noble/main amd64 libpam0g amd64 1.5.2-9.1ubuntu3 [65.9 kB] Get:59 http://ftpmaster.internal/ubuntu noble/main amd64 libseccomp2 amd64 2.5.5-1ubuntu1 [50.3 kB] Get:60 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 systemd-sysv amd64 255.4-1ubuntu1 [11.9 kB] Get:61 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 systemd-dev all 255.4-1ubuntu1 [103 kB] Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 systemd amd64 255.4-1ubuntu1 [3470 kB] Get:63 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsystemd-shared amd64 255.4-1ubuntu1 [2067 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main amd64 libargon2-1 amd64 0~20190702+dfsg-4 [21.4 kB] Get:65 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libudev1 amd64 255.4-1ubuntu1 [174 kB] Get:66 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libdevmapper1.02.1 amd64 2:1.02.185-3ubuntu1 [139 kB] Get:67 http://ftpmaster.internal/ubuntu noble/main amd64 libuuid1 amd64 2.39.3-6ubuntu2 [34.5 kB] Get:68 http://ftpmaster.internal/ubuntu noble/main amd64 libcryptsetup12 amd64 2:2.6.1-6ubuntu1 [242 kB] Get:69 http://ftpmaster.internal/ubuntu noble/main amd64 libfdisk1 amd64 2.39.3-6ubuntu2 [146 kB] Get:70 http://ftpmaster.internal/ubuntu noble/main amd64 mount amd64 2.39.3-6ubuntu2 [118 kB] Get:71 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsystemd0 amd64 255.4-1ubuntu1 [432 kB] Get:72 http://ftpmaster.internal/ubuntu noble/main amd64 libxxhash0 amd64 0.8.2-2 [25.5 kB] Get:73 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libapt-pkg6.0t64 amd64 2.7.12+nmu1 [985 kB] Get:74 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 apt amd64 2.7.12+nmu1 [1376 kB] Get:75 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 apt-utils amd64 2.7.12+nmu1 [217 kB] Get:76 http://ftpmaster.internal/ubuntu noble/main amd64 tar amd64 1.35+dfsg-3 [253 kB] Get:77 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 dpkg amd64 1.22.5ubuntu2 [1284 kB] Get:78 http://ftpmaster.internal/ubuntu noble/main amd64 dash amd64 0.5.12-6ubuntu4 [89.8 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main amd64 diffutils amd64 1:3.10-1 [176 kB] Get:80 http://ftpmaster.internal/ubuntu noble/main amd64 grep amd64 3.11-4 [176 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main amd64 gzip amd64 1.12-1ubuntu2 [98.8 kB] Get:82 http://ftpmaster.internal/ubuntu noble/main amd64 hostname amd64 3.23+nmu2ubuntu1 [11.0 kB] Get:83 http://ftpmaster.internal/ubuntu noble/main amd64 login amd64 1:4.13+dfsg1-4ubuntu1 [201 kB] Get:84 http://ftpmaster.internal/ubuntu noble/main amd64 ncurses-bin amd64 6.4+20240113-1ubuntu1 [188 kB] Get:85 http://ftpmaster.internal/ubuntu noble/main amd64 sed amd64 4.9-2 [204 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main amd64 util-linux amd64 2.39.3-6ubuntu2 [1127 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main amd64 libdebconfclient0 amd64 0.271ubuntu1 [11.3 kB] Get:88 http://ftpmaster.internal/ubuntu noble/main amd64 base-passwd amd64 3.6.3 [51.2 kB] Get:89 http://ftpmaster.internal/ubuntu noble/main amd64 init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:90 http://ftpmaster.internal/ubuntu noble/main amd64 ncurses-base all 6.4+20240113-1ubuntu1 [25.4 kB] Get:91 http://ftpmaster.internal/ubuntu noble/main amd64 sysvinit-utils amd64 3.08-6ubuntu2 [34.1 kB] Get:92 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gpgv amd64 2.4.4-2ubuntu8 [157 kB] Get:93 http://ftpmaster.internal/ubuntu noble/main amd64 ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:94 http://ftpmaster.internal/ubuntu noble/main amd64 libffi8 amd64 3.4.6-1 [24.7 kB] Get:95 http://ftpmaster.internal/ubuntu noble/main amd64 libp11-kit0 amd64 0.25.3-4ubuntu1 [299 kB] Get:96 http://ftpmaster.internal/ubuntu noble/main amd64 libunistring5 amd64 1.1-2 [537 kB] Get:97 http://ftpmaster.internal/ubuntu noble/main amd64 libidn2-0 amd64 2.3.7-2 [66.0 kB] Get:98 http://ftpmaster.internal/ubuntu noble/main amd64 libgnutls30 amd64 3.8.3-1ubuntu1 [996 kB] Get:99 http://ftpmaster.internal/ubuntu noble/main amd64 libpam-modules-bin amd64 1.5.2-9.1ubuntu3 [48.1 kB] Get:100 http://ftpmaster.internal/ubuntu noble/main amd64 libpam-modules amd64 1.5.2-9.1ubuntu3 [285 kB] Get:101 http://ftpmaster.internal/ubuntu noble/main amd64 init amd64 1.66ubuntu1 [6186 B] Get:102 http://ftpmaster.internal/ubuntu noble/main amd64 libsmartcols1 amd64 2.39.3-6ubuntu2 [64.1 kB] Get:103 http://ftpmaster.internal/ubuntu noble/main amd64 uuid-runtime amd64 2.39.3-6ubuntu2 [33.0 kB] Get:104 http://ftpmaster.internal/ubuntu noble/main amd64 libattr1 amd64 1:2.5.2-1 [11.4 kB] Get:105 http://ftpmaster.internal/ubuntu noble/main amd64 libmd0 amd64 1.1.0-2 [27.1 kB] Get:106 http://ftpmaster.internal/ubuntu noble/main amd64 libpam-runtime all 1.5.2-9.1ubuntu3 [40.4 kB] Get:107 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsemanage-common all 3.5-1build3 [10.1 kB] Get:108 http://ftpmaster.internal/ubuntu noble/main amd64 libsepol2 amd64 3.5-2 [300 kB] Get:109 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsemanage2 amd64 3.5-1build3 [93.0 kB] Get:110 http://ftpmaster.internal/ubuntu noble/main amd64 libncursesw6 amd64 6.4+20240113-1ubuntu1 [148 kB] Get:111 http://ftpmaster.internal/ubuntu noble/main amd64 libtinfo6 amd64 6.4+20240113-1ubuntu1 [108 kB] Get:112 http://ftpmaster.internal/ubuntu noble/main amd64 passwd amd64 1:4.13+dfsg1-4ubuntu1 [844 kB] Get:113 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 g++-13 amd64 13.2.0-16ubuntu1 [14.5 kB] Get:114 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gcc-13 amd64 13.2.0-16ubuntu1 [475 kB] Get:115 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 cpp-13 amd64 13.2.0-16ubuntu1 [1032 B] Get:116 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 cpp-13-x86-64-linux-gnu amd64 13.2.0-16ubuntu1 [11.2 MB] Get:117 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libcc1-0 amd64 14-20240221-2ubuntu1 [47.6 kB] Get:118 http://ftpmaster.internal/ubuntu noble/main amd64 libgprofng0 amd64 2.42-3ubuntu1 [851 kB] Get:119 http://ftpmaster.internal/ubuntu noble/main amd64 libctf0 amd64 2.42-3ubuntu1 [94.5 kB] Get:120 http://ftpmaster.internal/ubuntu noble/main amd64 libctf-nobfd0 amd64 2.42-3ubuntu1 [97.1 kB] Get:121 http://ftpmaster.internal/ubuntu noble/main amd64 libsframe1 amd64 2.42-3ubuntu1 [14.9 kB] Get:122 http://ftpmaster.internal/ubuntu noble/main amd64 binutils-x86-64-linux-gnu amd64 2.42-3ubuntu1 [2469 kB] Get:123 http://ftpmaster.internal/ubuntu noble/main amd64 libbinutils amd64 2.42-3ubuntu1 [573 kB] Get:124 http://ftpmaster.internal/ubuntu noble/main amd64 binutils amd64 2.42-3ubuntu1 [18.0 kB] Get:125 http://ftpmaster.internal/ubuntu noble/main amd64 binutils-common amd64 2.42-3ubuntu1 [239 kB] Get:126 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libstdc++-13-dev amd64 13.2.0-16ubuntu1 [2339 kB] Get:127 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libgomp1 amd64 14-20240221-2ubuntu1 [147 kB] Get:128 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libitm1 amd64 14-20240221-2ubuntu1 [29.1 kB] Get:129 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libatomic1 amd64 14-20240221-2ubuntu1 [10.4 kB] Get:130 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libasan8 amd64 14-20240221-2ubuntu1 [3025 kB] Get:131 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 liblsan0 amd64 14-20240221-2ubuntu1 [1309 kB] Get:132 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libgcc-13-dev amd64 13.2.0-16ubuntu1 [2687 kB] Get:133 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libtsan2 amd64 14-20240221-2ubuntu1 [2732 kB] Get:134 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libubsan1 amd64 14-20240221-2ubuntu1 [1171 kB] Get:135 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libhwasan0 amd64 14-20240221-2ubuntu1 [1629 kB] Get:136 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libquadmath0 amd64 14-20240221-2ubuntu1 [155 kB] Get:137 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gcc-13-x86-64-linux-gnu amd64 13.2.0-16ubuntu1 [21.8 MB] Get:138 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 g++-13-x86-64-linux-gnu amd64 13.2.0-16ubuntu1 [12.5 MB] Get:139 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gcc-13-base amd64 13.2.0-16ubuntu1 [47.2 kB] Get:140 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libproc2-0 amd64 2:4.0.4-4ubuntu1 [59.2 kB] Get:141 http://ftpmaster.internal/ubuntu noble/main amd64 mawk amd64 1.3.4.20240123-1 [127 kB] Get:142 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 procps amd64 2:4.0.4-4ubuntu1 [708 kB] Get:143 http://ftpmaster.internal/ubuntu noble/main amd64 sensible-utils all 0.0.22 [22.5 kB] Get:144 http://ftpmaster.internal/ubuntu noble/main amd64 openssl amd64 3.0.10-1ubuntu4 [1002 kB] Get:145 http://ftpmaster.internal/ubuntu noble/main amd64 ca-certificates all 20240203 [159 kB] Get:146 http://ftpmaster.internal/ubuntu noble/main amd64 krb5-locales all 1.20.1-5build1 [13.7 kB] Get:147 http://ftpmaster.internal/ubuntu noble/main amd64 libip4tc2 amd64 1.8.10-3ubuntu1 [23.3 kB] Get:148 http://ftpmaster.internal/ubuntu noble/main amd64 readline-common all 8.2-3 [56.2 kB] Get:149 http://ftpmaster.internal/ubuntu noble/main amd64 libreadline8 amd64 8.2-3 [152 kB] Get:150 http://ftpmaster.internal/ubuntu noble/main amd64 libsqlite3-0 amd64 3.45.1-1 [701 kB] Get:151 http://ftpmaster.internal/ubuntu noble/main amd64 tzdata all 2024a-1ubuntu1 [273 kB] Get:152 http://ftpmaster.internal/ubuntu noble/main amd64 bash-completion all 1:2.11-8 [180 kB] Get:153 http://ftpmaster.internal/ubuntu noble/main amd64 bsdextrautils amd64 2.39.3-6ubuntu2 [73.7 kB] Get:154 http://ftpmaster.internal/ubuntu noble/main amd64 libpng16-16 amd64 1.6.43-1 [186 kB] Get:155 http://ftpmaster.internal/ubuntu noble/main amd64 psmisc amd64 23.6-2 [178 kB] Get:156 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 xz-utils amd64 5.6.0-0.1 [272 kB] Get:157 http://ftpmaster.internal/ubuntu noble/main amd64 g++ amd64 4:13.2.0-7ubuntu1 [1100 B] Get:158 http://ftpmaster.internal/ubuntu noble/main amd64 gcc amd64 4:13.2.0-7ubuntu1 [5018 B] Get:159 http://ftpmaster.internal/ubuntu noble/main amd64 cpp amd64 4:13.2.0-7ubuntu1 [22.4 kB] Get:160 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [5326 B] Get:161 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1212 B] Get:162 http://ftpmaster.internal/ubuntu noble/main amd64 g++-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [964 B] Get:163 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 dpkg-dev all 1.22.5ubuntu2 [1061 kB] Get:164 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libdpkg-perl all 1.22.5ubuntu2 [269 kB] Get:165 http://ftpmaster.internal/ubuntu noble/main amd64 lto-disabled-list all 47 [12.4 kB] Get:166 http://ftpmaster.internal/ubuntu noble/main amd64 libfakeroot amd64 1.33-1 [32.4 kB] Get:167 http://ftpmaster.internal/ubuntu noble/main amd64 fakeroot amd64 1.33-1 [67.2 kB] Get:168 http://ftpmaster.internal/ubuntu noble/main amd64 pinentry-curses amd64 1.2.1-3ubuntu1 [34.9 kB] Get:169 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gpg amd64 2.4.4-2ubuntu8 [565 kB] Get:170 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gpgconf amd64 2.4.4-2ubuntu8 [103 kB] Get:171 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gpg-agent amd64 2.4.4-2ubuntu8 [227 kB] Get:172 http://ftpmaster.internal/ubuntu noble/main amd64 optipng amd64 0.7.8+ds-1 [110 kB] Preconfiguring packages ... 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Processing triggers for libc-bin (2.39-0ubuntu2) ... Processing triggers for debianutils (5.16) ... Processing triggers for ca-certificates (20240203) ... 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-27848328 amd64 noble-proposed -c chroot:build-PACKAGEBUILD-27848328 --arch=amd64 --dist=noble-proposed --nolog -A pyensembl_2.3.9-2.dsc Initiating build PACKAGEBUILD-27848328 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-172-generic #190-Ubuntu SMP Fri Feb 2 23:24:22 UTC 2024 x86_64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos03-amd64-040.buildd +==============================================================================+ | pyensembl 2.3.9-2 (amd64) Thu, 29 Feb 2024 05:35:12 +0000 | +==============================================================================+ Package: pyensembl Version: 2.3.9-2 Source Version: 2.3.9-2 Distribution: noble-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-27848328/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/pyensembl-nUffLw/resolver-HreQGW' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- pyensembl_2.3.9-2.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/pyensembl-nUffLw/pyensembl-2.3.9' with '<>' I: NOTICE: Log filtering will replace 'build/pyensembl-nUffLw' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3-setuptools, python3-all, python3-pandas, python3-numpy, python3-datacache, python3-serializable, python3-memoized-property, python3-gtfparse, python3-nose, python3-pytest, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3-setuptools, python3-all, python3-pandas, python3-numpy, python3-datacache, python3-serializable, python3-memoized-property, python3-gtfparse, python3-nose, python3-pytest, 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 [460 B] Get:5 copy:/<>/apt_archive ./ Packages [532 B] Fetched 1949 B in 0s (188 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: apt-utils bash-completion debconf-i18n krb5-locales libgpg-error-l10n libgpm2 libip4tc2 liblocale-gettext-perl libnss-nis libnss-nisplus libperl5.36 libtext-charwidth-perl libtext-iconv-perl libtext-wrapi18n-perl libunistring2 perl-modules-5.36 psmisc uuid-runtime Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libblas3 libdebhelper-perl libdw1 libelf1 libexpat1 libfile-stripnondeterminism-perl libgfortran5 libicu74 liblapack3 libmagic-mgc libmagic1 libpipeline1 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libpython3.12-minimal libpython3.12-stdlib libsub-override-perl libtool libuchardet0 libxml2 m4 man-db media-types netbase po-debconf python3 python3-all python3-appdirs python3-certifi python3-chardet python3-datacache python3-dateutil python3-distutils python3-gtfparse python3-idna python3-iniconfig python3-lib2to3 python3-memoized-property python3-minimal python3-nose python3-numpy python3-packaging python3-pandas python3-pandas-lib python3-pkg-resources python3-pluggy python3-pytest python3-requests python3-serializable python3-setuptools python3-simplejson python3-six python3-typechecks python3-tz python3-urllib3 python3-zombie-imp python3.11 python3.11-minimal python3.12 python3.12-minimal Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make flit python3-build python3-installer python3-wheel gettext-doc libasprintf-dev libgettextpo-dev groff libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python-nose-doc gfortran python3-dev python-pandas-doc python3-statsmodels python3-cryptography python3-openssl python3-socks python-requests-doc python-setuptools-doc python3-brotli python3.11-venv python3.11-doc binfmt-support python3.12-venv python3.12-doc Recommended packages: curl | wget | lynx libarchive-cpio-perl libltdl-dev libmail-sendmail-perl python3-scipy python3-matplotlib python3-bottleneck python3-numexpr python3-odf python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables python3-jinja2 python3-numba python3-pygments The following NEW packages will be installed: autoconf automake autopoint autotools-dev debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libblas3 libdebhelper-perl libdw1 libelf1 libexpat1 libfile-stripnondeterminism-perl libgfortran5 libicu74 liblapack3 libmagic-mgc libmagic1 libpipeline1 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libpython3.12-minimal libpython3.12-stdlib libsub-override-perl libtool libuchardet0 libxml2 m4 man-db media-types netbase po-debconf python3 python3-all python3-appdirs python3-certifi python3-chardet python3-datacache python3-dateutil python3-distutils python3-gtfparse python3-idna python3-iniconfig python3-lib2to3 python3-memoized-property python3-minimal python3-nose python3-numpy python3-packaging python3-pandas python3-pandas-lib python3-pkg-resources python3-pluggy python3-pytest python3-requests python3-serializable python3-setuptools python3-simplejson python3-six python3-typechecks python3-tz python3-urllib3 python3-zombie-imp python3.11 python3.11-minimal python3.12 python3.12-minimal sbuild-build-depends-main-dummy 0 upgraded, 78 newly installed, 0 to remove and 0 not upgraded. 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amd64 python3-pandas-lib amd64 2.1.4+dfsg-4ubuntu2 [8348 kB] Get:63 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main amd64 python3-idna all 3.6-2 [46.0 kB] Get:65 http://ftpmaster.internal/ubuntu noble/main amd64 python3-urllib3 all 2.0.7-1 [113 kB] Get:66 http://ftpmaster.internal/ubuntu noble/main amd64 python3-requests all 2.31.0+dfsg-1ubuntu1 [50.7 kB] Get:67 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-typechecks all 0.1.0+ds-3 [4440 B] Get:68 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-datacache all 1.2.1-2 [12.8 kB] Get:69 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-gtfparse all 1.3.0+ds-1 [10.1 kB] Get:70 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] Get:71 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-memoized-property all 1.0.3-2 [5286 B] Get:72 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-zombie-imp all 0.0.2-2 [11.9 kB] Get:73 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-nose all 1.3.7-12 [117 kB] Get:74 http://ftpmaster.internal/ubuntu noble/main amd64 python3-packaging all 23.2-1 [40.6 kB] Get:75 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-pluggy all 1.4.0-1 [20.4 kB] Get:76 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 python3-pytest all 8.0.2-1 [248 kB] Get:77 http://ftpmaster.internal/ubuntu noble/main amd64 python3-simplejson amd64 3.19.2-1build1 [62.8 kB] Get:78 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-serializable all 0.4.0+ds-1 [8210 B] Preconfiguring packages ... Fetched 54.9 MB in 3s (19.3 MB/s) Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... 15738 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.2-1_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.2-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.0-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.2-1_amd64.deb ... Unpacking python3.12-minimal (3.12.2-1) ... Setting up libpython3.12-minimal:amd64 (3.12.2-1) ... Setting up libexpat1:amd64 (2.6.0-1) ... Setting up python3.12-minimal (3.12.2-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 16056 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.12.1-0ubuntu2_amd64.deb ... 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Setting up autotools-dev (20220109.1) ... Setting up libblas3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up autopoint (0.21-14ubuntu1) ... Setting up libgfortran5:amd64 (14-20240221-2ubuntu1) ... Setting up autoconf (2.71-3) ... Setting up libicu74:amd64 (74.2-1ubuntu1) ... Setting up libuchardet0:amd64 (0.0.8-1) ... Setting up libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... Setting up libpython3.11-minimal:amd64 (3.11.8-1) ... Setting up libelf1:amd64 (0.190-1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3ubuntu1) ... Setting up automake (1:1.16.5-1.3ubuntu1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up python3.11-minimal (3.11.8-1) ... Setting up libdw1:amd64 (0.190-1) ... Setting up liblapack3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.21-14ubuntu1) ... Setting up libpython3.12-stdlib:amd64 (3.12.2-1) ... Setting up libtool (2.4.7-7) ... Setting up libpython3.11-stdlib:amd64 (3.11.8-1) ... Setting up python3.12 (3.12.2-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-3) ... Setting up debugedit (1:5.0-5) ... Setting up libpython3-stdlib:amd64 (3.12.1-0ubuntu2) ... Setting up python3.11 (3.11.8-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.12.1-0ubuntu2) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /usr/lib/systemd/system/man-db.timer. Setting up python3-tz (2024.1-2) ... Setting up python3-six (1.16.0-4) ... Setting up python3-simplejson (3.19.2-1build1) ... Setting up python3-packaging (23.2-1) ... Setting up python3-certifi (2023.11.17-1) ... Setting up python3-idna (3.6-2) ... Setting up python3-urllib3 (2.0.7-1) ... Setting up python3-pluggy (1.4.0-1) ... Setting up python3-dateutil (2.8.2-3) ... Setting up python3-lib2to3 (3.11.5-1) ... Setting up python3-appdirs (1.4.4-4) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.11.5-1) ... python3.12: can't get files for byte-compilation Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-zombie-imp (0.0.2-2) ... Setting up python3-setuptools (68.1.2-2) ... Setting up python3-typechecks (0.1.0+ds-3) ... Setting up python3-memoized-property (1.0.3-2) ... Setting up python3-pytest (8.0.2-1) ... Setting up python3-all (3.12.1-0ubuntu2) ... Setting up debhelper (13.14.1ubuntu1) ... Setting up python3-serializable (0.4.0+ds-1) ... Setting up python3-nose (1.3.7-12) ... /usr/lib/python3/dist-packages/nose/config.py:142: SyntaxWarning: invalid escape sequence '\.' """nose configuration. /usr/lib/python3/dist-packages/nose/ext/dtcompat.py:686: SyntaxWarning: invalid escape sequence '\S' _INDENT_RE = re.compile('^([ ]*)(?=\S)', re.MULTILINE) /usr/lib/python3/dist-packages/nose/ext/dtcompat.py:1021: SyntaxWarning: invalid escape sequence '\s' pat = re.compile('(^|.*:)\s*\w*("|\')') /usr/lib/python3/dist-packages/nose/ext/dtcompat.py:1430: SyntaxWarning: invalid escape sequence '\s' want = re.sub('(?m)^%s\s*?$' % re.escape(BLANKLINE_MARKER), /usr/lib/python3/dist-packages/nose/ext/dtcompat.py:1434: SyntaxWarning: invalid escape sequence '\s' got = re.sub('(?m)^\s*?$', '', got) /usr/lib/python3/dist-packages/nose/inspector.py:110: SyntaxWarning: invalid escape sequence '\ ' """Find lines in home that are inspectable. Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-requests (2.31.0+dfsg-1ubuntu1) ... Setting up python3-numpy (1:1.24.2-2) ... Setting up dh-python (6.20231223ubuntu1) ... Setting up python3-pandas-lib:amd64 (2.1.4+dfsg-4ubuntu2) ... Setting up python3-pandas (2.1.4+dfsg-4ubuntu2) ... Setting up python3-datacache (1.2.1-2) ... /usr/lib/python3/dist-packages/datacache/common.py:48: SyntaxWarning: invalid escape sequence '\?' filename = re.sub("/|\\|;|:|\?|=", "_", filename) Setting up python3-gtfparse (1.3.0+ds-1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for systemd (255.4-1ubuntu1) ... Processing triggers for libc-bin (2.39-0ubuntu2) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-172-generic #190-Ubuntu SMP Fri Feb 2 23:24:22 UTC 2024 amd64 (x86_64) Toolchain package versions: binutils_2.42-3ubuntu1 dpkg-dev_1.22.5ubuntu2 g++-13_13.2.0-16ubuntu1 gcc-13_13.2.0-16ubuntu1 libc6-dev_2.39-0ubuntu2 libstdc++-13-dev_13.2.0-16ubuntu1 libstdc++6_14-20240221-2ubuntu1 linux-libc-dev_6.8.0-11.11 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1 apt_2.7.12+nmu1 apt-utils_2.7.12+nmu1 autoconf_2.71-3 automake_1:1.16.5-1.3ubuntu1 autopoint_0.21-14ubuntu1 autotools-dev_20220109.1 base-files_13ubuntu7 base-passwd_3.6.3 bash_5.2.21-2ubuntu2 bash-completion_1:2.11-8 binutils_2.42-3ubuntu1 binutils-common_2.42-3ubuntu1 binutils-x86-64-linux-gnu_2.42-3ubuntu1 bsdextrautils_2.39.3-6ubuntu2 bsdutils_1:2.39.3-6ubuntu2 build-essential_12.10ubuntu1 bzip2_1.0.8-5ubuntu1 ca-certificates_20240203 coreutils_9.4-3ubuntu2 cpp_4:13.2.0-7ubuntu1 cpp-13_13.2.0-16ubuntu1 cpp-13-x86-64-linux-gnu_13.2.0-16ubuntu1 cpp-x86-64-linux-gnu_4:13.2.0-7ubuntu1 dash_0.5.12-6ubuntu4 debconf_1.5.86 debconf-i18n_1.5.86 debhelper_13.14.1ubuntu1 debianutils_5.16 debugedit_1:5.0-5 dh-autoreconf_20 dh-python_6.20231223ubuntu1 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dpkg_1.22.5ubuntu2 dpkg-dev_1.22.5ubuntu2 dwz_0.15-1 e2fsprogs_1.47.0-2ubuntu1 fakeroot_1.33-1 file_1:5.45-2 findutils_4.9.0-5 g++_4:13.2.0-7ubuntu1 g++-13_13.2.0-16ubuntu1 g++-13-x86-64-linux-gnu_13.2.0-16ubuntu1 g++-x86-64-linux-gnu_4:13.2.0-7ubuntu1 gcc_4:13.2.0-7ubuntu1 gcc-13_13.2.0-16ubuntu1 gcc-13-base_13.2.0-16ubuntu1 gcc-13-x86-64-linux-gnu_13.2.0-16ubuntu1 gcc-14-base_14-20240221-2ubuntu1 gcc-x86-64-linux-gnu_4:13.2.0-7ubuntu1 gettext_0.21-14ubuntu1 gettext-base_0.21-14ubuntu1 gpg_2.4.4-2ubuntu8 gpg-agent_2.4.4-2ubuntu8 gpgconf_2.4.4-2ubuntu8 gpgv_2.4.4-2ubuntu8 grep_3.11-4 groff-base_1.23.0-3 gzip_1.12-1ubuntu2 hostname_3.23+nmu2ubuntu1 init_1.66ubuntu1 init-system-helpers_1.66ubuntu1 intltool-debian_0.35.0+20060710.6 krb5-locales_1.20.1-5build1 libacl1_2.3.2-1 libapparmor1_4.0.0~alpha4-0ubuntu1 libapt-pkg6.0t64_2.7.12+nmu1 libarchive-zip-perl_1.68-1 libargon2-1_0~20190702+dfsg-4 libasan8_14-20240221-2ubuntu1 libassuan0_2.5.6-1 libatomic1_14-20240221-2ubuntu1 libattr1_1:2.5.2-1 libaudit-common_1:3.1.2-2.1 libaudit1_1:3.1.2-2.1 libbinutils_2.42-3ubuntu1 libblas3_3.12.0-3 libblkid1_2.39.3-6ubuntu2 libbz2-1.0_1.0.8-5ubuntu1 libc-bin_2.39-0ubuntu2 libc-dev-bin_2.39-0ubuntu2 libc6_2.39-0ubuntu2 libc6-dev_2.39-0ubuntu2 libcap-ng0_0.8.4-2 libcap2_1:2.66-5ubuntu1 libcc1-0_14-20240221-2ubuntu1 libcom-err2_1.47.0-2ubuntu1 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libcryptsetup12_2:2.6.1-6ubuntu1 libctf-nobfd0_2.42-3ubuntu1 libctf0_2.42-3ubuntu1 libdb5.3_5.3.28+dfsg2-4 libdebconfclient0_0.271ubuntu1 libdebhelper-perl_13.14.1ubuntu1 libdevmapper1.02.1_2:1.02.185-3ubuntu1 libdpkg-perl_1.22.5ubuntu2 libdw1_0.190-1 libelf1_0.190-1 libexpat1_2.6.0-1 libext2fs2_1.47.0-2ubuntu1 libfakeroot_1.33-1 libfdisk1_2.39.3-6ubuntu2 libffi8_3.4.6-1 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-13-dev_13.2.0-16ubuntu1 libgcc-s1_14-20240221-2ubuntu1 libgcrypt20_1.10.3-2 libgdbm-compat4_1.23-5 libgdbm6_1.23-5 libgfortran5_14-20240221-2ubuntu1 libgmp10_2:6.3.0+dfsg-2ubuntu4 libgnutls30_3.8.3-1ubuntu1 libgomp1_14-20240221-2ubuntu1 libgpg-error-l10n_1.47-3build1 libgpg-error0_1.47-3build1 libgpm2_1.20.7-10build1 libgprofng0_2.42-3ubuntu1 libgssapi-krb5-2_1.20.1-5build1 libhogweed6_3.9.1-2 libhwasan0_14-20240221-2ubuntu1 libicu74_74.2-1ubuntu1 libidn2-0_2.3.7-2 libip4tc2_1.8.10-3ubuntu1 libisl23_0.26-3 libitm1_14-20240221-2ubuntu1 libjansson4_2.14-2 libjson-c5_0.17-1 libk5crypto3_1.20.1-5build1 libkeyutils1_1.6.3-3 libkmod2_30+20230601-2ubuntu1 libkrb5-3_1.20.1-5build1 libkrb5support0_1.20.1-5build1 liblapack3_3.12.0-3 liblocale-gettext-perl_1.07-6build1 liblockfile-bin_1.17-1build2 liblockfile1_1.17-1build2 liblsan0_14-20240221-2ubuntu1 liblz4-1_1.9.4-1 liblzma5_5.6.0-0.1 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmd0_1.1.0-2 libmount1_2.39.3-6ubuntu2 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libncursesw6_6.4+20240113-1ubuntu1 libnettle8_3.9.1-2 libnpth0_1.6-3build2 libnsl-dev_1.3.0-3 libnsl2_1.3.0-3 libnss-nis_3.1-0ubuntu6 libnss-nisplus_1.3-0ubuntu6 libp11-kit0_0.25.3-4ubuntu1 libpam-modules_1.5.2-9.1ubuntu3 libpam-modules-bin_1.5.2-9.1ubuntu3 libpam-runtime_1.5.2-9.1ubuntu3 libpam0g_1.5.2-9.1ubuntu3 libpcre2-8-0_10.42-4ubuntu1 libperl5.36_5.36.0-9ubuntu1 libperl5.38_5.38.2-3 libpipeline1_1.5.7-1 libpng16-16_1.6.43-1 libproc2-0_2:4.0.4-4ubuntu1 libpython3-stdlib_3.12.1-0ubuntu2 libpython3.11-minimal_3.11.8-1 libpython3.11-stdlib_3.11.8-1 libpython3.12-minimal_3.12.2-1 libpython3.12-stdlib_3.12.2-1 libquadmath0_14-20240221-2ubuntu1 libreadline8_8.2-3 libseccomp2_2.5.5-1ubuntu1 libselinux1_3.5-2build2 libsemanage-common_3.5-1build3 libsemanage2_3.5-1build3 libsepol2_3.5-2 libsframe1_2.42-3ubuntu1 libsmartcols1_2.39.3-6ubuntu2 libsqlite3-0_3.45.1-1 libss2_1.47.0-2ubuntu1 libssl3_3.0.10-1ubuntu4 libstdc++-13-dev_13.2.0-16ubuntu1 libstdc++6_14-20240221-2ubuntu1 libsub-override-perl_0.10-1 libsystemd-shared_255.4-1ubuntu1 libsystemd0_255.4-1ubuntu1 libtasn1-6_4.19.0-3 libtext-charwidth-perl_0.04-11build1 libtext-iconv-perl_1.7-8build1 libtext-wrapi18n-perl_0.06-10 libtinfo6_6.4+20240113-1ubuntu1 libtirpc-common_1.3.4+ds-1build1 libtirpc-dev_1.3.4+ds-1build1 libtirpc3_1.3.4+ds-1build1 libtool_2.4.7-7 libtsan2_14-20240221-2ubuntu1 libubsan1_14-20240221-2ubuntu1 libuchardet0_0.0.8-1 libudev1_255.4-1ubuntu1 libunistring2_1.0-2 libunistring5_1.1-2 libuuid1_2.39.3-6ubuntu2 libxml2_2.9.14+dfsg-1.3ubuntu1 libxxhash0_0.8.2-2 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.8.0-11.11 lockfile-progs_0.1.19build1 login_1:4.13+dfsg1-4ubuntu1 logsave_1.47.0-2ubuntu1 lto-disabled-list_47 m4_1.4.19-4 make_4.3-4.1build1 man-db_2.12.0-3 mawk_1.3.4.20240123-1 media-types_10.1.0 mount_2.39.3-6ubuntu2 ncurses-base_6.4+20240113-1ubuntu1 ncurses-bin_6.4+20240113-1ubuntu1 netbase_6.4 openssl_3.0.10-1ubuntu4 optipng_0.7.8+ds-1 passwd_1:4.13+dfsg1-4ubuntu1 patch_2.7.6-7build2 perl_5.38.2-3 perl-base_5.38.2-3 perl-modules-5.36_5.36.0-9ubuntu1 perl-modules-5.38_5.38.2-3 pinentry-curses_1.2.1-3ubuntu1 pkgbinarymangler_154 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:4.0.4-4ubuntu1 psmisc_23.6-2 python3_3.12.1-0ubuntu2 python3-all_3.12.1-0ubuntu2 python3-appdirs_1.4.4-4 python3-certifi_2023.11.17-1 python3-chardet_5.2.0+dfsg-1 python3-datacache_1.2.1-2 python3-dateutil_2.8.2-3 python3-distutils_3.11.5-1 python3-gtfparse_1.3.0+ds-1 python3-idna_3.6-2 python3-iniconfig_1.1.1-2 python3-lib2to3_3.11.5-1 python3-memoized-property_1.0.3-2 python3-minimal_3.12.1-0ubuntu2 python3-nose_1.3.7-12 python3-numpy_1:1.24.2-2 python3-packaging_23.2-1 python3-pandas_2.1.4+dfsg-4ubuntu2 python3-pandas-lib_2.1.4+dfsg-4ubuntu2 python3-pkg-resources_68.1.2-2 python3-pluggy_1.4.0-1 python3-pytest_8.0.2-1 python3-requests_2.31.0+dfsg-1ubuntu1 python3-serializable_0.4.0+ds-1 python3-setuptools_68.1.2-2 python3-simplejson_3.19.2-1build1 python3-six_1.16.0-4 python3-typechecks_0.1.0+ds-3 python3-tz_2024.1-2 python3-urllib3_2.0.7-1 python3-zombie-imp_0.0.2-2 python3.11_3.11.8-1 python3.11-minimal_3.11.8-1 python3.12_3.12.2-1 python3.12-minimal_3.12.2-1 readline-common_8.2-3 rpcsvc-proto_1.4.2-0ubuntu6 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.22 systemd_255.4-1ubuntu1 systemd-dev_255.4-1ubuntu1 systemd-sysv_255.4-1ubuntu1 sysvinit-utils_3.08-6ubuntu2 tar_1.35+dfsg-3 tzdata_2024a-1ubuntu1 ubuntu-keyring_2023.11.28.1 util-linux_2.39.3-6ubuntu2 uuid-runtime_2.39.3-6ubuntu2 xz-utils_5.6.0-0.1 zlib1g_1:1.3.dfsg-3ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: pyensembl Binary: pyensembl Architecture: all Version: 2.3.9-2 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Étienne Mollier Homepage: https://github.com/openvax/pyensembl Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/pyensembl Vcs-Git: https://salsa.debian.org/med-team/pyensembl.git Testsuite: autopkgtest, autopkgtest-pkg-pybuild Testsuite-Triggers: python3-all, python3-nose, python3-pytest Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3-setuptools, python3-all, python3-pandas, python3-numpy, python3-datacache, python3-serializable, python3-memoized-property, python3-gtfparse, python3-nose , python3-pytest Package-List: pyensembl deb science optional arch=all Checksums-Sha1: 2bbd0580c71ba3ffa047a0f94a728ce8f0fccf60 60248 pyensembl_2.3.9.orig.tar.xz af81844c3b1862019a5c1e22d8def62a5f7735d6 5284 pyensembl_2.3.9-2.debian.tar.xz Checksums-Sha256: b0f37e5e3376f0bcce1a2140e4a517ab0f7062cfb9c5e30dc4ce8469ac235e80 60248 pyensembl_2.3.9.orig.tar.xz b236d33ab3c62221f31f3f2bda5a1253d57321a5d28018373927460a03d81ae2 5284 pyensembl_2.3.9-2.debian.tar.xz Files: bcd307daaa29b436b95179add4f6d548 60248 pyensembl_2.3.9.orig.tar.xz 5c6596057de25ed54708b66509c5d32b 5284 pyensembl_2.3.9-2.debian.tar.xz Dgit: d2e88e64084c5459bcb87a008495545b9b901826 debian archive/debian/2.3.9-2 https://git.dgit.debian.org/pyensembl -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmXfoLoUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdrnHBAAkXipb3O2KKelcrhDbZ7LiHVGn+RV OS03TZvJXaBkCFeCz+0qAqiQrwYOtmHplRRrbZ8ym+TAZojdNg6SI6HD7kDo+2FD JEDuG9GcoR1lEOie48sMXnyPwT+LNfXUjRx7BIfynPmh4tyuiFN8vPpl4+Vcso6l RLbotDCTuuBYRsIOl4jRHEjIEivMl74oahcRR9U0BHQoZtucE07OyDgIK0ZyhrMu 7xxMtZQFqgKe9SLqEIXTR2M4NYLkfVI9LhaRY4RLUOgUYLfyt44/SOWpjhfve0cD 89oT05SZG5MPyEta1q02uu9Y7/RD9CYFl954EtdZgJ7zmVWs7MFNH3HqqqwweI3G xSGTzbw31fPlmwDBFKkAdGOpGx5syk70gqn/nny0BEJlyQCW+n88JvdjW7cJlyH/ F5hoVCxXRj8yb6MsXewUDjWlz6oCHyfX+bUBOELawZq1s/wO6pS1n9hdl9HWG8OM N5wco6v7SxbhwxlEl1nv5Uk15LAoKAP17Ed9pB5W1ta4+qBUcMPFsM47x6Ek0P8W pUHNNwOP3v2DHYh+v8RVFEZS+DOn6kWkXnD/yOoeV+Poy1lx4UhusqrYS7Uqxlzf 308lk4KxHZ4dSB+9LZw0Rt9q5xGoTUnQSMYzJwUbu2wkNtoWVfMFAJiWJc37iDxk r8EeAdvOMz4Tw4E= =+NNJ -----END PGP SIGNATURE----- gpgv: Signature made Wed Feb 28 21:08:10 2024 UTC gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./pyensembl_2.3.9-2.dsc: no acceptable signature found dpkg-source: info: extracting pyensembl in /<> dpkg-source: info: unpacking pyensembl_2.3.9.orig.tar.xz dpkg-source: info: unpacking pyensembl_2.3.9-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying skip-benchmark.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-27848328 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-27848328 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-27848328 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 pyensembl dpkg-buildpackage: info: source version 2.3.9-2 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from pyensembl-2.3.9/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean pybuild --clean -i python{version} -p 3.12 I: pybuild base:305: python3.12 setup.py clean running clean removing '/<>/.pybuild/cpython3_3.12_pyensembl/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it rm -rf .pybuild/ find . -name \*.pyc -exec rm {} \; rm -f pyensembl.egg-info/SOURCES.txt pyensembl.egg-info/requires.txt make[1]: Leaving directory '/<>' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/pyensembl.substvars debian/files rm -fr -- debian/pyensembl/ debian/tmp/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild pybuild --configure -i python{version} -p 3.12 I: pybuild base:305: python3.12 setup.py config running config dh_auto_build -O--buildsystem=pybuild pybuild --build -i python{version} -p 3.12 I: pybuild base:305: /usr/bin/python3 setup.py build running build running build_py creating /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl copying pyensembl/sequence_data.py -> /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl copying pyensembl/shell.py -> /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl copying pyensembl/download_cache.py -> /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl copying pyensembl/version.py -> /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl copying pyensembl/normalization.py -> /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl copying pyensembl/genome.py -> /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl copying pyensembl/species.py -> /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl copying pyensembl/fasta.py -> /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl copying pyensembl/database.py -> /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl copying pyensembl/locus.py -> /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl copying pyensembl/gene.py -> /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl copying pyensembl/common.py -> /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl copying pyensembl/transcript.py -> /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl copying pyensembl/ensembl_release.py -> /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl copying pyensembl/reference_name.py -> /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl copying pyensembl/exon.py -> /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl copying pyensembl/__init__.py -> /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl copying pyensembl/ensembl_url_templates.py -> /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl copying pyensembl/locus_with_genome.py -> /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl copying pyensembl/search.py -> /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl copying pyensembl/ensembl_versions.py -> /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl copying pyensembl/logging.conf -> /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl copying pyensembl/../requirements.txt -> /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/.. dh_auto_test -O--buildsystem=pybuild pybuild --test --test-pytest -i python{version} -p 3.12 I: pybuild base:305: cd /<>/.pybuild/cpython3_3.12_pyensembl/build; python3.12 -m pytest -v -k 'not test_download_cache.py and not test_gene_ids.py and not test_gene_names.py and not test_gene_objects.py and not test_id_length.py and not test_search.py and not test_serialization.py and not test_transcript_ids.py and not test_transcript_objects.py and not test_contigs.py and not test_exon_id.py and not test_exon_object.py and not test_string_representation.py and not test_timings.py and not test_transcript_sequences.py and not test_transcript_support_level.py' ============================= test session starts ============================== platform linux -- Python 3.12.2, pytest-8.0.2, pluggy-1.4.0 -- /usr/bin/python3.12 cachedir: .pytest_cache rootdir: /<> collecting ... collected 126 items / 98 deselected / 28 selected tests/test_ensembl_object_properties.py::test_human_reference_name PASSED [ 3%] tests/test_locus.py::test_normalize_chromosome PASSED [ 7%] tests/test_locus.py::test_locus_overlaps PASSED [ 10%] tests/test_locus.py::test_locus_contains PASSED [ 14%] tests/test_locus.py::test_position_offset PASSED [ 17%] tests/test_locus.py::test_range_offset PASSED [ 21%] tests/test_locus.py::test_locus_distance PASSED [ 25%] tests/test_missing_genome_sources.py::test_transcript_fasta_only PASSED [ 28%] tests/test_missing_genome_sources.py::test_protein_fasta_only PASSED [ 32%] tests/test_missing_genome_sources.py::test_gtf_only PASSED [ 35%] tests/test_missing_genome_sources.py::test_gtf_transcript_only PASSED [ 39%] tests/test_missing_genome_sources.py::test_gtf_protein_only PASSED [ 42%] tests/test_mouse.py::test_mouse_ENSMUSG00000017167 PASSED [ 46%] tests/test_release_versions.py::test_version_too_old_1 PASSED [ 50%] tests/test_release_versions.py::test_version_too_old_47 PASSED [ 53%] tests/test_release_versions.py::test_version_is_not_numeric PASSED [ 57%] tests/test_release_versions.py::test_version_is_none PASSED [ 60%] tests/test_release_versions.py::test_max_ensembl_release PASSED [ 64%] tests/test_release_versions.py::test_int_version PASSED [ 67%] tests/test_release_versions.py::test_str_version PASSED [ 71%] tests/test_sequence_data.py::test_sequence_type PASSED [ 75%] tests/test_sequence_data.py::test_missing_sequence PASSED [ 78%] tests/test_sequence_data.py::test_clear_cache PASSED [ 82%] tests/test_shell.py::test_genome_selection_grch38 PASSED [ 85%] tests/test_ucsc_gtf.py::test_ucsc_gencode_gtf PASSED [ 89%] tests/test_ucsc_gtf.py::test_ucsc_gencode_genome PASSED [ 92%] tests/test_ucsc_gtf.py::test_ucsc_refseq_gtf PASSED [ 96%] tests/test_ucsc_gtf.py::test_ucsc_refseq_genome PASSED [100%] =============================== warnings summary =============================== ../../../../../../usr/lib/python3/dist-packages/dateutil/tz/tz.py:37 /usr/lib/python3/dist-packages/dateutil/tz/tz.py:37: DeprecationWarning: datetime.datetime.utcfromtimestamp() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.fromtimestamp(timestamp, datetime.UTC). EPOCH = datetime.datetime.utcfromtimestamp(0) pyensembl/shell.py:43 /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/shell.py:43: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import pkg_resources pyensembl/shell.py:65 /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/shell.py:65: DeprecationWarning: Nesting argument groups is deprecated. release_group = root_group.add_argument_group() pyensembl/shell.py:87 /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/shell.py:87: DeprecationWarning: Nesting argument groups is deprecated. path_group = root_group.add_argument_group() -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ================ 28 passed, 98 deselected, 4 warnings in 0.66s ================= rm -fr -- /tmp/dh-xdg-rundir-QnqEtISw create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild rm -f -- debian/pyensembl.substvars rm -fr -- debian/.debhelper/generated/pyensembl/ debian/pyensembl/ debian/tmp/ dh_auto_install --destdir=debian/pyensembl/ -O--buildsystem=pybuild install -m0755 -d /<>/debian/pyensembl pybuild --install -i python{version} -p 3.12 --dest-dir /<>/debian/pyensembl I: pybuild base:305: /usr/bin/python3 setup.py install --root /<>/debian/pyensembl running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running install_lib creating /<>/debian/pyensembl/usr creating /<>/debian/pyensembl/usr/lib creating /<>/debian/pyensembl/usr/lib/python3.12 creating /<>/debian/pyensembl/usr/lib/python3.12/dist-packages creating /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/sequence_data.py -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/shell.py -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/download_cache.py -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/version.py -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/normalization.py -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/genome.py -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/species.py -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/fasta.py -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/database.py -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/locus.py -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/gene.py -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/common.py -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/transcript.py -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/ensembl_release.py -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/reference_name.py -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/logging.conf -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/exon.py -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/__init__.py -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/ensembl_url_templates.py -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/locus_with_genome.py -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl creating /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/__pycache__ copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/__pycache__/fasta.cpython-312.pyc -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/__pycache__ copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/__pycache__/ensembl_versions.cpython-312.pyc -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/__pycache__ copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/__pycache__/ensembl_url_templates.cpython-312.pyc -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/__pycache__ copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/__pycache__/genome.cpython-312.pyc -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/__pycache__ copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/__pycache__/sequence_data.cpython-312.pyc -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/__pycache__ copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/__pycache__/database.cpython-312.pyc -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/__pycache__ copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/__pycache__/shell.cpython-312.pyc -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/__pycache__ copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/__pycache__/transcript.cpython-312.pyc -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/__pycache__ copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/__pycache__/gene.cpython-312.pyc -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/__pycache__ copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/__pycache__/search.cpython-312.pyc -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/__pycache__ copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/__pycache__/download_cache.cpython-312.pyc -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/__pycache__ copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/__pycache__/normalization.cpython-312.pyc -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/__pycache__ copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/__pycache__/ensembl_release.cpython-312.pyc -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/__pycache__ copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/__pycache__/species.cpython-312.pyc -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/__pycache__ copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/__pycache__/exon.cpython-312.pyc -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/__pycache__ copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/__pycache__/locus_with_genome.cpython-312.pyc -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/__pycache__ copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/__pycache__/__init__.cpython-312.pyc -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/__pycache__ copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/__pycache__/common.cpython-312.pyc -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/__pycache__ copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/__pycache__/locus.cpython-312.pyc -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/__pycache__ copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/__pycache__/reference_name.cpython-312.pyc -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/__pycache__ copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/__pycache__/version.cpython-312.pyc -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/__pycache__ copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/search.py -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl copying /<>/.pybuild/cpython3_3.12_pyensembl/build/pyensembl/ensembl_versions.py -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl copying /<>/.pybuild/cpython3_3.12_pyensembl/build/requirements.txt -> /<>/debian/pyensembl/usr/lib/python3.12/dist-packages byte-compiling /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/sequence_data.py to sequence_data.cpython-312.pyc byte-compiling /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/shell.py to shell.cpython-312.pyc byte-compiling /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/download_cache.py to download_cache.cpython-312.pyc byte-compiling /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/version.py to version.cpython-312.pyc byte-compiling /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/normalization.py to normalization.cpython-312.pyc byte-compiling /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/genome.py to genome.cpython-312.pyc byte-compiling /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/species.py to species.cpython-312.pyc byte-compiling /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/fasta.py to fasta.cpython-312.pyc byte-compiling /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/database.py to database.cpython-312.pyc byte-compiling /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/locus.py to locus.cpython-312.pyc byte-compiling /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/gene.py to gene.cpython-312.pyc byte-compiling /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/common.py to common.cpython-312.pyc byte-compiling /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/transcript.py to transcript.cpython-312.pyc byte-compiling /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/ensembl_release.py to ensembl_release.cpython-312.pyc byte-compiling /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/reference_name.py to reference_name.cpython-312.pyc byte-compiling /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/exon.py to exon.cpython-312.pyc byte-compiling /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/__init__.py to __init__.cpython-312.pyc byte-compiling /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/ensembl_url_templates.py to ensembl_url_templates.cpython-312.pyc byte-compiling /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/locus_with_genome.py to locus_with_genome.cpython-312.pyc byte-compiling /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/search.py to search.cpython-312.pyc byte-compiling /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl/ensembl_versions.py to ensembl_versions.cpython-312.pyc running install_egg_info running egg_info creating pyensembl.egg-info writing pyensembl.egg-info/PKG-INFO writing dependency_links to pyensembl.egg-info/dependency_links.txt writing entry points to pyensembl.egg-info/entry_points.txt writing requirements to pyensembl.egg-info/requires.txt writing top-level names to pyensembl.egg-info/top_level.txt writing manifest file 'pyensembl.egg-info/SOURCES.txt' reading manifest file 'pyensembl.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'pyensembl.egg-info/SOURCES.txt' Copying pyensembl.egg-info to /<>/debian/pyensembl/usr/lib/python3.12/dist-packages/pyensembl-2.3.9.egg-info Skipping SOURCES.txt running install_scripts Installing pyensembl script to /<>/debian/pyensembl/usr/bin debian/rules override_dh_install make[1]: Entering directory '/<>' dh_install find debian -name requirements.txt -delete make[1]: Leaving directory '/<>' dh_installdocs -O--buildsystem=pybuild install -m0755 -d debian/pyensembl/usr/share/doc/pyensembl install -p -m0644 debian/copyright debian/pyensembl/usr/share/doc/pyensembl/copyright dh_installchangelogs -O--buildsystem=pybuild install -m0755 -d debian/pyensembl/usr/share/doc/pyensembl install -p -m0644 debian/.debhelper/generated/pyensembl/dh_installchangelogs.dch.trimmed debian/pyensembl/usr/share/doc/pyensembl/changelog.Debian dh_installman -O--buildsystem=pybuild install -m0755 -d debian/pyensembl/usr/share/man/man1/ install -p -m0644 ./debian/pyensembl.1 debian/pyensembl/usr/share/man/man1/pyensembl.1 man-recode --to-code UTF-8 --suffix .dh-new debian/pyensembl/usr/share/man/man1/pyensembl.1 mv debian/pyensembl/usr/share/man/man1/pyensembl.1.dh-new debian/pyensembl/usr/share/man/man1/pyensembl.1 chmod 0644 -- debian/pyensembl/usr/share/man/man1/pyensembl.1 dh_python3 -O--buildsystem=pybuild D: dh_python3 dh_python3:179: version: 6.20231223ubuntu1 D: dh_python3 dh_python3:180: argv: ['/usr/bin/dh_python3', '-O--buildsystem=pybuild'] D: dh_python3 dh_python3:181: options: Namespace(guess_deps=True, skip_private=False, verbose=True, arch=None, package=None, no_package=None, remaining_packages=False, compile_all=False, vrange=None, regexpr=None, accept_upstream_versions=False, depends=None, depends_section=None, recommends=None, recommends_section=None, suggests=None, suggests_section=None, requires=None, shebang=None, ignore_shebangs=False, clean_dbg_pkg=True, no_ext_rename=False, no_shebang_rewrite=False, private_dir=None, O=['--buildsystem=pybuild']) D: dh_python3 dh_python3:182: supported Python versions: 3.12 (default=3.12) D: dh_python3 debhelper:183: source=pyensembl, binary packages=['pyensembl'] D: dh_python3 dh_python3:204: processing package pyensembl... D: dh_python3 fs:50: moving files from debian/pyensembl/usr/lib/python3.12/dist-packages to debian/pyensembl/usr/lib/python3/dist-packages/ D: dh_python3 fs:348: package pyensembl details = {'requires.txt': {'debian/pyensembl/usr/lib/python3/dist-packages/pyensembl-2.3.9.egg-info/requires.txt'}, 'egg-info': {'debian/pyensembl/usr/lib/python3/dist-packages/pyensembl-2.3.9.egg-info/PKG-INFO'}, 'dist-info': set(), 'nsp.txt': set(), 'shebangs': {/usr/bin/python3}, 'public_vers': {Version('3')}, 'private_dirs': {}, 'compile': True, 'ext_vers': set(), 'ext_no_version': set()} D: dh_python3 depends:117: generating dependencies for package pyensembl D: dh_python3 pydist:173: trying to find dependency for datacache<2.0.0,>=1.4.0 (python=None) D: dh_python3 pydist:207: dependency: module seems to be installed D: dh_python3 pydist:270: dependency: included in build-deps D: dh_python3 pydist:173: trying to find dependency for gtfparse<3.0.0,>=2.5.0 (python=None) D: dh_python3 pydist:207: dependency: module seems to be installed D: dh_python3 pydist:270: dependency: included in build-deps D: dh_python3 pydist:173: trying to find dependency for memoized-property>=1.0.2 (python=None) D: dh_python3 pydist:207: dependency: module seems to be installed D: dh_python3 pydist:270: dependency: included in build-deps D: dh_python3 pydist:173: trying to find dependency for pylint<3.0.0,>=2.17.2 (python=None) D: dh_python3 pydist:207: dependency: module seems to be installed D: dh_python3 pydist:270: dependency: included in build-deps D: dh_python3 pydist:173: trying to find dependency for serializable<1.0.0,>=0.2.1 (python=None) D: dh_python3 pydist:207: dependency: module seems to be installed D: dh_python3 pydist:270: dependency: included in build-deps D: dh_python3 pydist:173: trying to find dependency for tinytimer<1.0.0,>=0.0.0 (python=None) D: dh_python3 pydist:277: invoking dpkg -S *python3/*/[Tt][Ii][Nn][Yy][Tt][Ii][Mm][Ee][Rr]-?*.*-info D: dh_python3 pydist:299: dpkg -S did not find package for tinytimer: dpkg-query: no path found matching pattern *python3/*/[Tt][Ii][Nn][Yy][Tt][Ii][Mm][Ee][Rr]-?*.*-info I: dh_python3 pydist:302: Cannot find package that provides tinytimer. Please add package that provides it to Build-Depends or add "tinytimer python3-tinytimer" line to debian/py3dist-overrides or add proper dependency to Depends by hand and ignore this info. D: dh_python3 pydist:173: trying to find dependency for typechecks<1.0.0,>=0.0.2 (python=None) D: dh_python3 pydist:207: dependency: module seems to be installed D: dh_python3 pydist:270: dependency: included in build-deps D: dh_python3 depends:284: D={'python3-datacache', 'python3-typechecks', 'python3-gtfparse', 'python3-memoized-property', 'python3-serializable', 'pylint', 'python3:any'}; R=[]; S=[]; E=[], B=[]; RT=[] dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild cd debian/pyensembl chmod a-x usr/share/doc/pyensembl/changelog.Debian usr/share/man/man1/pyensembl.1 gzip -9nf usr/share/doc/pyensembl/changelog.Debian usr/share/man/man1/pyensembl.1 cd '/<>' dh_fixperms -O--buildsystem=pybuild find debian/pyensembl ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/pyensembl/usr/share/doc -type f -a -true -a ! -regex 'debian/pyensembl/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/pyensembl/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/pyensembl/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/pyensembl -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/pyensembl/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/pyensembl/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w dh_missing -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild install -m0755 -d debian/pyensembl/DEBIAN printf '#!/bin/sh\nset -e\n' > debian/pyensembl/DEBIAN/postinst cat debian/pyensembl.postinst.debhelper >> debian/pyensembl/DEBIAN/postinst chmod 0755 -- debian/pyensembl/DEBIAN/postinst printf '#!/bin/sh\nset -e\n' > debian/pyensembl/DEBIAN/prerm cat debian/pyensembl.prerm.debhelper >> debian/pyensembl/DEBIAN/prerm chmod 0755 -- debian/pyensembl/DEBIAN/prerm dh_gencontrol -O--buildsystem=pybuild install -m0755 -d debian/pyensembl/DEBIAN echo misc:Depends= >> debian/pyensembl.substvars echo misc:Pre-Depends= >> debian/pyensembl.substvars dpkg-gencontrol -ppyensembl -ldebian/changelog -Tdebian/pyensembl.substvars -Pdebian/pyensembl chmod 0644 -- debian/pyensembl/DEBIAN/control dh_md5sums -O--buildsystem=pybuild install -m0755 -d debian/pyensembl/DEBIAN cd debian/pyensembl >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/pyensembl/DEBIAN/md5sums dh_builddeb -O--buildsystem=pybuild dpkg-deb --root-owner-group --build debian/pyensembl .. INFO: pkgstriptranslations version 154 pkgstriptranslations: processing pyensembl (in debian/pyensembl); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/pyensembl/DEBIAN/control, package pyensembl, directory debian/pyensembl pkgstripfiles: Running PNG optimization (using 4 cpus) for package pyensembl ... pkgstripfiles: No PNG files. dpkg-deb: building package 'pyensembl' in '../pyensembl_2.3.9-2_all.deb'. dpkg-genbuildinfo --build=binary -O../pyensembl_2.3.9-2_amd64.buildinfo dpkg-genchanges --build=binary -mLaunchpad Build Daemon -O../pyensembl_2.3.9-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from pyensembl-2.3.9/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2024-02-29T05:35:36Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ pyensembl_2.3.9-2_amd64.changes: -------------------------------- Format: 1.8 Date: Wed, 28 Feb 2024 22:01:31 +0100 Source: pyensembl Binary: pyensembl Built-For-Profiles: noudeb Architecture: all Version: 2.3.9-2 Distribution: noble-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Étienne Mollier Description: pyensembl - installs data from the Ensembl genome database Changes: pyensembl (2.3.9-2) unstable; urgency=medium . * d/t/run-unit-test: update test directory name. Put manual autopkgtest back in working conditions. Checksums-Sha1: 014ee06a2fbfb49544154b89480944fd054208bf 36764 pyensembl_2.3.9-2_all.deb 6ae9aa718b90a0b9b573e0f5ba90031fe3eb0729 7502 pyensembl_2.3.9-2_amd64.buildinfo Checksums-Sha256: c620bb749349bb9e8e432a60ecc4beeee49608259cf682e890bb5dd5227911ab 36764 pyensembl_2.3.9-2_all.deb b484be71403f09f395ad6cd28702e9e8416179dc92f21914d442561092b4eac9 7502 pyensembl_2.3.9-2_amd64.buildinfo Files: 3d57ec13bbfdef9c9b1ea7ebffc4752a 36764 science optional pyensembl_2.3.9-2_all.deb 745053c46e734b60ffed620868940595 7502 science optional pyensembl_2.3.9-2_amd64.buildinfo /<>/pyensembl_2.3.9-2_amd64.changes.new could not be renamed to /<>/pyensembl_2.3.9-2_amd64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: pyensembl Binary: pyensembl Architecture: all Version: 2.3.9-2 Checksums-Md5: 3d57ec13bbfdef9c9b1ea7ebffc4752a 36764 pyensembl_2.3.9-2_all.deb Checksums-Sha1: 014ee06a2fbfb49544154b89480944fd054208bf 36764 pyensembl_2.3.9-2_all.deb Checksums-Sha256: c620bb749349bb9e8e432a60ecc4beeee49608259cf682e890bb5dd5227911ab 36764 pyensembl_2.3.9-2_all.deb Build-Origin: Ubuntu Build-Architecture: amd64 Build-Date: Thu, 29 Feb 2024 05:35:36 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3ubuntu1), autopoint (= 0.21-14ubuntu1), autotools-dev (= 20220109.1), base-files (= 13ubuntu7), base-passwd (= 3.6.3), bash (= 5.2.21-2ubuntu2), binutils (= 2.42-3ubuntu1), binutils-common (= 2.42-3ubuntu1), binutils-x86-64-linux-gnu (= 2.42-3ubuntu1), bsdextrautils (= 2.39.3-6ubuntu2), bsdutils (= 1:2.39.3-6ubuntu2), build-essential (= 12.10ubuntu1), bzip2 (= 1.0.8-5ubuntu1), ca-certificates (= 20240203), coreutils (= 9.4-3ubuntu2), cpp (= 4:13.2.0-7ubuntu1), cpp-13 (= 13.2.0-16ubuntu1), cpp-13-x86-64-linux-gnu (= 13.2.0-16ubuntu1), cpp-x86-64-linux-gnu (= 4:13.2.0-7ubuntu1), dash (= 0.5.12-6ubuntu4), debconf (= 1.5.86), debhelper (= 13.14.1ubuntu1), debianutils (= 5.16), debugedit (= 1:5.0-5), dh-autoreconf (= 20), dh-python (= 6.20231223ubuntu1), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.10-1), dpkg (= 1.22.5ubuntu2), dpkg-dev (= 1.22.5ubuntu2), dwz (= 0.15-1), file (= 1:5.45-2), findutils (= 4.9.0-5), g++ (= 4:13.2.0-7ubuntu1), g++-13 (= 13.2.0-16ubuntu1), g++-13-x86-64-linux-gnu (= 13.2.0-16ubuntu1), g++-x86-64-linux-gnu (= 4:13.2.0-7ubuntu1), gcc (= 4:13.2.0-7ubuntu1), gcc-13 (= 13.2.0-16ubuntu1), gcc-13-base (= 13.2.0-16ubuntu1), gcc-13-x86-64-linux-gnu (= 13.2.0-16ubuntu1), gcc-14-base (= 14-20240221-2ubuntu1), gcc-x86-64-linux-gnu (= 4:13.2.0-7ubuntu1), gettext (= 0.21-14ubuntu1), gettext-base (= 0.21-14ubuntu1), grep (= 3.11-4), groff-base (= 1.23.0-3), gzip (= 1.12-1ubuntu2), hostname (= 3.23+nmu2ubuntu1), init-system-helpers (= 1.66ubuntu1), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-1), libarchive-zip-perl (= 1.68-1), libasan8 (= 14-20240221-2ubuntu1), libatomic1 (= 14-20240221-2ubuntu1), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:3.1.2-2.1), libaudit1 (= 1:3.1.2-2.1), libbinutils (= 2.42-3ubuntu1), libblas3 (= 3.12.0-3), libblkid1 (= 2.39.3-6ubuntu2), libbz2-1.0 (= 1.0.8-5ubuntu1), libc-bin (= 2.39-0ubuntu2), libc-dev-bin (= 2.39-0ubuntu2), libc6 (= 2.39-0ubuntu2), libc6-dev (= 2.39-0ubuntu2), libcap-ng0 (= 0.8.4-2), libcap2 (= 1:2.66-5ubuntu1), libcc1-0 (= 14-20240221-2ubuntu1), libcom-err2 (= 1.47.0-2ubuntu1), libcrypt-dev (= 1:4.4.36-4), libcrypt1 (= 1:4.4.36-4), libctf-nobfd0 (= 2.42-3ubuntu1), libctf0 (= 2.42-3ubuntu1), libdb5.3 (= 5.3.28+dfsg2-4), libdebconfclient0 (= 0.271ubuntu1), libdebhelper-perl (= 13.14.1ubuntu1), libdpkg-perl (= 1.22.5ubuntu2), libdw1 (= 0.190-1), libelf1 (= 0.190-1), libexpat1 (= 2.6.0-1), libffi8 (= 3.4.6-1), libfile-stripnondeterminism-perl (= 1.13.1-1), libgcc-13-dev (= 13.2.0-16ubuntu1), libgcc-s1 (= 14-20240221-2ubuntu1), libgcrypt20 (= 1.10.3-2), libgdbm-compat4 (= 1.23-5), libgdbm6 (= 1.23-5), libgfortran5 (= 14-20240221-2ubuntu1), libgmp10 (= 2:6.3.0+dfsg-2ubuntu4), libgomp1 (= 14-20240221-2ubuntu1), libgpg-error0 (= 1.47-3build1), libgprofng0 (= 2.42-3ubuntu1), libgssapi-krb5-2 (= 1.20.1-5build1), libhwasan0 (= 14-20240221-2ubuntu1), libicu74 (= 74.2-1ubuntu1), libisl23 (= 0.26-3), libitm1 (= 14-20240221-2ubuntu1), libjansson4 (= 2.14-2), libk5crypto3 (= 1.20.1-5build1), libkeyutils1 (= 1.6.3-3), libkrb5-3 (= 1.20.1-5build1), libkrb5support0 (= 1.20.1-5build1), liblapack3 (= 3.12.0-3), liblsan0 (= 14-20240221-2ubuntu1), liblz4-1 (= 1.9.4-1), liblzma5 (= 5.6.0-0.1), libmagic-mgc (= 1:5.45-2), libmagic1 (= 1:5.45-2), libmd0 (= 1.1.0-2), libmount1 (= 2.39.3-6ubuntu2), libmpc3 (= 1.3.1-1), libmpfr6 (= 4.2.1-1), libncursesw6 (= 6.4+20240113-1ubuntu1), libnsl-dev (= 1.3.0-3), libnsl2 (= 1.3.0-3), libpam-modules (= 1.5.2-9.1ubuntu3), libpam-modules-bin (= 1.5.2-9.1ubuntu3), libpam-runtime (= 1.5.2-9.1ubuntu3), libpam0g (= 1.5.2-9.1ubuntu3), libpcre2-8-0 (= 10.42-4ubuntu1), libperl5.38 (= 5.38.2-3), libpipeline1 (= 1.5.7-1), libpython3-stdlib (= 3.12.1-0ubuntu2), libpython3.11-minimal (= 3.11.8-1), libpython3.11-stdlib (= 3.11.8-1), libpython3.12-minimal (= 3.12.2-1), libpython3.12-stdlib (= 3.12.2-1), libquadmath0 (= 14-20240221-2ubuntu1), libreadline8 (= 8.2-3), libseccomp2 (= 2.5.5-1ubuntu1), libselinux1 (= 3.5-2build2), libsframe1 (= 2.42-3ubuntu1), libsmartcols1 (= 2.39.3-6ubuntu2), libsqlite3-0 (= 3.45.1-1), libssl3 (= 3.0.10-1ubuntu4), libstdc++-13-dev (= 13.2.0-16ubuntu1), libstdc++6 (= 14-20240221-2ubuntu1), libsub-override-perl (= 0.10-1), libsystemd0 (= 255.4-1ubuntu1), libtinfo6 (= 6.4+20240113-1ubuntu1), libtirpc-common (= 1.3.4+ds-1build1), libtirpc-dev (= 1.3.4+ds-1build1), libtirpc3 (= 1.3.4+ds-1build1), libtool (= 2.4.7-7), libtsan2 (= 14-20240221-2ubuntu1), libubsan1 (= 14-20240221-2ubuntu1), libuchardet0 (= 0.0.8-1), libudev1 (= 255.4-1ubuntu1), libunistring5 (= 1.1-2), libuuid1 (= 2.39.3-6ubuntu2), libxml2 (= 2.9.14+dfsg-1.3ubuntu1), libzstd1 (= 1.5.5+dfsg2-2), linux-libc-dev (= 6.8.0-11.11), login (= 1:4.13+dfsg1-4ubuntu1), lto-disabled-list (= 47), m4 (= 1.4.19-4), make (= 4.3-4.1build1), man-db (= 2.12.0-3), mawk (= 1.3.4.20240123-1), media-types (= 10.1.0), ncurses-base (= 6.4+20240113-1ubuntu1), ncurses-bin (= 6.4+20240113-1ubuntu1), netbase (= 6.4), openssl (= 3.0.10-1ubuntu4), patch (= 2.7.6-7build2), perl (= 5.38.2-3), perl-base (= 5.38.2-3), perl-modules-5.38 (= 5.38.2-3), po-debconf (= 1.0.21+nmu1), python3 (= 3.12.1-0ubuntu2), python3-all (= 3.12.1-0ubuntu2), python3-appdirs (= 1.4.4-4), python3-certifi (= 2023.11.17-1), python3-chardet (= 5.2.0+dfsg-1), python3-datacache (= 1.2.1-2), python3-dateutil (= 2.8.2-3), python3-distutils (= 3.11.5-1), python3-gtfparse (= 1.3.0+ds-1), python3-idna (= 3.6-2), python3-iniconfig (= 1.1.1-2), python3-lib2to3 (= 3.11.5-1), python3-memoized-property (= 1.0.3-2), python3-minimal (= 3.12.1-0ubuntu2), python3-nose (= 1.3.7-12), python3-numpy (= 1:1.24.2-2), python3-packaging (= 23.2-1), python3-pandas (= 2.1.4+dfsg-4ubuntu2), python3-pandas-lib (= 2.1.4+dfsg-4ubuntu2), python3-pkg-resources (= 68.1.2-2), python3-pluggy (= 1.4.0-1), python3-pytest (= 8.0.2-1), python3-requests (= 2.31.0+dfsg-1ubuntu1), python3-serializable (= 0.4.0+ds-1), python3-setuptools (= 68.1.2-2), python3-simplejson (= 3.19.2-1build1), python3-six (= 1.16.0-4), python3-typechecks (= 0.1.0+ds-3), python3-tz (= 2024.1-2), python3-urllib3 (= 2.0.7-1), python3-zombie-imp (= 0.0.2-2), python3.11 (= 3.11.8-1), python3.11-minimal (= 3.11.8-1), python3.12 (= 3.12.2-1), python3.12-minimal (= 3.12.2-1), readline-common (= 8.2-3), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.9-2), sensible-utils (= 0.0.22), sysvinit-utils (= 3.08-6ubuntu2), tar (= 1.35+dfsg-3), tzdata (= 2024a-1ubuntu1), util-linux (= 2.39.3-6ubuntu2), xz-utils (= 5.6.0-0.1), zlib1g (= 1:1.3.dfsg-3ubuntu1) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1709154091" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ pyensembl_2.3.9-2_all.deb ------------------------- new Debian package, version 2.0. size 36764 bytes: control archive=1951 bytes. 930 bytes, 20 lines control 2714 bytes, 31 lines md5sums 253 bytes, 12 lines * postinst #!/bin/sh 366 bytes, 12 lines * prerm #!/bin/sh Package: pyensembl Version: 2.3.9-2 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 203 Depends: pylint, python3-datacache, python3-gtfparse, python3-memoized-property, python3-serializable, python3-typechecks, python3:any Section: science Priority: optional Homepage: https://github.com/openvax/pyensembl Description: installs data from the Ensembl genome database The Ensembl genome database is an established reference for genomic sequences and their automated annotation. To have this data local has advantages for bulk analyses, e.g. for the mapping of reads from RNA-seq against the latest golden path - or a previous one to compare analyses. . This package provides a reproducible way to insatll this data and thus simplify the automation of respective workflows. drwxr-xr-x root/root 0 2024-02-28 21:01 ./ drwxr-xr-x root/root 0 2024-02-28 21:01 ./usr/ drwxr-xr-x root/root 0 2024-02-28 21:01 ./usr/bin/ -rwxr-xr-x root/root 968 2024-02-28 21:01 ./usr/bin/pyensembl drwxr-xr-x root/root 0 2024-02-28 21:01 ./usr/lib/ drwxr-xr-x root/root 0 2024-02-28 21:01 ./usr/lib/python3/ drwxr-xr-x root/root 0 2024-02-28 21:01 ./usr/lib/python3/dist-packages/ drwxr-xr-x root/root 0 2024-02-28 21:01 ./usr/lib/python3/dist-packages/pyensembl-2.3.9.egg-info/ -rw-r--r-- root/root 9155 2024-02-28 21:01 ./usr/lib/python3/dist-packages/pyensembl-2.3.9.egg-info/PKG-INFO -rw-r--r-- root/root 1 2024-02-28 21:01 ./usr/lib/python3/dist-packages/pyensembl-2.3.9.egg-info/dependency_links.txt -rw-r--r-- root/root 50 2024-02-28 21:01 ./usr/lib/python3/dist-packages/pyensembl-2.3.9.egg-info/entry_points.txt -rw-r--r-- root/root 24 2024-02-28 21:01 ./usr/lib/python3/dist-packages/pyensembl-2.3.9.egg-info/requires.txt -rw-r--r-- root/root 10 2024-02-28 21:01 ./usr/lib/python3/dist-packages/pyensembl-2.3.9.egg-info/top_level.txt drwxr-xr-x root/root 0 2024-02-28 21:01 ./usr/lib/python3/dist-packages/pyensembl/ -rw-r--r-- root/root 1809 2024-01-17 05:34 ./usr/lib/python3/dist-packages/pyensembl/__init__.py -rw-r--r-- root/root 2619 2024-01-17 05:34 ./usr/lib/python3/dist-packages/pyensembl/common.py -rw-r--r-- root/root 21986 2024-01-17 05:34 ./usr/lib/python3/dist-packages/pyensembl/database.py -rw-r--r-- root/root 11807 2024-01-17 05:34 ./usr/lib/python3/dist-packages/pyensembl/download_cache.py -rw-r--r-- root/root 5168 2024-01-17 05:34 ./usr/lib/python3/dist-packages/pyensembl/ensembl_release.py -rw-r--r-- root/root 5418 2024-01-17 05:34 ./usr/lib/python3/dist-packages/pyensembl/ensembl_url_templates.py -rw-r--r-- root/root 1053 2024-01-17 05:34 ./usr/lib/python3/dist-packages/pyensembl/ensembl_versions.py -rw-r--r-- root/root 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+------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 1560 Build-Time: 5 Distribution: noble-proposed Host Architecture: amd64 Install-Time: 18 Job: pyensembl_2.3.9-2.dsc Machine Architecture: amd64 Package: pyensembl Package-Time: 24 Source-Version: 2.3.9-2 Space: 1560 Status: successful Version: 2.3.9-2 -------------------------------------------------------------------------------- Finished at 2024-02-29T05:35:36Z Build needed 00:00:24, 1560k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27848328 Scanning for processes to kill in build PACKAGEBUILD-27848328