https://launchpad.net/ubuntu/+source/python-pairix/0.3.7-6/+build/24887997 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lcy02-amd64-098 5.4.0-132-generic #148-Ubuntu SMP Mon Oct 17 16:02:06 UTC 2022 x86_64 Buildd toolchain package versions: launchpad-buildd_223~593~ubuntu20.04.1 python3-lpbuildd_223~593~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.6 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 1 Dec 05:22:31 ntpdate[1941]: adjust time server 10.131.248.1 offset -0.000752 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=lunar --arch=amd64 PACKAGEBUILD-24887997 --image-type chroot /home/buildd/filecache-default/b509365b3a13e4aa6176e31a361b75cab8d51910 Creating target for build PACKAGEBUILD-24887997 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=lunar --arch=amd64 PACKAGEBUILD-24887997 Starting target for build PACKAGEBUILD-24887997 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=lunar --arch=amd64 PACKAGEBUILD-24887997 'deb http://ftpmaster.internal/ubuntu lunar main universe' 'deb http://ftpmaster.internal/ubuntu lunar-security main universe' 'deb http://ftpmaster.internal/ubuntu lunar-updates main universe' 'deb http://ftpmaster.internal/ubuntu lunar-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-24887997 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=lunar --arch=amd64 PACKAGEBUILD-24887997 Updating target for build PACKAGEBUILD-24887997 Get:1 http://ftpmaster.internal/ubuntu lunar InRelease [267 kB] Get:2 http://ftpmaster.internal/ubuntu lunar-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu lunar-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu lunar-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu lunar/main amd64 Packages [1394 kB] Get:6 http://ftpmaster.internal/ubuntu lunar/main Translation-en [511 kB] Get:7 http://ftpmaster.internal/ubuntu lunar/universe amd64 Packages [14.1 MB] Get:8 http://ftpmaster.internal/ubuntu lunar/universe Translation-en [5843 kB] Get:9 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 Packages [303 kB] Get:10 http://ftpmaster.internal/ubuntu lunar-proposed/main Translation-en [111 kB] Get:11 http://ftpmaster.internal/ubuntu lunar-proposed/universe amd64 Packages [1589 kB] Get:12 http://ftpmaster.internal/ubuntu lunar-proposed/universe Translation-en [622 kB] Fetched 25.1 MB in 3s (9030 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: libperl5.34 perl-modules-5.34 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libperl5.36 perl-modules-5.36 The following packages will be upgraded: adduser advancecomp apt binutils binutils-common binutils-x86-64-linux-gnu debconf debianutils e2fsprogs fakeroot gpg gpg-agent gpgconf gpgv grep init init-system-helpers libapparmor1 libapt-pkg6.0 libassuan0 libaudit-common libaudit1 libbinutils libcap-ng0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libext2fs2 libfakeroot libffi8 libgpg-error0 libgprofng0 libgssapi-krb5-2 libip4tc2 libjson-c5 libk5crypto3 libkrb5-3 libkrb5support0 liblz4-1 liblzma5 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpng16-16 libreadline8 libseccomp2 libselinux1 libsqlite3-0 libss2 libssl3 linux-libc-dev login logsave openssl passwd perl perl-base pinentry-curses readline-common tar tzdata usrmerge xz-utils zlib1g 68 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 28.5 MB of archives. After this operation, 46.5 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 debianutils amd64 5.7-0.4 [103 kB] Get:2 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 grep amd64 3.8-3 [159 kB] Get:3 http://ftpmaster.internal/ubuntu lunar/main amd64 login amd64 1:4.13+dfsg1-1ubuntu1 [199 kB] Get:4 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 perl-modules-5.36 all 5.36.0-4ubuntu2 [2984 kB] Get:5 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libperl5.36 amd64 5.36.0-4ubuntu2 [4808 kB] Get:6 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 perl amd64 5.36.0-4ubuntu2 [235 kB] Get:7 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 perl-base amd64 5.36.0-4ubuntu2 [1779 kB] Get:8 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libcrypt-dev amd64 1:4.4.33-1 [113 kB] Get:9 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libcrypt1 amd64 1:4.4.33-1 [80.8 kB] Get:10 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 zlib1g amd64 1:1.2.13.dfsg-1ubuntu2 [61.1 kB] Get:11 http://ftpmaster.internal/ubuntu lunar/main amd64 tar amd64 1.34+dfsg-1.1 [292 kB] Get:12 http://ftpmaster.internal/ubuntu lunar/main amd64 usrmerge all 33ubuntu1 [57.0 kB] Get:13 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 init-system-helpers all 1.65.2 [38.1 kB] Get:14 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 liblz4-1 amd64 1.9.4-1 [63.1 kB] Get:15 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 liblzma5 amd64 5.2.8-0.0 [102 kB] Get:16 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libapt-pkg6.0 amd64 2.5.4 [902 kB] Get:17 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libaudit-common all 1:3.0.7-1ubuntu2 [5018 B] Get:18 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libcap-ng0 amd64 0.8.3-1build1 [15.2 kB] Get:19 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libaudit1 amd64 1:3.0.7-1ubuntu2 [45.4 kB] Get:20 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 debconf all 1.5.80 [125 kB] Get:21 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libpam0g amd64 1.5.2-5ubuntu1 [60.2 kB] Get:22 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libselinux1 amd64 3.4-1build1 [77.9 kB] Get:23 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libpam-modules-bin amd64 1.5.2-5ubuntu1 [45.5 kB] Get:24 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libpam-modules amd64 1.5.2-5ubuntu1 [282 kB] Get:25 http://ftpmaster.internal/ubuntu lunar/main amd64 passwd amd64 1:4.13+dfsg1-1ubuntu1 [842 kB] Get:26 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 adduser all 3.129ubuntu1 [59.0 kB] Get:27 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libgpg-error0 amd64 1.46-1 [68.9 kB] Get:28 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 gpgv amd64 2.2.40-1ubuntu1 [137 kB] Get:29 http://ftpmaster.internal/ubuntu lunar/main amd64 libseccomp2 amd64 2.5.4-1ubuntu2 [46.2 kB] Get:30 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 apt amd64 2.5.4 [1378 kB] Get:31 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 logsave amd64 1.46.6~rc1-1ubuntu1 [10.5 kB] Get:32 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libext2fs2 amd64 1.46.6~rc1-1ubuntu1 [207 kB] Get:33 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 e2fsprogs amd64 1.46.6~rc1-1ubuntu1 [590 kB] Get:34 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 init amd64 1.65.2 [4808 B] Get:35 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libpam-runtime all 1.5.2-5ubuntu1 [40.0 kB] Get:36 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libffi8 amd64 3.4.4-1 [23.8 kB] Get:37 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libcom-err2 amd64 1.46.6~rc1-1ubuntu1 [9650 B] Get:38 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libss2 amd64 1.46.6~rc1-1ubuntu1 [12.2 kB] Get:39 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libapparmor1 amd64 3.0.7-1ubuntu4 [36.7 kB] Get:40 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libjson-c5 amd64 0.16-2 [32.8 kB] Get:41 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libssl3 amd64 3.0.5-2ubuntu2 [1893 kB] Get:42 http://ftpmaster.internal/ubuntu lunar/main amd64 libcryptsetup12 amd64 2:2.5.0-6ubuntu1 [222 kB] Get:43 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libgssapi-krb5-2 amd64 1.20.1-1 [142 kB] Get:44 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libkrb5-3 amd64 1.20.1-1 [346 kB] Get:45 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libkrb5support0 amd64 1.20.1-1 [31.4 kB] Get:46 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libk5crypto3 amd64 1.20.1-1 [81.1 kB] Get:47 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libip4tc2 amd64 1.8.7-1ubuntu7 [19.7 kB] Get:48 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 readline-common all 8.2-1.2 [55.2 kB] Get:49 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libreadline8 amd64 8.2-1.2 [150 kB] Get:50 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libsqlite3-0 amd64 3.40.0-1 [653 kB] Get:51 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 openssl amd64 3.0.5-2ubuntu2 [1178 kB] Get:52 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 tzdata all 2022g-0ubuntu1 [401 kB] Get:53 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libpng16-16 amd64 1.6.39-1 [186 kB] Get:54 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 xz-utils amd64 5.2.8-0.0 [142 kB] Get:55 http://ftpmaster.internal/ubuntu lunar/main amd64 advancecomp amd64 2.4-1 [180 kB] Get:56 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libctf-nobfd0 amd64 2.39-8ubuntu2 [99.9 kB] Get:57 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libgprofng0 amd64 2.39-8ubuntu2 [897 kB] Get:58 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libctf0 amd64 2.39-8ubuntu2 [97.4 kB] Get:59 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 binutils-x86-64-linux-gnu amd64 2.39-8ubuntu2 [2402 kB] Get:60 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libbinutils amd64 2.39-8ubuntu2 [610 kB] Get:61 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 binutils amd64 2.39-8ubuntu2 [3240 B] Get:62 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 binutils-common amd64 2.39-8ubuntu2 [233 kB] Get:63 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libfakeroot amd64 1.30.1-1ubuntu1 [30.9 kB] Get:64 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 fakeroot amd64 1.30.1-1ubuntu1 [60.1 kB] Get:65 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libassuan0 amd64 2.5.5-5 [37.2 kB] Get:66 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 pinentry-curses amd64 1.2.1-1ubuntu1 [34.6 kB] Get:67 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 gpg amd64 2.2.40-1ubuntu1 [523 kB] Get:68 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 gpgconf amd64 2.2.40-1ubuntu1 [93.8 kB] Get:69 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 gpg-agent amd64 2.2.40-1ubuntu1 [217 kB] Get:70 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 linux-libc-dev amd64 5.19.0-23.24 [1345 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 28.5 MB in 0s (116 MB/s) (Reading database ... 13556 files and directories currently installed.) 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Setting up binutils (2.39-8ubuntu2) ... Processing triggers for libc-bin (2.36-0ubuntu4) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-24887997 amd64 lunar-proposed -c chroot:build-PACKAGEBUILD-24887997 --arch=amd64 --dist=lunar-proposed --nolog -A python-pairix_0.3.7-6.dsc Initiating build PACKAGEBUILD-24887997 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-132-generic #148-Ubuntu SMP Mon Oct 17 16:02:06 UTC 2022 x86_64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on lcy02-amd64-098.buildd +==============================================================================+ | python-pairix 0.3.7-6 (amd64) Thu, 01 Dec 2022 05:22:54 +0000 | +==============================================================================+ Package: python-pairix Version: 0.3.7-6 Source Version: 0.3.7-6 Distribution: lunar-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-24887997/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/python-pairix-bdua9g/resolver-LihodQ' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- python-pairix_0.3.7-6.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/python-pairix-bdua9g/python-pairix-0.3.7' with '<>' I: NOTICE: Log filtering will replace 'build/python-pairix-bdua9g' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-python, python3-all-dev, python3-setuptools, zlib1g-dev, python3-pytest, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), dh-python, python3-all-dev, python3-setuptools, zlib1g-dev, 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 [413 B] Get:5 copy:/<>/apt_archive ./ Packages [488 B] Fetched 1858 B in 0s (0 B/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: libperl5.34 perl-modules-5.34 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libdw1 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libicu71 libjs-jquery libjs-sphinxdoc libjs-underscore libmagic-mgc libmagic1 libmpdec3 libpipeline1 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.10 libpython3.10-dev libpython3.10-minimal libpython3.10-stdlib libpython3.11 libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib libsub-override-perl libtool libuchardet0 libxml2 m4 man-db media-types po-debconf python3 python3-all python3-all-dev python3-attr python3-dev python3-distutils python3-iniconfig python3-lib2to3 python3-minimal python3-more-itertools python3-packaging python3-pkg-resources python3-pluggy python3-py python3-pyparsing python3-pytest python3-setuptools python3-tomli python3.10 python3.10-dev python3.10-minimal python3.11 python3.11-dev python3.11-minimal zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make flit python3-build python3-installer 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-attr-doc subversion python-pyparsing-doc python-setuptools-doc python3.10-venv python3.10-doc binfmt-support python3.11-venv python3.11-doc Recommended packages: curl | wget | lynx libarchive-cpio-perl javascript-common libltdl-dev libmail-sendmail-perl python3-pygments The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libdw1 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libicu71 libjs-jquery libjs-sphinxdoc libjs-underscore libmagic-mgc libmagic1 libmpdec3 libpipeline1 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.10 libpython3.10-dev libpython3.10-minimal libpython3.10-stdlib libpython3.11 libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib libsub-override-perl libtool libuchardet0 libxml2 m4 man-db media-types po-debconf python3 python3-all python3-all-dev python3-attr python3-dev python3-distutils python3-iniconfig python3-lib2to3 python3-minimal python3-more-itertools python3-packaging python3-pkg-resources python3-pluggy python3-py python3-pyparsing python3-pytest python3-setuptools python3-tomli python3.10 python3.10-dev python3.10-minimal python3.11 python3.11-dev python3.11-minimal sbuild-build-depends-main-dummy zlib1g-dev 0 upgraded, 76 newly installed, 0 to remove and 0 not upgraded. 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http://ftpmaster.internal/ubuntu lunar/main amd64 python3-pyparsing all 3.0.7-3 [82.1 kB] Get:71 http://ftpmaster.internal/ubuntu lunar/main amd64 python3-packaging all 21.3-1.1 [30.6 kB] Get:72 http://ftpmaster.internal/ubuntu lunar/universe amd64 python3-pluggy all 1.0.0+repack-1 [15.1 kB] Get:73 http://ftpmaster.internal/ubuntu lunar/universe amd64 python3-py all 1.11.0-1 [73.2 kB] Get:74 http://ftpmaster.internal/ubuntu lunar/universe amd64 python3-tomli all 2.0.1-1 [16.6 kB] Get:75 http://ftpmaster.internal/ubuntu lunar/universe amd64 python3-pytest all 7.1.2-2ubuntu1 [219 kB] Get:76 http://ftpmaster.internal/ubuntu lunar/main amd64 python3-setuptools all 59.6.0-1.2 [339 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 47.7 MB in 0s (154 MB/s) Selecting previously unselected package libpython3.10-minimal:amd64. 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Processing triggers for systemd (251.4-1ubuntu7) ... Processing triggers for libc-bin (2.36-0ubuntu4) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-132-generic #148-Ubuntu SMP Mon Oct 17 16:02:06 UTC 2022 amd64 (x86_64) Toolchain package versions: binutils_2.39-8ubuntu2 dpkg-dev_1.21.9ubuntu1 g++-12_12.2.0-9ubuntu1 gcc-12_12.2.0-9ubuntu1 libc6-dev_2.36-0ubuntu4 libstdc++-12-dev_12.2.0-9ubuntu1 libstdc++6_12.2.0-9ubuntu1 linux-libc-dev_5.19.0-23.24 Package versions: adduser_3.129ubuntu1 advancecomp_2.4-1 apt_2.5.4 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-10 autotools-dev_20220109.1 base-files_12.3ubuntu1 base-passwd_3.6.1 bash_5.2-1ubuntu2 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sed_4.8-1ubuntu2 sensible-utils_0.0.17 systemd_251.4-1ubuntu7 systemd-sysv_251.4-1ubuntu7 sysvinit-utils_3.04-1ubuntu1 tar_1.34+dfsg-1.1 tzdata_2022g-0ubuntu1 ubuntu-keyring_2021.03.26 usrmerge_33ubuntu1 util-linux_2.38-4ubuntu1 util-linux-extra_2.38-4ubuntu1 xz-utils_5.2.8-0.0 zlib1g_1:1.2.13.dfsg-1ubuntu2 zlib1g-dev_1:1.2.13.dfsg-1ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: python-pairix Binary: python3-pairix, python-pairix-examples Architecture: any all Version: 0.3.7-6 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/4dn-dcic/pairix Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/python-pairix Vcs-Git: https://salsa.debian.org/med-team/python-pairix.git Testsuite: autopkgtest Testsuite-Triggers: python3-pytest Build-Depends: debhelper-compat (= 13), dh-python, python3-all-dev, python3-setuptools, zlib1g-dev, python3-pytest Package-List: python-pairix-examples deb science optional arch=all python3-pairix deb python optional arch=any Checksums-Sha1: eb863fe1eeedbfdf4fc98a93b264c158c6870694 175413839 python-pairix_0.3.7.orig.tar.gz 72974c50b5214c2d7357001fb379462361b811cc 4828 python-pairix_0.3.7-6.debian.tar.xz Checksums-Sha256: c0de5fb5baea2bf90a6179f9c81c911e2fb951b716b38574f73ac5b23ac84969 175413839 python-pairix_0.3.7.orig.tar.gz 5680a5d9f1396b5a57d3047c72b15cad88df104de5b34d28fe99018cd7cc5d34 4828 python-pairix_0.3.7-6.debian.tar.xz Files: a1f9b3c7b13d904dfe736cf5e66c2385 175413839 python-pairix_0.3.7.orig.tar.gz e7444b9b8a43853393517927bc019e18 4828 python-pairix_0.3.7-6.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmOHya8RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHP2w//WFUcOuDbog9ArbR+i0JWNo7mX5tX+HJ+ 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in /<> dpkg-source: info: unpacking python-pairix_0.3.7.orig.tar.gz dpkg-source: info: unpacking python-pairix_0.3.7-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying python3.10 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-24887997 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-24887997 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-24887997 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-pairix dpkg-buildpackage: info: source version 0.3.7-6 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:240: python3.11 setup.py clean /usr/lib/python3/dist-packages/setuptools/dist.py:723: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead warnings.warn( running clean removing '/<>/.pybuild/cpython3_3.11_pairix/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it I: pybuild base:240: python3.10 setup.py clean /usr/lib/python3/dist-packages/setuptools/dist.py:723: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead warnings.warn( running clean removing '/<>/.pybuild/cpython3_3.10_pairix/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.10' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:240: python3.11 setup.py config /usr/lib/python3/dist-packages/setuptools/dist.py:723: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead warnings.warn( running config I: pybuild base:240: python3.10 setup.py config /usr/lib/python3/dist-packages/setuptools/dist.py:723: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead warnings.warn( running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:240: /usr/bin/python3.11 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:723: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead warnings.warn( running build running build_ext building 'pypairix' extension creating build creating build/temp.linux-x86_64-3.11 creating build/temp.linux-x86_64-3.11/src x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Isrc -I/usr/include/python3.11 -c src/bgzf.c -o build/temp.linux-x86_64-3.11/src/bgzf.o src/bgzf.c: In function ‘bgzf_block_length’: src/bgzf.c:331:34: warning: unused variable ‘remaining’ [-Wunused-variable] 331 | int count, block_length, remaining; | ^~~~~~~~~ src/bgzf.c:330:47: warning: unused variable ‘compressed_block’ [-Wunused-variable] 330 | uint8_t header[BLOCK_HEADER_LENGTH], *compressed_block; | ^~~~~~~~~~~~~~~~ src/bgzf.c: In function ‘bgzf_flush’: src/bgzf.c:419:75: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 419 | if (fwrite(fp->compressed_block, 1, block_length, fp->fp) != block_length) { | ^~ src/bgzf.c: In function ‘bgzf_close’: src/bgzf.c:456:18: warning: variable ‘count’ set but not used [-Wunused-but-set-variable] 456 | int ret, count, block_length; | ^~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Isrc -I/usr/include/python3.11 -c src/bgzip.c -o build/temp.linux-x86_64-3.11/src/bgzip.o src/bgzip.c: In function ‘main’: src/bgzip.c:198:25: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 198 | write(f_dst, buffer, c); | ^~~~~~~~~~~~~~~~~~~~~~~ src/bgzip.c: In function ‘write_open’: src/bgzip.c:57:25: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 57 | scanf("%c", &c); | ^~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Isrc -I/usr/include/python3.11 -c src/index.c -o build/temp.linux-x86_64-3.11/src/index.o src/index.c: In function ‘merge_chunks’: src/index.c:354:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 354 | for (l = 1; l < p->n; ++l) { | ^ src/index.c: In function ‘ti_index_core’: src/index.c:393:42: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int32_t’ {aka ‘int’} changes value from ‘last_bin = 4294967295’ to ‘-1’ [-Woverflow] 393 | save_bin = save_tid = last_tid = last_bin = 0xffffffffu; | ^~~~~~~~ src/index.c:399:28: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 399 | if (lineno <= idx->conf.line_skip || str->s[0] == idx->conf.meta_char) { | ^~ src/index.c:423:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 423 | if (intv.bin != last_bin) { // then possibly write the binning index | ^~ src/index.c:431:35: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 431 | if (bgzf_tell(fp) <= last_off) { | ^~ src/index.c: In function ‘ti_index_save’: src/index.c:510:31: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘khint_t’ {aka ‘unsigned int’} [-Wsign-compare] 510 | for (i = 0; i < kh_size(idx->tname); ++i) | ^ src/index.c:514:31: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘khint_t’ {aka ‘unsigned int’} [-Wsign-compare] 514 | for (i = 0; i < kh_size(idx->tname); ++i) | ^ src/index.c:534:60: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 534 | for (x = 0; (int)x < p->n; ++x) { | ^ src/index.c:539:60: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 539 | for (x = 0; (int)x < p->n; ++x) { | ^ src/index.c: In function ‘ti_index_load_core’: src/index.c:659:47: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 659 | for (x = 0; x < p->n; ++x) { | ^ src/index.c: In function ‘ti_parse_region2d’: src/index.c:864:69: warning: passing argument 1 of ‘ti_get_region_split_character’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 864 | char region_split_character = ti_get_region_split_character(idx); | ^~~ In file included from src/index.c:11: src/pairix.h:218:56: note: expected ‘ti_index_t *’ {aka ‘struct __ti_index_t *’} but argument is of type ‘const ti_index_t *’ {aka ‘const struct __ti_index_t *’} 218 | char ti_get_region_split_character(ti_index_t *idx); | ~~~~~~~~~~~~^~~ src/index.c:878:30: warning: passing argument 1 of ‘ti_get_sc2’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 878 | int dim = ti_get_sc2(idx)+1==0?1:2; | ^~~ src/pairix.h:209:36: note: expected ‘ti_index_t *’ {aka ‘struct __ti_index_t *’} but argument is of type ‘const ti_index_t *’ {aka ‘const struct __ti_index_t *’} 209 | int ti_get_sc2(ti_index_t *idx); | ~~~~~~~~~~~~^~~ src/index.c: In function ‘reg2bins’: src/index.c:974:56: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 974 | for (k = 1 + (beg>>TAD_LIDX_SHIFT_PL12); k <= 1 + (end>>TAD_LIDX_SHIFT_PL12); ++k) list[i++] = k; | ^~ src/index.c:975:55: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 975 | for (k = 9 + (beg>>TAD_LIDX_SHIFT_PL9); k <= 9 + (end>>TAD_LIDX_SHIFT_PL9); ++k) list[i++] = k; | ^~ src/index.c:976:55: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 976 | for (k = 73 + (beg>>TAD_LIDX_SHIFT_PL6); k <= 73 + (end>>TAD_LIDX_SHIFT_PL6); ++k) list[i++] = k; | ^~ src/index.c:977:55: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 977 | for (k = 585 + (beg>>TAD_LIDX_SHIFT_PL3); k <= 585 + (end>>TAD_LIDX_SHIFT_PL3); ++k) list[i++] = k; | ^~ src/index.c:978:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 978 | for (k = 4681 + (beg>>TAD_LIDX_SHIFT); k <= 4681 + (end>>TAD_LIDX_SHIFT); ++k) list[i++] = k; | ^~ src/index.c: In function ‘ti_iter_query’: src/index.c:1038:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 1038 | for (j = 0; j < p->n; ++j) | ^ src/index.c: In function ‘ti_querys_2d_general’: src/index.c:1219:31: warning: initialization of ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 1219 | char **chrpairlist = ti_seqname(t->idx, &n_seqpair_list); | ^~~~~~~~~~ src/index.c:1236:59: warning: passing argument 2 of ‘ti_querys_2d_multi’ from incompatible pointer type [-Wincompatible-pointer-types] 1236 | sequential_iter_t *siter = ti_querys_2d_multi(t, regions, n_sub_list); | ^~~~~~~ | | | char ** src/pairix.h:131:73: note: expected ‘const char **’ but argument is of type ‘char **’ 131 | sequential_iter_t *ti_querys_2d_multi(pairix_t *t, const char **regs, int nRegs); | ~~~~~~~~~~~~~^~~~ src/index.c:1242:30: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1242 | *sp=0; char *chr1 = reg; | ^~~ src/index.c:1246:31: warning: initialization of ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 1246 | char **chrpairlist = ti_seqname(t->idx, &n_seqpair_list); | ^~~~~~~~~~ src/index.c:1263:59: warning: passing argument 2 of ‘ti_querys_2d_multi’ from incompatible pointer type [-Wincompatible-pointer-types] 1263 | sequential_iter_t *siter = ti_querys_2d_multi(t, regions, n_sub_list); | ^~~~~~~ | | | char ** src/pairix.h:131:73: note: expected ‘const char **’ but argument is of type ‘char **’ 131 | sequential_iter_t *ti_querys_2d_multi(pairix_t *t, const char **regs, int nRegs); | ~~~~~~~~~~~~~^~~~ src/index.c: In function ‘ti_query_2d_tid’: src/index.c:1417:31: warning: returning ‘ti_iter_t’ {aka ‘struct __ti_iter_t *’} from a function with return type ‘int’ makes integer from pointer without a cast [-Wint-conversion] 1417 | if (name == 0) return ti_iter_first(); | ^~~~~~~~~~~~~~~ src/index.c: In function ‘create_merged_iter’: src/index.c:1469:10: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 1469 | if( miter->iu = calloc(n,sizeof(iter_unit*))) { | ^~~~~ src/index.c: In function ‘merged_ti_read’: src/index.c:1537:19: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1537 | miu[i]->s = ti_iter_read(miu[i]->t->fp, miu[i]->iter, miu[i]->len, seqonly); | ^ src/index.c:1543:17: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1543 | miu[0]->s = ti_iter_read(miu[0]->t->fp, miu[0]->iter, miu[0]->len, seqonly); // get next entry for the flushed iter | ^ src/index.c: In function ‘sequential_ti_read’: src/index.c:1573:15: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1573 | char *s = ti_iter_read(siter->t->fp,siter->iter[siter->curr], len, 0); | ^~~~~~~~~~~~ src/index.c:1576:9: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1576 | s = ti_iter_read(siter->t->fp,siter->iter[siter->curr], len, 0); | ^ src/index.c: In function ‘get_unique_merged_seqname’: src/index.c:1643:22: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 1643 | seqnames = ti_seqname(tbs[i]->idx,&len); | ^ src/index.c: In function ‘flip_region’: src/index.c:1744:19: warning: variable ‘split_pos’ set but not used [-Wunused-but-set-variable] 1744 | int l, i, l2, split_pos; | ^~~~~~~~~ src/index.c: In function ‘querys_2D_wrapper’: src/index.c:1911:34: warning: passing argument 1 of ‘flip_region’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1911 | char *reg2 = flip_region(reg, get_region_split_character(tb)); | ^~~ src/index.c:1743:27: note: expected ‘char *’ but argument is of type ‘const char *’ 1743 | char *flip_region ( char* s, char region_split_character) { | ~~~~~~^ src/index.c: In function ‘check_triangle’: src/index.c:1971:23: warning: initialization of ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 1971 | char **seqnames = ti_seqname(idx,&len); | ^~~~~~~~~~ src/index.c:1977:64: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1977 | if(ti_get_tid(idx, reg2)!=-1) { free(seqnames); free(reg2); return(0); } // not a triangle | ^~~~ In file included from src/khash.h:94, from src/index.c:4: /usr/include/stdlib.h:568:25: note: expected ‘void *’ but argument is of type ‘const char *’ 568 | extern void free (void *__ptr) __THROW; | ~~~~~~^~~~~ src/index.c:1978:14: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1978 | free(reg2); | ^~~~ /usr/include/stdlib.h:568:25: note: expected ‘void *’ but argument is of type ‘const char *’ 568 | extern void free (void *__ptr) __THROW; | ~~~~~~^~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Isrc -I/usr/include/python3.11 -c src/knetfile.c -o build/temp.linux-x86_64-3.11/src/knetfile.o In file included from src/knetfile.c:49: src/knetfile.c: In function ‘kftp_send_cmd’: src/knetfile.h:9:32: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) | ^~~~~~~~~~~~~~~~~~~ src/knetfile.c:239:9: note: in expansion of macro ‘netwrite’ 239 | netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); | ^~~~~~~~ src/knetfile.c: In function ‘khttp_connect_file’: src/knetfile.h:9:32: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) | ^~~~~~~~~~~~~~~~~~~ src/knetfile.c:418:9: note: in expansion of macro ‘netwrite’ 418 | netwrite(fp->fd, buf, l); | ^~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Isrc -I/usr/include/python3.11 -c src/kstring.c -o build/temp.linux-x86_64-3.11/src/kstring.o src/kstring.c: In function ‘ksprintf’: src/kstring.c:15:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 15 | if (l + 1 > s->m - s->l) { | ^ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Isrc -I/usr/include/python3.11 -c src/pairixmodule.c -o build/temp.linux-x86_64-3.11/src/pairixmodule.o src/pairixmodule.c: In function ‘pairix_new’: src/pairixmodule.c:367:9: warning: unused variable ‘i’ [-Wunused-variable] 367 | int i; | ^ src/pairixmodule.c: In function ‘pairix_querys_2D’: src/pairixmodule.c:559:28: warning: passing argument 1 of ‘flip_region’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 559 | reg2 = flip_region(reg, get_region_split_character(self->tb)); | ^~~ In file included from src/pairixmodule.c:34: src/pairix.h:223:33: note: expected ‘char *’ but argument is of type ‘const char *’ 223 | char* flip_region(char *s, char region_split_character); | ~~~~~~^ src/pairixmodule.c: In function ‘pairix_get_blocknames’: src/pairixmodule.c:603:23: warning: initialization of ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 603 | char **blocknames = ti_seqname(self->tb->idx, &n); | ^~~~~~~~~~ src/pairixmodule.c: In function ‘pairix_get_header’: src/pairixmodule.c:693:15: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 693 | while ((s = sequential_ti_read(siter, &len)) != 0) { | ^ src/pairixmodule.c:704:15: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 704 | while ((s = sequential_ti_read(siter, &len)) != 0) { | ^ src/pairixmodule.c: In function ‘pairix_get_chromsize’: src/pairixmodule.c:726:15: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 726 | while ((s = sequential_ti_read(siter, &len)) != 0) { | ^ src/pairixmodule.c:738:15: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 738 | while ((s = sequential_ti_read(siter, &len)) != 0) { | ^ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.11/src/bgzf.o build/temp.linux-x86_64-3.11/src/bgzip.o build/temp.linux-x86_64-3.11/src/index.o build/temp.linux-x86_64-3.11/src/knetfile.o build/temp.linux-x86_64-3.11/src/kstring.o build/temp.linux-x86_64-3.11/src/pairixmodule.o -lz -o /<>/.pybuild/cpython3_3.11_pairix/build/pypairix.cpython-311-x86_64-linux-gnu.so I: pybuild base:240: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:723: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead warnings.warn( running build running build_ext building 'pypairix' extension creating build/temp.linux-x86_64-3.10 creating build/temp.linux-x86_64-3.10/src x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Isrc -I/usr/include/python3.10 -c src/bgzf.c -o build/temp.linux-x86_64-3.10/src/bgzf.o src/bgzf.c: In function ‘bgzf_block_length’: src/bgzf.c:331:34: warning: unused variable ‘remaining’ [-Wunused-variable] 331 | int count, block_length, remaining; | ^~~~~~~~~ src/bgzf.c:330:47: warning: unused variable ‘compressed_block’ [-Wunused-variable] 330 | uint8_t header[BLOCK_HEADER_LENGTH], *compressed_block; | ^~~~~~~~~~~~~~~~ src/bgzf.c: In function ‘bgzf_flush’: src/bgzf.c:419:75: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 419 | if (fwrite(fp->compressed_block, 1, block_length, fp->fp) != block_length) { | ^~ src/bgzf.c: In function ‘bgzf_close’: src/bgzf.c:456:18: warning: variable ‘count’ set but not used [-Wunused-but-set-variable] 456 | int ret, count, block_length; | ^~~~~ x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Isrc -I/usr/include/python3.10 -c src/bgzip.c -o build/temp.linux-x86_64-3.10/src/bgzip.o x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Isrc -I/usr/include/python3.10 -c src/index.c -o build/temp.linux-x86_64-3.10/src/index.o src/index.c: In function ‘merge_chunks’: src/index.c:354:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 354 | for (l = 1; l < p->n; ++l) { | ^ src/index.c: In function ‘ti_index_core’: src/index.c:393:42: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int32_t’ {aka ‘int’} changes value from ‘last_bin = 4294967295’ to ‘-1’ [-Woverflow] 393 | save_bin = save_tid = last_tid = last_bin = 0xffffffffu; | ^~~~~~~~ src/index.c:399:28: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 399 | if (lineno <= idx->conf.line_skip || str->s[0] == idx->conf.meta_char) { | ^~ src/index.c:423:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 423 | if (intv.bin != last_bin) { // then possibly write the binning index | ^~ src/index.c:431:35: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 431 | if (bgzf_tell(fp) <= last_off) { | ^~ src/index.c: In function ‘ti_index_save’: src/index.c:510:31: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘khint_t’ {aka ‘unsigned int’} [-Wsign-compare] 510 | for (i = 0; i < kh_size(idx->tname); ++i) | ^ src/index.c:514:31: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘khint_t’ {aka ‘unsigned int’} [-Wsign-compare] 514 | for (i = 0; i < kh_size(idx->tname); ++i) | ^ src/index.c:534:60: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 534 | for (x = 0; (int)x < p->n; ++x) { | ^ src/index.c:539:60: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 539 | for (x = 0; (int)x < p->n; ++x) { | ^ src/index.c: In function ‘ti_index_load_core’: src/index.c:659:47: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 659 | for (x = 0; x < p->n; ++x) { | ^ src/index.c: In function ‘ti_parse_region2d’: src/index.c:864:69: warning: passing argument 1 of ‘ti_get_region_split_character’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 864 | char region_split_character = ti_get_region_split_character(idx); | ^~~ In file included from src/index.c:11: src/pairix.h:218:56: note: expected ‘ti_index_t *’ {aka ‘struct __ti_index_t *’} but argument is of type ‘const ti_index_t *’ {aka ‘const struct __ti_index_t *’} 218 | char ti_get_region_split_character(ti_index_t *idx); | ~~~~~~~~~~~~^~~ src/index.c:878:30: warning: passing argument 1 of ‘ti_get_sc2’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 878 | int dim = ti_get_sc2(idx)+1==0?1:2; | ^~~ src/pairix.h:209:36: note: expected ‘ti_index_t *’ {aka ‘struct __ti_index_t *’} but argument is of type ‘const ti_index_t *’ {aka ‘const struct __ti_index_t *’} 209 | int ti_get_sc2(ti_index_t *idx); | ~~~~~~~~~~~~^~~ src/index.c: In function ‘reg2bins’: src/index.c:974:56: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 974 | for (k = 1 + (beg>>TAD_LIDX_SHIFT_PL12); k <= 1 + (end>>TAD_LIDX_SHIFT_PL12); ++k) list[i++] = k; | ^~ src/index.c:975:55: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 975 | for (k = 9 + (beg>>TAD_LIDX_SHIFT_PL9); k <= 9 + (end>>TAD_LIDX_SHIFT_PL9); ++k) list[i++] = k; | ^~ src/index.c:976:55: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 976 | for (k = 73 + (beg>>TAD_LIDX_SHIFT_PL6); k <= 73 + (end>>TAD_LIDX_SHIFT_PL6); ++k) list[i++] = k; | ^~ src/index.c:977:55: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 977 | for (k = 585 + (beg>>TAD_LIDX_SHIFT_PL3); k <= 585 + (end>>TAD_LIDX_SHIFT_PL3); ++k) list[i++] = k; | ^~ src/index.c:978:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 978 | for (k = 4681 + (beg>>TAD_LIDX_SHIFT); k <= 4681 + (end>>TAD_LIDX_SHIFT); ++k) list[i++] = k; | ^~ src/index.c: In function ‘ti_iter_query’: src/index.c:1038:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 1038 | for (j = 0; j < p->n; ++j) | ^ src/index.c: In function ‘ti_querys_2d_general’: src/index.c:1219:31: warning: initialization of ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 1219 | char **chrpairlist = ti_seqname(t->idx, &n_seqpair_list); | ^~~~~~~~~~ src/index.c:1236:59: warning: passing argument 2 of ‘ti_querys_2d_multi’ from incompatible pointer type [-Wincompatible-pointer-types] 1236 | sequential_iter_t *siter = ti_querys_2d_multi(t, regions, n_sub_list); | ^~~~~~~ | | | char ** src/pairix.h:131:73: note: expected ‘const char **’ but argument is of type ‘char **’ 131 | sequential_iter_t *ti_querys_2d_multi(pairix_t *t, const char **regs, int nRegs); | ~~~~~~~~~~~~~^~~~ src/index.c:1242:30: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1242 | *sp=0; char *chr1 = reg; | ^~~ src/index.c:1246:31: warning: initialization of ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 1246 | char **chrpairlist = ti_seqname(t->idx, &n_seqpair_list); | ^~~~~~~~~~ src/index.c:1263:59: warning: passing argument 2 of ‘ti_querys_2d_multi’ from incompatible pointer type [-Wincompatible-pointer-types] 1263 | sequential_iter_t *siter = ti_querys_2d_multi(t, regions, n_sub_list); | ^~~~~~~ | | | char ** src/pairix.h:131:73: note: expected ‘const char **’ but argument is of type ‘char **’ 131 | sequential_iter_t *ti_querys_2d_multi(pairix_t *t, const char **regs, int nRegs); | ~~~~~~~~~~~~~^~~~ src/index.c: In function ‘ti_query_2d_tid’: src/index.c:1417:31: warning: returning ‘ti_iter_t’ {aka ‘struct __ti_iter_t *’} from a function with return type ‘int’ makes integer from pointer without a cast [-Wint-conversion] 1417 | if (name == 0) return ti_iter_first(); | ^~~~~~~~~~~~~~~ src/index.c: In function ‘create_merged_iter’: src/index.c:1469:10: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 1469 | if( miter->iu = calloc(n,sizeof(iter_unit*))) { | ^~~~~ src/index.c: In function ‘merged_ti_read’: src/index.c:1537:19: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1537 | miu[i]->s = ti_iter_read(miu[i]->t->fp, miu[i]->iter, miu[i]->len, seqonly); | ^ src/index.c:1543:17: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1543 | miu[0]->s = ti_iter_read(miu[0]->t->fp, miu[0]->iter, miu[0]->len, seqonly); // get next entry for the flushed iter | ^ src/index.c: In function ‘sequential_ti_read’: src/index.c:1573:15: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1573 | char *s = ti_iter_read(siter->t->fp,siter->iter[siter->curr], len, 0); | ^~~~~~~~~~~~ src/index.c:1576:9: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1576 | s = ti_iter_read(siter->t->fp,siter->iter[siter->curr], len, 0); | ^ src/index.c: In function ‘get_unique_merged_seqname’: src/index.c:1643:22: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 1643 | seqnames = ti_seqname(tbs[i]->idx,&len); | ^ src/index.c: In function ‘flip_region’: src/index.c:1744:19: warning: variable ‘split_pos’ set but not used [-Wunused-but-set-variable] 1744 | int l, i, l2, split_pos; | ^~~~~~~~~ src/index.c: In function ‘querys_2D_wrapper’: src/index.c:1911:34: warning: passing argument 1 of ‘flip_region’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1911 | char *reg2 = flip_region(reg, get_region_split_character(tb)); | ^~~ src/index.c:1743:27: note: expected ‘char *’ but argument is of type ‘const char *’ 1743 | char *flip_region ( char* s, char region_split_character) { | ~~~~~~^ src/index.c: In function ‘check_triangle’: src/index.c:1971:23: warning: initialization of ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 1971 | char **seqnames = ti_seqname(idx,&len); | ^~~~~~~~~~ src/index.c:1977:64: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1977 | if(ti_get_tid(idx, reg2)!=-1) { free(seqnames); free(reg2); return(0); } // not a triangle | ^~~~ In file included from src/khash.h:94, from src/index.c:4: /usr/include/stdlib.h:568:25: note: expected ‘void *’ but argument is of type ‘const char *’ 568 | extern void free (void *__ptr) __THROW; | ~~~~~~^~~~~ src/index.c:1978:14: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1978 | free(reg2); | ^~~~ /usr/include/stdlib.h:568:25: note: expected ‘void *’ but argument is of type ‘const char *’ 568 | extern void free (void *__ptr) __THROW; | ~~~~~~^~~~~ x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Isrc -I/usr/include/python3.10 -c src/knetfile.c -o build/temp.linux-x86_64-3.10/src/knetfile.o x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Isrc -I/usr/include/python3.10 -c src/kstring.c -o build/temp.linux-x86_64-3.10/src/kstring.o src/kstring.c: In function ‘ksprintf’: src/kstring.c:15:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 15 | if (l + 1 > s->m - s->l) { | ^ x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Isrc -I/usr/include/python3.10 -c src/pairixmodule.c -o build/temp.linux-x86_64-3.10/src/pairixmodule.o src/pairixmodule.c: In function ‘pairix_new’: src/pairixmodule.c:367:9: warning: unused variable ‘i’ [-Wunused-variable] 367 | int i; | ^ src/pairixmodule.c: In function ‘pairix_querys_2D’: src/pairixmodule.c:559:28: warning: passing argument 1 of ‘flip_region’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 559 | reg2 = flip_region(reg, get_region_split_character(self->tb)); | ^~~ In file included from src/pairixmodule.c:34: src/pairix.h:223:33: note: expected ‘char *’ but argument is of type ‘const char *’ 223 | char* flip_region(char *s, char region_split_character); | ~~~~~~^ src/pairixmodule.c: In function ‘pairix_get_blocknames’: src/pairixmodule.c:603:23: warning: initialization of ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 603 | char **blocknames = ti_seqname(self->tb->idx, &n); | ^~~~~~~~~~ src/pairixmodule.c: In function ‘pairix_get_header’: src/pairixmodule.c:693:15: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 693 | while ((s = sequential_ti_read(siter, &len)) != 0) { | ^ src/pairixmodule.c:704:15: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 704 | while ((s = sequential_ti_read(siter, &len)) != 0) { | ^ src/pairixmodule.c: In function ‘pairix_get_chromsize’: src/pairixmodule.c:726:15: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 726 | while ((s = sequential_ti_read(siter, &len)) != 0) { | ^ src/pairixmodule.c:738:15: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 738 | while ((s = sequential_ti_read(siter, &len)) != 0) { | ^ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/src/bgzf.o build/temp.linux-x86_64-3.10/src/bgzip.o build/temp.linux-x86_64-3.10/src/index.o build/temp.linux-x86_64-3.10/src/knetfile.o build/temp.linux-x86_64-3.10/src/kstring.o build/temp.linux-x86_64-3.10/src/pairixmodule.o -lz -o /<>/.pybuild/cpython3_3.10_pairix/build/pypairix.cpython-310-x86_64-linux-gnu.so dh_auto_test -O--buildsystem=pybuild I: pybuild pybuild:300: cp -a /<>/samples /<>/.pybuild/cpython3_3.11_pairix/build; cp -a /<>/VERSION.txt /<>/.pybuild/cpython3_3.11_pairix/build; I: pybuild base:240: cd /<>/.pybuild/cpython3_3.11_pairix/build; python3.11 -m pytest test ============================= test session starts ============================== platform linux -- Python 3.11.0+, pytest-7.1.2, pluggy-1.0.0+repack rootdir: /<> collected 48 items test/test_oldindex.py ........................ [ 50%] test/test_oldindex2.py ........................ [100%] =============================== warnings summary =============================== test/test_oldindex.py:60 /<>/.pybuild/cpython3_3.11_pairix/build/test/test_oldindex.py:60: DeprecationWarning: invalid escape sequence '\s' fields = line.rstrip().split('\s+') test/test_oldindex2.py:59 /<>/.pybuild/cpython3_3.11_pairix/build/test/test_oldindex2.py:59: DeprecationWarning: invalid escape sequence '\s' fields = line.rstrip().split('\s+') -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ======================== 48 passed, 2 warnings in 5.62s ======================== The file is a triangle. The file is a triangle. The file is not a triangle. The file is a triangle. The file is a triangle. The file is not a triangle. I: pybuild pybuild:300: cp -a /<>/samples /<>/.pybuild/cpython3_3.10_pairix/build; cp -a /<>/VERSION.txt /<>/.pybuild/cpython3_3.10_pairix/build; I: pybuild base:240: cd /<>/.pybuild/cpython3_3.10_pairix/build; python3.10 -m pytest test ============================= test session starts ============================== platform linux -- Python 3.10.8, pytest-7.1.2, pluggy-1.0.0+repack rootdir: /<> collected 48 items test/test_oldindex.py ........................ [ 50%] test/test_oldindex2.py ........................ [100%] =============================== warnings summary =============================== test/test_oldindex.py:60 /<>/.pybuild/cpython3_3.10_pairix/build/test/test_oldindex.py:60: DeprecationWarning: invalid escape sequence '\s' fields = line.rstrip().split('\s+') test/test_oldindex2.py:59 /<>/.pybuild/cpython3_3.10_pairix/build/test/test_oldindex2.py:59: DeprecationWarning: invalid escape sequence '\s' fields = line.rstrip().split('\s+') -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ======================== 48 passed, 2 warnings in 6.51s ======================== The file is a triangle. The file is a triangle. The file is not a triangle. The file is a triangle. The file is a triangle. The file is not a triangle. create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:240: /usr/bin/python3.11 setup.py install --root /<>/debian/python3-pairix /usr/lib/python3/dist-packages/setuptools/dist.py:723: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead warnings.warn( running install /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_ext running install_lib creating /<>/debian/python3-pairix creating /<>/debian/python3-pairix/usr creating /<>/debian/python3-pairix/usr/lib creating /<>/debian/python3-pairix/usr/lib/python3.11 creating /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages copying /<>/.pybuild/cpython3_3.11_pairix/build/VERSION.txt -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages copying /<>/.pybuild/cpython3_3.11_pairix/build/pypairix.cpython-311-x86_64-linux-gnu.so -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages creating /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/test_old_merged_nodups.pairs -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/merged_nodups.space.chrblock_sorted.subsample3.bsorted.ff.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/merged_nodups.space.chrblock_sorted.subsample2.txt.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/merged_nodup.tab.chrblock_sorted.txt.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/merged_nodups.space.chrblock_sorted.subsample1.txt.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/merged_nodups.space.chrblock_sorted.subsample3.bsorted.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/merged_nodups.space.chrblock_sorted.subsample3.pairs -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples creating /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index2 copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index2/merged_nodup.tab.chrblock_sorted.txt.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index2 copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index2/merged_nodups.space.chrblock_sorted.subsample1.txt.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index2 copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index2/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index2 copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index2/mock.largechr.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index2 copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index2/4dn.bsorted.chr21_22_only.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index2 copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index2/4dn.bsorted.chr21_22_only.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index2 copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index2/merged_nodups.space.chrblock_sorted.subsample1.txt.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index2 copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index2/SRR1171591.variants.snp.vqsr.p.vcf.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index2 copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index2/merged_nodup.tab.chrblock_sorted.txt.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index2 copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index2/SRR1171591.variants.snp.vqsr.p.vcf.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index2 copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index2/mock.largechr.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index2 copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index2/test_4dn.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index2 copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index2/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index2 copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index2/test_4dn.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index2 copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/merged_nodups.space.chrblock_sorted.subsample3.bsorted.ff.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/test_merged_nodups.txt.bsorted.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/hg19.chrom.sizes.chr21_22_only:50000 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/merged_nodups.space.chrblock_sorted.subsample3.bsorted.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/test_4dn_2.bsorted.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/merged_nodups.space.chrblock_sorted.subsample3.txt.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/test.bed -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/mock.largechr.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/test_merged_nodups.pairs -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/test_juicer_shortform.bsorted.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/merged_nodups.space.chrblock_sorted.subsample3.bsorted.nofrag.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/4dn.bsorted.chr21_22_only.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/test_4dn.cp.pairs -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples creating /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/test_old_merged_nodups.pairs -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/merged_nodups.space.chrblock_sorted.subsample3.bsorted.ff.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/merged_nodups.space.chrblock_sorted.subsample2.txt.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/merged_nodup.tab.chrblock_sorted.txt.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/merged_nodups.space.chrblock_sorted.subsample1.txt.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/merged_nodups.space.chrblock_sorted.subsample3.bsorted.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/merged_nodups.space.chrblock_sorted.subsample3.pairs -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/merged_nodups.space.chrblock_sorted.subsample3.bsorted.ff.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/test_merged_nodups.txt.bsorted.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/hg19.chrom.sizes.chr21_22_only:50000 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/merged_nodups.space.chrblock_sorted.subsample3.bsorted.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/test_4dn_2.bsorted.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/merged_nodups.space.chrblock_sorted.subsample3.txt.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/test.bed -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/mock.largechr.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/test_merged_nodups.pairs -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/test_juicer_shortform.bsorted.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/merged_nodups.space.chrblock_sorted.subsample3.bsorted.nofrag.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/4dn.bsorted.chr21_22_only.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/test_4dn.cp.pairs -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/hg19.chrom.sizes.chr21_22_only -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/test_merged_nodups.txt -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/test_merged_nodups.bsorted.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/4dn.bsorted.chr21_22_only.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/test.regions -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/test_juicer_shortform.bsorted.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/test_old_merged_nodups.txt.bsorted.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/merged_nodups.space.chrblock_sorted.subsample1.txt.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/test_old_merged_nodups.bsorted.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/test_merged_nodups.bsorted.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/SRR1171591.variants.snp.vqsr.p.vcf.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/merged_nodups.space.chrblock_sorted.subsample2.txt.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/hg19.chrom.sizes.-chr -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/merged_nodup.tab.chrblock_sorted.txt.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/merged_nodups.space.chrblock_sorted.subsample3.txt.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/test_old_merged_nodups.txt -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/test_old_merged_nodups.bsorted.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/SRR1171591.variants.snp.vqsr.p.vcf.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/mock.largechr.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/test_4dn_2.bsorted.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/test_old_merged_nodups.txt.bsorted.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/merged_nodups.space.chrblock_sorted.subsample3.bsorted.nofrag.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/test_juicer_shortform.pairs -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/test_4dn.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/test_merged_nodups.txt.bsorted.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/test_4dn.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/test_juicer_shortform.txt -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/old_index/test.regions2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/hg19.chrom.sizes.chr21_22_only -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/test_merged_nodups.txt -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/test_merged_nodups.bsorted.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/4dn.bsorted.chr21_22_only.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/test.regions -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/test_juicer_shortform.bsorted.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/4dn.bsorted.chr21_22_only.largechr.pairs -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/test_old_merged_nodups.txt.bsorted.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/merged_nodups.space.chrblock_sorted.subsample1.txt.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/test_old_merged_nodups.bsorted.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/test_merged_nodups.bsorted.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/SRR1171591.variants.snp.vqsr.p.vcf.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/merged_nodups.space.chrblock_sorted.subsample2.txt.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/hg19.chrom.sizes.-chr -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/merged_nodup.tab.chrblock_sorted.txt.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/merged_nodups.space.chrblock_sorted.subsample3.txt.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/test_old_merged_nodups.txt -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/test_old_merged_nodups.bsorted.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/SRR1171591.variants.snp.vqsr.p.vcf.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/mock.largechr.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/test_4dn_2.bsorted.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/test_old_merged_nodups.txt.bsorted.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/merged_nodups.space.chrblock_sorted.subsample3.bsorted.nofrag.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/test_juicer_shortform.pairs -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/test_4dn.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/test_merged_nodups.txt.bsorted.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/test_4dn.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/test_juicer_shortform.txt -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples copying /<>/.pybuild/cpython3_3.11_pairix/build/samples/test.regions2 -> /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/samples running install_egg_info running egg_info creating pypairix.egg-info writing pypairix.egg-info/PKG-INFO writing dependency_links to pypairix.egg-info/dependency_links.txt writing top-level names to pypairix.egg-info/top_level.txt writing manifest file 'pypairix.egg-info/SOURCES.txt' reading manifest file 'pypairix.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE.txt' writing manifest file 'pypairix.egg-info/SOURCES.txt' Copying pypairix.egg-info to /<>/debian/python3-pairix/usr/lib/python3.11/dist-packages/pypairix-0.3.7.egg-info Skipping SOURCES.txt running install_scripts I: pybuild base:240: /usr/bin/python3 setup.py install --root /<>/debian/python3-pairix /usr/lib/python3/dist-packages/setuptools/dist.py:723: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead warnings.warn( running install /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_ext running install_lib creating /<>/debian/python3-pairix/usr/lib/python3.10 creating /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages copying /<>/.pybuild/cpython3_3.10_pairix/build/VERSION.txt -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages creating /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/test_old_merged_nodups.pairs -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/merged_nodups.space.chrblock_sorted.subsample3.bsorted.ff.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/merged_nodups.space.chrblock_sorted.subsample2.txt.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/merged_nodup.tab.chrblock_sorted.txt.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/merged_nodups.space.chrblock_sorted.subsample1.txt.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/merged_nodups.space.chrblock_sorted.subsample3.bsorted.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/merged_nodups.space.chrblock_sorted.subsample3.pairs -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples creating /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index2 copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index2/merged_nodup.tab.chrblock_sorted.txt.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index2 copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index2/merged_nodups.space.chrblock_sorted.subsample1.txt.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index2 copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index2/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index2 copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index2/mock.largechr.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index2 copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index2/4dn.bsorted.chr21_22_only.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index2 copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index2/4dn.bsorted.chr21_22_only.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index2 copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index2/merged_nodups.space.chrblock_sorted.subsample1.txt.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index2 copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index2/SRR1171591.variants.snp.vqsr.p.vcf.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index2 copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index2/merged_nodup.tab.chrblock_sorted.txt.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index2 copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index2/SRR1171591.variants.snp.vqsr.p.vcf.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index2 copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index2/mock.largechr.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index2 copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index2/test_4dn.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index2 copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index2/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index2 copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index2/test_4dn.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index2 copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/merged_nodups.space.chrblock_sorted.subsample3.bsorted.ff.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/test_merged_nodups.txt.bsorted.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/hg19.chrom.sizes.chr21_22_only:50000 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/merged_nodups.space.chrblock_sorted.subsample3.bsorted.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/test_4dn_2.bsorted.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/merged_nodups.space.chrblock_sorted.subsample3.txt.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/test.bed -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/mock.largechr.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/test_merged_nodups.pairs -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/test_juicer_shortform.bsorted.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/merged_nodups.space.chrblock_sorted.subsample3.bsorted.nofrag.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/4dn.bsorted.chr21_22_only.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/test_4dn.cp.pairs -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples creating /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/test_old_merged_nodups.pairs -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/merged_nodups.space.chrblock_sorted.subsample3.bsorted.ff.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/merged_nodups.space.chrblock_sorted.subsample2.txt.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/merged_nodup.tab.chrblock_sorted.txt.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/merged_nodups.space.chrblock_sorted.subsample1.txt.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/merged_nodups.space.chrblock_sorted.subsample3.bsorted.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/merged_nodups.space.chrblock_sorted.subsample3.pairs -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/merged_nodups.space.chrblock_sorted.subsample3.bsorted.ff.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/test_merged_nodups.txt.bsorted.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/hg19.chrom.sizes.chr21_22_only:50000 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/merged_nodups.space.chrblock_sorted.subsample3.bsorted.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/test_4dn_2.bsorted.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/merged_nodups.space.chrblock_sorted.subsample3.txt.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/test.bed -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/mock.largechr.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/test_merged_nodups.pairs -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/test_juicer_shortform.bsorted.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/merged_nodups.space.chrblock_sorted.subsample3.bsorted.nofrag.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/4dn.bsorted.chr21_22_only.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/test_4dn.cp.pairs -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/hg19.chrom.sizes.chr21_22_only -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/test_merged_nodups.txt -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/test_merged_nodups.bsorted.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/4dn.bsorted.chr21_22_only.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/test.regions -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/test_juicer_shortform.bsorted.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/test_old_merged_nodups.txt.bsorted.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/merged_nodups.space.chrblock_sorted.subsample1.txt.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/test_old_merged_nodups.bsorted.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/test_merged_nodups.bsorted.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/SRR1171591.variants.snp.vqsr.p.vcf.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/merged_nodups.space.chrblock_sorted.subsample2.txt.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/hg19.chrom.sizes.-chr -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/merged_nodup.tab.chrblock_sorted.txt.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/merged_nodups.space.chrblock_sorted.subsample3.txt.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/test_old_merged_nodups.txt -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/test_old_merged_nodups.bsorted.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/SRR1171591.variants.snp.vqsr.p.vcf.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/mock.largechr.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/test_4dn_2.bsorted.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/test_old_merged_nodups.txt.bsorted.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/merged_nodups.space.chrblock_sorted.subsample3.bsorted.nofrag.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/test_juicer_shortform.pairs -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/test_4dn.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/test_merged_nodups.txt.bsorted.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/test_4dn.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/test_juicer_shortform.txt -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/old_index/test.regions2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples/old_index copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/hg19.chrom.sizes.chr21_22_only -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/test_merged_nodups.txt -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/test_merged_nodups.bsorted.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/4dn.bsorted.chr21_22_only.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/test.regions -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/test_juicer_shortform.bsorted.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/4dn.bsorted.chr21_22_only.largechr.pairs -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/test_old_merged_nodups.txt.bsorted.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/merged_nodups.space.chrblock_sorted.subsample1.txt.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/test_old_merged_nodups.bsorted.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/test_merged_nodups.bsorted.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/SRR1171591.variants.snp.vqsr.p.vcf.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/merged_nodups.space.chrblock_sorted.subsample2.txt.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/hg19.chrom.sizes.-chr -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/merged_nodup.tab.chrblock_sorted.txt.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/merged_nodups.space.chrblock_sorted.subsample3.txt.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/test_old_merged_nodups.txt -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/test_old_merged_nodups.bsorted.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/SRR1171591.variants.snp.vqsr.p.vcf.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/mock.largechr.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/test_4dn_2.bsorted.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/test_old_merged_nodups.txt.bsorted.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/merged_nodups.space.chrblock_sorted.subsample3.bsorted.nofrag.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/test_juicer_shortform.pairs -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/test_4dn.pairs.gz -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/test_merged_nodups.txt.bsorted.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/test_4dn.pairs.gz.px2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/test_juicer_shortform.txt -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/samples/test.regions2 -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/samples copying /<>/.pybuild/cpython3_3.10_pairix/build/pypairix.cpython-310-x86_64-linux-gnu.so -> /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages running install_egg_info running egg_info writing pypairix.egg-info/PKG-INFO writing dependency_links to pypairix.egg-info/dependency_links.txt writing top-level names to pypairix.egg-info/top_level.txt reading manifest file 'pypairix.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE.txt' writing manifest file 'pypairix.egg-info/SOURCES.txt' Copying pypairix.egg-info to /<>/debian/python3-pairix/usr/lib/python3.10/dist-packages/pypairix-0.3.7.egg-info Skipping SOURCES.txt running install_scripts debian/rules override_dh_install make[1]: Entering directory '/<>' tar caf samples.tar.xz samples --mode=go=rX,u+rw,a-s --owner=0 --group=0 --numeric-owner --sort=name dh_install find debian/python3-pairix/usr/lib -name samples -type d | xargs rm -rf find debian/*/usr/lib -name VERSION.txt -delete make[1]: Leaving directory '/<>' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild debugedit: debian/python3-pairix/usr/lib/python3/dist-packages/pypairix.cpython-311-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 e03469408fab4906365813afa74985f1dfe4618c debugedit: debian/python3-pairix/usr/lib/python3/dist-packages/pypairix.cpython-310-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 4e9087199f09a97ff80d55eebac10881099b1216 dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: Depends field of package python3-pairix: substitution variable ${shlib:Depends} used, but is not defined dpkg-gencontrol: warning: package python3-pairix: substitution variable ${shlibs:Depends} unused, but is defined dpkg-gencontrol: warning: Depends field of package python3-pairix: substitution variable ${shlib:Depends} used, but is not defined dpkg-gencontrol: warning: package python3-pairix: substitution variable ${shlibs:Depends} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 pkgstriptranslations: processing python-pairix-examples (in debian/python-pairix-examples); do_strip: , oemstrip: pkgstriptranslations: processing python3-pairix (in debian/python3-pairix); do_strip: , oemstrip: pkgstriptranslations: processing python3-pairix-dbgsym (in debian/.debhelper/python3-pairix/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/python-pairix-examples/DEBIAN/control, package python-pairix-examples, directory debian/python-pairix-examples INFO: pkgstripfiles: waiting for lock (python-pairix-examples) ... pkgstripfiles: processing control file: debian/.debhelper/python3-pairix/dbgsym-root/DEBIAN/control, package python3-pairix-dbgsym, directory debian/.debhelper/python3-pairix/dbgsym-root dpkg-deb: building package 'python3-pairix-dbgsym' in 'debian/.debhelper/scratch-space/build-python3-pairix/python3-pairix-dbgsym_0.3.7-6_amd64.deb'. Renaming python3-pairix-dbgsym_0.3.7-6_amd64.deb to python3-pairix-dbgsym_0.3.7-6_amd64.ddeb INFO: pkgstripfiles: waiting for lock (python-pairix-examples) ... INFO: pkgstripfiles: waiting for lock (python-pairix-examples) ... INFO: pkgstripfiles: waiting for lock (python-pairix-examples) ... INFO: pkgstripfiles: waiting for lock (python-pairix-examples) ... pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/python3-pairix/DEBIAN/control, package python3-pairix, directory debian/python3-pairix pkgstripfiles: Running PNG optimization (using 4 cpus) for package python3-pairix ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python3-pairix' in '../python3-pairix_0.3.7-6_amd64.deb'. pkgstripfiles: Running PNG optimization (using 4 cpus) for package python-pairix-examples ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python-pairix-examples' in '../python-pairix-examples_0.3.7-6_all.deb'. dpkg-genbuildinfo --build=binary -O../python-pairix_0.3.7-6_amd64.buildinfo dpkg-genchanges --build=binary -mLaunchpad Build Daemon -O../python-pairix_0.3.7-6_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2022-12-01T05:26:13Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ python-pairix_0.3.7-6_amd64.changes: ------------------------------------ Format: 1.8 Date: Wed, 30 Nov 2022 21:06:43 +0100 Source: python-pairix Binary: python-pairix-examples python3-pairix Built-For-Profiles: noudeb Architecture: all amd64 Version: 0.3.7-6 Distribution: lunar-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: python-pairix-examples - 1D/2D indexing and querying with a pair of genomic coordinates (e python3-pairix - 1D/2D indexing and querying with a pair of genomic coordinates Changes: python-pairix (0.3.7-6) unstable; urgency=medium . * Fix watch file 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python3-distutils (= 3.10.8-1), python3-iniconfig (= 1.1.1-2), python3-lib2to3 (= 3.10.8-1), python3-minimal (= 3.10.6-1ubuntu1), python3-more-itertools (= 8.10.0-2), python3-packaging (= 21.3-1.1), python3-pkg-resources (= 59.6.0-1.2), python3-pluggy (= 1.0.0+repack-1), python3-py (= 1.11.0-1), python3-pyparsing (= 3.0.7-3), python3-pytest (= 7.1.2-2ubuntu1), python3-setuptools (= 59.6.0-1.2), python3-tomli (= 2.0.1-1), python3.10 (= 3.10.8-3), python3.10-dev (= 3.10.8-3), python3.10-minimal (= 3.10.8-3), python3.11 (= 3.11.0-3), python3.11-dev (= 3.11.0-3), python3.11-minimal (= 3.11.0-3), readline-common (= 8.2-1.2), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.8-1ubuntu2), sensible-utils (= 0.0.17), sysvinit-utils (= 3.04-1ubuntu1), tar (= 1.34+dfsg-1.1), usrmerge (= 33ubuntu1), util-linux (= 2.38-4ubuntu1), util-linux-extra (= 2.38-4ubuntu1), xz-utils (= 5.2.8-0.0), zlib1g (= 1:1.2.13.dfsg-1ubuntu2), zlib1g-dev (= 1:1.2.13.dfsg-1ubuntu2) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1669838803" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ python-pairix-examples_0.3.7-6_all.deb -------------------------------------- new Debian package, version 2.0. size 172545100 bytes: control archive=1270 bytes. 1376 bytes, 31 lines control 1119 bytes, 12 lines md5sums Package: python-pairix-examples Source: python-pairix Version: 0.3.7-6 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 168532 Enhances: python3-pairix Section: science Priority: optional Multi-Arch: foreign Homepage: https://github.com/4dn-dcic/pairix Description: 1D/2D indexing and querying with a pair of genomic coordinates (examples) Pairix is a tool for indexing and querying on a block-compressed text file containing pairs of genomic coordinates. . Pairix is a stand-alone C program that was written on top of tabix as a tool for the 4DN-standard pairs file format describing Hi-C data: pairs_format_specification.md . However, Pairix can be used as a generic tool for indexing and querying any bgzipped text file containing genomic coordinates, for either 2D- or 1D- indexing and querying. . For example: given the custom text file below, you want to extract specific lines from the Pairs file further below. An awk command would read the Pairs file from beginning to end. Pairix creates an index and uses it to access the file from a relevant position by taking advantage of bgzf compression, allowing for a fast query on large files. . This package contains some example data to test the package. drwxr-xr-x root/root 0 2022-11-30 20:06 ./ drwxr-xr-x root/root 0 2022-11-30 20:06 ./usr/ drwxr-xr-x root/root 0 2022-11-30 20:06 ./usr/share/ drwxr-xr-x root/root 0 2022-11-30 20:06 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-11-30 20:06 ./usr/share/doc/python-pairix-examples/ -rw-r--r-- root/root 752 2022-11-30 20:06 ./usr/share/doc/python-pairix-examples/changelog.Debian.gz -rw-r--r-- root/root 1995 2022-11-30 20:06 ./usr/share/doc/python-pairix-examples/copyright drwxr-xr-x root/root 0 2022-11-30 20:06 ./usr/share/doc/python3-pairix/ drwxr-xr-x root/root 0 2022-11-30 20:06 ./usr/share/doc/python3-pairix/examples/ -rw-r--r-- root/root 6 2019-04-11 14:48 ./usr/share/doc/python3-pairix/examples/VERSION.txt -rw-r--r-- root/root 172542932 2022-11-30 20:06 ./usr/share/doc/python3-pairix/examples/samples.tar.xz drwxr-xr-x root/root 0 2022-11-30 20:06 ./usr/share/doc/python3-pairix/examples/test/ -rwxr-xr-x root/root 908 2019-04-11 14:48 ./usr/share/doc/python3-pairix/examples/test/inefficient-merger-for-testing -rw-r--r-- root/root 609 2019-04-11 14:48 ./usr/share/doc/python3-pairix/examples/test/reindex_samples.sh -rw-r--r-- root/root 3800 2019-04-11 14:48 ./usr/share/doc/python3-pairix/examples/test/test.py.gz -rw-r--r-- root/root 1280 2019-04-11 14:48 ./usr/share/doc/python3-pairix/examples/test/test_c.sh.gz -rw-r--r-- root/root 1920 2019-04-11 14:48 ./usr/share/doc/python3-pairix/examples/test/test_c_oldindex.sh.gz -rw-r--r-- root/root 1035 2019-04-11 14:48 ./usr/share/doc/python3-pairix/examples/test/test_c_oldindex2.sh.gz -rw-r--r-- root/root 3238 2022-11-30 20:06 ./usr/share/doc/python3-pairix/examples/test/test_oldindex.py.gz -rw-r--r-- root/root 3218 2022-11-30 20:06 ./usr/share/doc/python3-pairix/examples/test/test_oldindex2.py.gz python3-pairix_0.3.7-6_amd64.deb -------------------------------- new Debian package, version 2.0. size 44298 bytes: control archive=1172 bytes. 1309 bytes, 29 lines control 751 bytes, 8 lines md5sums Package: python3-pairix Source: python-pairix Version: 0.3.7-6 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 218 Depends: python3 (<< 3.12), python3 (>= 3.10~) Section: python Priority: optional Multi-Arch: same Homepage: https://github.com/4dn-dcic/pairix Description: 1D/2D indexing and querying with a pair of genomic coordinates Pairix is a tool for indexing and querying on a block-compressed text file containing pairs of genomic coordinates. . Pairix is a stand-alone C program that was written on top of tabix as a tool for the 4DN-standard pairs file format describing Hi-C data: pairs_format_specification.md . However, Pairix can be used as a generic tool for indexing and querying any bgzipped text file containing genomic coordinates, for either 2D- or 1D- indexing and querying. . For example: given the custom text file below, you want to extract specific lines from the Pairs file further below. An awk command would read the Pairs file from beginning to end. Pairix creates an index and uses it to access the file from a relevant position by taking advantage of bgzf compression, allowing for a fast query on large files. drwxr-xr-x root/root 0 2022-11-30 20:06 ./ drwxr-xr-x root/root 0 2022-11-30 20:06 ./usr/ drwxr-xr-x root/root 0 2022-11-30 20:06 ./usr/lib/ drwxr-xr-x root/root 0 2022-11-30 20:06 ./usr/lib/python3/ drwxr-xr-x root/root 0 2022-11-30 20:06 ./usr/lib/python3/dist-packages/ drwxr-xr-x root/root 0 2022-11-30 20:06 ./usr/lib/python3/dist-packages/pypairix-0.3.7.egg-info/ -rw-r--r-- root/root 1089 2022-11-30 20:06 ./usr/lib/python3/dist-packages/pypairix-0.3.7.egg-info/PKG-INFO -rw-r--r-- root/root 1 2022-11-30 20:06 ./usr/lib/python3/dist-packages/pypairix-0.3.7.egg-info/dependency_links.txt -rw-r--r-- root/root 9 2022-11-30 20:06 ./usr/lib/python3/dist-packages/pypairix-0.3.7.egg-info/top_level.txt -rw-r--r-- root/root 101304 2022-11-30 20:06 ./usr/lib/python3/dist-packages/pypairix.cpython-310-x86_64-linux-gnu.so -rw-r--r-- root/root 101304 2022-11-30 20:06 ./usr/lib/python3/dist-packages/pypairix.cpython-311-x86_64-linux-gnu.so drwxr-xr-x root/root 0 2022-11-30 20:06 ./usr/share/ drwxr-xr-x root/root 0 2022-11-30 20:06 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-11-30 20:06 ./usr/share/doc/python3-pairix/ -rw-r--r-- root/root 752 2022-11-30 20:06 ./usr/share/doc/python3-pairix/changelog.Debian.gz -rw-r--r-- root/root 1995 2022-11-30 20:06 ./usr/share/doc/python3-pairix/copyright drwxr-xr-x root/root 0 2022-11-30 20:06 ./usr/share/lintian/ drwxr-xr-x root/root 0 2022-11-30 20:06 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 137 2022-11-30 20:06 ./usr/share/lintian/overrides/python3-pairix +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 1046004 Build-Time: 177 Distribution: lunar-proposed Host Architecture: amd64 Install-Time: 19 Job: python-pairix_0.3.7-6.dsc Machine Architecture: amd64 Package: python-pairix Package-Time: 199 Source-Version: 0.3.7-6 Space: 1046004 Status: successful Version: 0.3.7-6 -------------------------------------------------------------------------------- Finished at 2022-12-01T05:26:13Z Build needed 00:03:19, 1046004k disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=lunar --arch=amd64 PACKAGEBUILD-24887997 Scanning for processes to kill in build PACKAGEBUILD-24887997