Running as unit: rb-build-arm64_12-127530.service; invocation ID: f1912b18bf654fd2ba57c7efb57a9dfa ==================================================================================== Sat Nov 1 14:08:25 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_12) on jenkins, called using "codethink04-arm64 codethink03-arm64" as arguments. Sat Nov 1 14:08:25 UTC 2025 - actually running "reproducible_build.sh" (md5sum bcb6fe1b50cf4e8eedacd0971a9eb63f) as "/tmp/jenkins-script-v6p6DqWv" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sat Nov 1 14:08:25 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Sat Nov 1 14:08:25 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-egpsG2' Sat Nov 1 14:08:26 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Sat Nov 1 14:08:26 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-61i1rm' ok, let's check if python-gffutils is building anywhere yet… ok, python-gffutils is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of python-gffutils in forky on arm64 on jenkins now. 1st build will be done on codethink04-arm64.debian.net. 2nd build will be done on codethink03-arm64.debian.net. ============================================================================= Sat Nov 1 14:08:34 UTC 2025 I: starting to build python-gffutils/forky/arm64 on jenkins on '2025-11-01 14:08' Sat Nov 1 14:08:34 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_12/127530/console.log 1762006114 arm64 forky python-gffutils Sat Nov 1 14:08:34 UTC 2025 I: Downloading source for forky/python-gffutils=0.13-3 --2025-11-01 14:08:34-- http://deb.debian.org/debian/pool/main/p/python-gffutils/python-gffutils_0.13-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2331 (2.3K) [text/prs.lines.tag] Saving to: ‘python-gffutils_0.13-3.dsc’ 0K .. 100% 275M=0s 2025-11-01 14:08:34 (275 MB/s) - ‘python-gffutils_0.13-3.dsc’ saved [2331/2331] --2025-11-01 14:08:34-- http://deb.debian.org/debian/pool/main/p/python-gffutils/python-gffutils_0.13-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2331 (2.3K) [text/prs.lines.tag] Saving to: ‘python-gffutils_0.13-3.dsc’ 0K .. 100% 275M=0s 2025-11-01 14:08:34 (275 MB/s) - ‘python-gffutils_0.13-3.dsc’ saved [2331/2331] Sat Nov 1 14:08:34 UTC 2025 I: python-gffutils_0.13-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: python-gffutils Binary: python3-gffutils Architecture: all Version: 0.13-3 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Steffen Moeller , Étienne Mollier Homepage: https://daler.github.io/gffutils Standards-Version: 4.7.2 Vcs-Browser: https://salsa.debian.org/med-team/python-gffutils Vcs-Git: https://salsa.debian.org/med-team/python-gffutils.git Testsuite: autopkgtest Testsuite-Triggers: python3-pytest Build-Depends: debhelper-compat (= 13), dh-sequence-python3, bedtools, python3-all, python3-setuptools, python3-argcomplete, python3-argh, python3-pyfaidx, python3-pytest, python3-biopython, python3-pybedtools, help2man Package-List: python3-gffutils deb science optional arch=all Checksums-Sha1: 1a4b4308dea940cc8306d3d75ea0b760e6abbe9d 1560489 python-gffutils_0.13.orig.tar.gz 4649561864368ec28c21d5b4fed7251adde651ae 5460 python-gffutils_0.13-3.debian.tar.xz Checksums-Sha256: b0d52f35c014cc0330fb5c4e3c6fea127c90ccf4c5384a825cdb5c8ff330d4eb 1560489 python-gffutils_0.13.orig.tar.gz 30347bc916ffce407f67527b3451490a1c0f30d34ddefb289aa2d19a96d159a9 5460 python-gffutils_0.13-3.debian.tar.xz Files: 13970382f37c65378765b7a5e522b9ec 1560489 python-gffutils_0.13.orig.tar.gz 4e660b5980f8fde0311782b77af955ba 5460 python-gffutils_0.13-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEEj23hBDd/OxHnQXSHMfMURUShdBoFAmip9bwRHHRjaGV0QGRl Ymlhbi5vcmcACgkQMfMURUShdBrrSRAArJd4sBLNjeGPmd2jWLv0Mm9IJgCiPFgH UQc5Sht6KTIqWxYVNytiKH7ntv5UZh9VQtnLvnKW/B4Mx9VWJW1ZNKf7C3lJ+25H OVIPCiWxJFgHCtEV3D7G4eCrlSMjPAu568C8NusMXZK6uOCotsn6SiBCmcJtX8Nw IorGpDZ9hJ6OjQeePebNd28qLuAKL819We3yvgIpQ8vxuHq+ZJwXSAei1pTiA1Ku jgNksSJskFydVq9S/0QAPmm/9adtrGUa60qtsTFWjvEV2maabrsglEBWY8lpWJET 2rgx9RvzP3OzTSRbvvdz9Ox6O4EI2An5Ei/x2NheOsqtBP3QY9iTdQaWSQeSMuwH PcQ8O5nmug6t/KCV4mZO+l8DK1ztgrISjmD7TBteszmstJQqUxbPAXiU7XMZ/Lml PwlovorjlCG2NAH9D12SEcYWXEFUsPCoxnLtuHFW4pLC9BxV6pj/fSfUSxcBX88b 8oddwpF3QpOjGqmdrMedPhTnNJCVuh5hQsNUtMIsZ6ni5rxbXxZaF4qNACYVQ6dk BUIy1WWcLUqwqFXiveiB6mcOb2yAzSOjN7CNZh8i+JFx3kWfwMECpsIXpktk6mio hidyaXuIhSVacWjjVeA4odTV0ntNrgDcgrRDjtlCDqCfouMyOOPdy5HizCF6E01w jT7Pqrym4rA= =X3aC -----END PGP SIGNATURE----- Sat Nov 1 14:08:34 UTC 2025 I: Checking whether the package is not for us Sat Nov 1 14:08:34 UTC 2025 I: Starting 1st build on remote node codethink04-arm64.debian.net. Sat Nov 1 14:08:34 UTC 2025 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Sat Nov 1 14:08:34 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Sat Nov 1 14:08:34 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-bijTye' ==================================================================================== Sat Nov 1 14:08:35 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink04-arm64, called using "1 python-gffutils forky /srv/reproducible-results/rbuild-debian/r-b-build.p5Ol6mnr 0.13-3" as arguments. Sat Nov 1 14:08:35 UTC 2025 - actually running "reproducible_build.sh" (md5sum bcb6fe1b50cf4e8eedacd0971a9eb63f) as "/tmp/jenkins-script-fJ1GIyuC" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sat Nov 1 14:08:35 UTC 2025 I: Downloading source for forky/python-gffutils=0.13-3 Reading package lists... NOTICE: 'python-gffutils' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/python-gffutils.git Please use: git clone https://salsa.debian.org/med-team/python-gffutils.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1568 kB of source archives. Get:1 http://deb.debian.org/debian forky/main python-gffutils 0.13-3 (dsc) [2331 B] Get:2 http://deb.debian.org/debian forky/main python-gffutils 0.13-3 (tar) [1560 kB] Get:3 http://deb.debian.org/debian forky/main python-gffutils 0.13-3 (diff) [5460 B] Fetched 1568 kB in 0s (23.1 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'python-gffutils' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/python-gffutils.git Please use: git clone https://salsa.debian.org/med-team/python-gffutils.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1568 kB of source archives. Get:1 http://deb.debian.org/debian forky/main python-gffutils 0.13-3 (dsc) [2331 B] Get:2 http://deb.debian.org/debian forky/main python-gffutils 0.13-3 (tar) [1560 kB] Get:3 http://deb.debian.org/debian forky/main python-gffutils 0.13-3 (diff) [5460 B] Fetched 1568 kB in 0s (23.1 MB/s) Download complete and in download only mode ============================================================================= Building python-gffutils in forky on arm64 on codethink04-arm64 now. Date: Sat Nov 1 14:08:36 GMT 2025 Date UTC: Sat Nov 1 14:08:36 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Sat Nov 1 02:08:36 -12 2025 I: pbuilder-time-stamp: 1762006116 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [python-gffutils_0.13-3.dsc] I: copying [./python-gffutils_0.13.orig.tar.gz] I: copying [./python-gffutils_0.13-3.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./python-gffutils_0.13-3.dsc: no acceptable signature found dpkg-source: info: extracting python-gffutils in python-gffutils-0.13 dpkg-source: info: unpacking python-gffutils_0.13.orig.tar.gz dpkg-source: info: unpacking python-gffutils_0.13-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying python3 dpkg-source: info: applying fix-version.patch dpkg-source: info: applying pr235.patch dpkg-source: info: applying pytest8.4.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1698365/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='3ba4072e2ae845ec8735b330ca0151fd' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1698365' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.p5Ol6mnr/pbuilderrc_VXr4 --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.p5Ol6mnr/b1 --logfile b1/build.log python-gffutils_0.13-3.dsc' SUDO_GID='109' SUDO_HOME='/var/lib/jenkins' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1698365/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, bedtools, python3-all, python3-setuptools, python3-argcomplete, python3-argh, python3-pyfaidx, python3-pytest, python3-biopython, python3-pybedtools, help2man dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19971 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on bedtools; however: Package bedtools is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-argcomplete; however: Package python3-argcomplete is not installed. pbuilder-satisfydepends-dummy depends on python3-argh; however: Package python3-argh is not installed. pbuilder-satisfydepends-dummy depends on python3-pyfaidx; however: Package python3-pyfaidx is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-pybedtools; however: Package python3-pybedtools is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bedtools{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libabsl20240722{a} libaom3{a} libarchive-zip-perl{a} libavif16{a} libblas3{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libcurl3t64-gnutls{a} libdav1d7{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgfortran5{a} libglib2.0-0t64{a} libgnutls30t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhts3t64{a} libhtscodecs2{a} libidn2-0{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblcms2-2{a} libldap2{a} liblerc4{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libopenjp2-7{a} libp11-kit0{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libraqm0{a} librav1e0.8{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libssh2-1t64{a} libsvtav1enc2{a} libtasn1-6{a} libtiff6{a} libtool{a} libuchardet0{a} libunistring5{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2-16{a} libxrender1{a} libyuv0{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-all{a} python3-argcomplete{a} python3-argh{a} python3-autocommand{a} python3-biopython{a} python3-cairo{a} python3-charset-normalizer{a} python3-freetype{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-numpy-dev{a} python3-packaging{a} python3-pil{a} python3-pkg-resources{a} python3-pluggy{a} python3-pybedtools{a} python3-pyfaidx{a} python3-pygments{a} python3-pysam{a} python3-pytest{a} python3-reportlab{a} python3-rlpycairo{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} tzdata{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl fonts-dejavu-extra krb5-locales libarchive-cpio-perl libglib2.0-data libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx ncbi-blast+ publicsuffix python-biopython-doc python3-olefile shared-mime-info wget xdg-user-dirs 0 packages upgraded, 155 newly installed, 0 to remove and 0 not upgraded. Need to get 76.9 MB of archives. After unpacking 273 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main arm64 libexpat1 arm64 2.7.3-1 [96.5 kB] Get: 2 http://deb.debian.org/debian forky/main arm64 liblocale-gettext-perl arm64 1.07-7+b1 [15.2 kB] Get: 3 http://deb.debian.org/debian forky/main arm64 libpython3.13-minimal arm64 3.13.9-1 [858 kB] Get: 4 http://deb.debian.org/debian forky/main arm64 python3.13-minimal arm64 3.13.9-1 [2061 kB] Get: 5 http://deb.debian.org/debian forky/main arm64 python3-minimal arm64 3.13.7-1 [27.2 kB] Get: 6 http://deb.debian.org/debian forky/main arm64 media-types all 14.0.0 [30.8 kB] Get: 7 http://deb.debian.org/debian forky/main arm64 netbase all 6.5 [12.4 kB] Get: 8 http://deb.debian.org/debian forky/main arm64 tzdata all 2025b-5 [260 kB] Get: 9 http://deb.debian.org/debian forky/main arm64 libffi8 arm64 3.5.2-2 [21.5 kB] Get: 10 http://deb.debian.org/debian forky/main arm64 readline-common all 8.3-3 [74.8 kB] Get: 11 http://deb.debian.org/debian forky/main arm64 libreadline8t64 arm64 8.3-3 [169 kB] Get: 12 http://deb.debian.org/debian forky/main arm64 libpython3.13-stdlib arm64 3.13.9-1 [1900 kB] Get: 13 http://deb.debian.org/debian forky/main arm64 python3.13 arm64 3.13.9-1 [764 kB] Get: 14 http://deb.debian.org/debian forky/main arm64 libpython3-stdlib arm64 3.13.7-1 [10.2 kB] Get: 15 http://deb.debian.org/debian forky/main arm64 python3 arm64 3.13.7-1 [28.3 kB] Get: 16 http://deb.debian.org/debian forky/main arm64 python3-numpy-dev arm64 1:2.3.3+ds-3 [135 kB] Get: 17 http://deb.debian.org/debian forky/main arm64 libblas3 arm64 3.12.1-7 [135 kB] Get: 18 http://deb.debian.org/debian forky/main arm64 libgfortran5 arm64 15.2.0-7 [371 kB] Get: 19 http://deb.debian.org/debian forky/main arm64 liblapack3 arm64 3.12.1-7 [1846 kB] Get: 20 http://deb.debian.org/debian forky/main arm64 python3-numpy arm64 1:2.3.3+ds-3 [3589 kB] Get: 21 http://deb.debian.org/debian forky/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get: 22 http://deb.debian.org/debian forky/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 23 http://deb.debian.org/debian forky/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 24 http://deb.debian.org/debian forky/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 25 http://deb.debian.org/debian forky/main arm64 gettext-base arm64 0.23.1-2+b1 [241 kB] Get: 26 http://deb.debian.org/debian forky/main arm64 libuchardet0 arm64 0.0.8-2 [69.0 kB] Get: 27 http://deb.debian.org/debian forky/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 28 http://deb.debian.org/debian forky/main arm64 bsdextrautils arm64 2.41.2-4 [97.3 kB] Get: 29 http://deb.debian.org/debian forky/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 30 http://deb.debian.org/debian forky/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 31 http://deb.debian.org/debian forky/main arm64 m4 arm64 1.4.20-2 [315 kB] Get: 32 http://deb.debian.org/debian forky/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 33 http://deb.debian.org/debian forky/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 34 http://deb.debian.org/debian forky/main arm64 automake all 1:1.18.1-2 [877 kB] Get: 35 http://deb.debian.org/debian forky/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 36 http://deb.debian.org/debian forky/main arm64 bedtools arm64 2.31.1+dfsg-2+b1 [601 kB] Get: 37 http://deb.debian.org/debian forky/main arm64 libdebhelper-perl all 13.28 [92.4 kB] Get: 38 http://deb.debian.org/debian forky/main arm64 libtool all 2.5.4-7 [540 kB] Get: 39 http://deb.debian.org/debian forky/main arm64 dh-autoreconf all 21 [12.2 kB] Get: 40 http://deb.debian.org/debian forky/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 41 http://deb.debian.org/debian forky/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 42 http://deb.debian.org/debian forky/main arm64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 43 http://deb.debian.org/debian forky/main arm64 libelf1t64 arm64 0.193-3 [189 kB] Get: 44 http://deb.debian.org/debian forky/main arm64 dwz arm64 0.16-2 [100 kB] Get: 45 http://deb.debian.org/debian forky/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 46 http://deb.debian.org/debian forky/main arm64 libxml2-16 arm64 2.14.6+dfsg-0.1 [601 kB] Get: 47 http://deb.debian.org/debian forky/main arm64 gettext arm64 0.23.1-2+b1 [1612 kB] Get: 48 http://deb.debian.org/debian forky/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 49 http://deb.debian.org/debian forky/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 50 http://deb.debian.org/debian forky/main arm64 debhelper all 13.28 [941 kB] Get: 51 http://deb.debian.org/debian forky/main arm64 dh-python all 6.20250414 [116 kB] Get: 52 http://deb.debian.org/debian forky/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 53 http://deb.debian.org/debian forky/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 54 http://deb.debian.org/debian forky/main arm64 libfontenc1 arm64 1:1.1.8-1+b2 [22.5 kB] Get: 55 http://deb.debian.org/debian forky/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 56 http://deb.debian.org/debian forky/main arm64 libpng16-16t64 arm64 1.6.50-1 [275 kB] Get: 57 http://deb.debian.org/debian forky/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 58 http://deb.debian.org/debian forky/main arm64 x11-common all 1:7.7+26 [217 kB] Get: 59 http://deb.debian.org/debian forky/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 60 http://deb.debian.org/debian forky/main arm64 xfonts-utils arm64 1:7.7+7 [89.3 kB] Get: 61 http://deb.debian.org/debian forky/main arm64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 62 http://deb.debian.org/debian forky/main arm64 fontconfig-config arm64 2.15.0-2.4 [318 kB] Get: 63 http://deb.debian.org/debian forky/main arm64 help2man arm64 1.49.3+b1 [198 kB] Get: 64 http://deb.debian.org/debian forky/main arm64 libabsl20240722 arm64 20240722.0-4 [452 kB] Get: 65 http://deb.debian.org/debian forky/main arm64 libaom3 arm64 3.13.1-2 [1632 kB] Get: 66 http://deb.debian.org/debian forky/main arm64 libdav1d7 arm64 1.5.1-1 [252 kB] Get: 67 http://deb.debian.org/debian forky/main arm64 libgav1-1 arm64 0.19.0-3+b1 [491 kB] Get: 68 http://deb.debian.org/debian forky/main arm64 librav1e0.8 arm64 0.8.1-5 [688 kB] Get: 69 http://deb.debian.org/debian forky/main arm64 libsvtav1enc2 arm64 2.3.0+dfsg-1 [1558 kB] Get: 70 http://deb.debian.org/debian forky/main arm64 libjpeg62-turbo arm64 1:2.1.5-4 [173 kB] Get: 71 http://deb.debian.org/debian forky/main arm64 libyuv0 arm64 0.0.1919.20250919-1 [138 kB] Get: 72 http://deb.debian.org/debian forky/main arm64 libavif16 arm64 1.3.0-1+b1 [127 kB] Get: 73 http://deb.debian.org/debian forky/main arm64 libfontconfig1 arm64 2.15.0-2.4 [387 kB] Get: 74 http://deb.debian.org/debian forky/main arm64 libpixman-1-0 arm64 0.46.4-1 [174 kB] Get: 75 http://deb.debian.org/debian forky/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 76 http://deb.debian.org/debian forky/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 77 http://deb.debian.org/debian forky/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 78 http://deb.debian.org/debian forky/main arm64 libx11-data all 2:1.8.12-1 [343 kB] Get: 79 http://deb.debian.org/debian forky/main arm64 libx11-6 arm64 2:1.8.12-1 [795 kB] Get: 80 http://deb.debian.org/debian forky/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 81 http://deb.debian.org/debian forky/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 82 http://deb.debian.org/debian forky/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB] Get: 83 http://deb.debian.org/debian forky/main arm64 libxrender1 arm64 1:0.9.12-1 [27.0 kB] Get: 84 http://deb.debian.org/debian forky/main arm64 libcairo2 arm64 1.18.4-1+b1 [483 kB] Get: 85 http://deb.debian.org/debian forky/main arm64 libcom-err2 arm64 1.47.2-3+b3 [24.9 kB] Get: 86 http://deb.debian.org/debian forky/main arm64 libnghttp3-9 arm64 1.12.0-1 [63.6 kB] Get: 87 http://deb.debian.org/debian forky/main arm64 libngtcp2-16 arm64 1.16.0-1 [123 kB] Get: 88 http://deb.debian.org/debian forky/main arm64 libidn2-0 arm64 2.3.8-4 [108 kB] Get: 89 http://deb.debian.org/debian forky/main arm64 libp11-kit0 arm64 0.25.9-2 [420 kB] Get: 90 http://deb.debian.org/debian forky/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 91 http://deb.debian.org/debian forky/main arm64 libgnutls30t64 arm64 3.8.10-3 [1384 kB] Get: 92 http://deb.debian.org/debian forky/main arm64 libkrb5support0 arm64 1.21.3-5 [32.4 kB] Get: 93 http://deb.debian.org/debian forky/main arm64 libk5crypto3 arm64 1.21.3-5 [81.2 kB] Get: 94 http://deb.debian.org/debian forky/main arm64 libkeyutils1 arm64 1.6.3-6 [9716 B] Get: 95 http://deb.debian.org/debian forky/main arm64 libkrb5-3 arm64 1.21.3-5 [308 kB] Get: 96 http://deb.debian.org/debian forky/main arm64 libgssapi-krb5-2 arm64 1.21.3-5 [127 kB] Get: 97 http://deb.debian.org/debian forky/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-10 [19.8 kB] Get: 98 http://deb.debian.org/debian forky/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-10 [55.0 kB] Get: 99 http://deb.debian.org/debian forky/main arm64 libldap2 arm64 2.6.10+dfsg-1 [179 kB] Get: 100 http://deb.debian.org/debian forky/main arm64 libnghttp2-14 arm64 1.64.0-1.1+b1 [71.7 kB] Get: 101 http://deb.debian.org/debian forky/main arm64 libngtcp2-crypto-gnutls8 arm64 1.16.0-1 [23.8 kB] Get: 102 http://deb.debian.org/debian forky/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 103 http://deb.debian.org/debian forky/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-3 [56.3 kB] Get: 104 http://deb.debian.org/debian forky/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 105 http://deb.debian.org/debian forky/main arm64 libcurl3t64-gnutls arm64 8.17.0~rc3-1 [362 kB] Get: 106 http://deb.debian.org/debian forky/main arm64 libdeflate0 arm64 1.23-2 [42.4 kB] Get: 107 http://deb.debian.org/debian forky/main arm64 libfribidi0 arm64 1.0.16-3 [26.5 kB] Get: 108 http://deb.debian.org/debian forky/main arm64 libglib2.0-0t64 arm64 2.86.1-1 [1436 kB] Get: 109 http://deb.debian.org/debian forky/main arm64 libgraphite2-3 arm64 1.3.14-11 [70.8 kB] Get: 110 http://deb.debian.org/debian forky/main arm64 libharfbuzz0b arm64 12.1.0-1 [486 kB] Get: 111 http://deb.debian.org/debian forky/main arm64 libhtscodecs2 arm64 1.6.1-2 [74.7 kB] Get: 112 http://deb.debian.org/debian forky/main arm64 libhts3t64 arm64 1.22.1+ds2-1 [434 kB] Get: 113 http://deb.debian.org/debian forky/main arm64 libimagequant0 arm64 4.4.0-3 [216 kB] Get: 114 http://deb.debian.org/debian forky/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 115 http://deb.debian.org/debian forky/main arm64 liblcms2-2 arm64 2.16-2 [151 kB] Get: 116 http://deb.debian.org/debian forky/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 117 http://deb.debian.org/debian forky/main arm64 libopenjp2-7 arm64 2.5.3-2.1 [189 kB] Get: 118 http://deb.debian.org/debian forky/main arm64 libraqm0 arm64 0.10.3-1 [13.6 kB] Get: 119 http://deb.debian.org/debian forky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [114 kB] Get: 120 http://deb.debian.org/debian forky/main arm64 libwebp7 arm64 1.5.0-0.1 [271 kB] Get: 121 http://deb.debian.org/debian forky/main arm64 libtiff6 arm64 4.7.1-1 [334 kB] Get: 122 http://deb.debian.org/debian forky/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [113 kB] Get: 123 http://deb.debian.org/debian forky/main arm64 libwebpmux3 arm64 1.5.0-0.1 [125 kB] Get: 124 http://deb.debian.org/debian forky/main arm64 python3-all arm64 3.13.7-1 [1044 B] Get: 125 http://deb.debian.org/debian forky/main arm64 python3-argcomplete all 3.6.2-1 [40.9 kB] Get: 126 http://deb.debian.org/debian forky/main arm64 python3-argh all 0.31.3-1 [26.6 kB] Get: 127 http://deb.debian.org/debian forky/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 128 http://deb.debian.org/debian forky/main arm64 python3-charset-normalizer arm64 3.4.3-1 [123 kB] Get: 129 http://deb.debian.org/debian forky/main arm64 python3-pil arm64 11.3.0-1 [507 kB] Get: 130 http://deb.debian.org/debian forky/main arm64 python3-cairo arm64 1.27.0-2 [114 kB] Get: 131 http://deb.debian.org/debian forky/main arm64 python3-freetype all 2.5.1-2 [89.4 kB] Get: 132 http://deb.debian.org/debian forky/main arm64 python3-rlpycairo all 0.3.0-4 [10.1 kB] Get: 133 http://deb.debian.org/debian forky/main arm64 python3-reportlab all 4.4.4-2 [1170 kB] Get: 134 http://deb.debian.org/debian forky/main arm64 sgml-base all 1.31+nmu1 [10.9 kB] Get: 135 http://deb.debian.org/debian forky/main arm64 xml-core all 0.19 [20.1 kB] Get: 136 http://deb.debian.org/debian forky/main arm64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 137 http://deb.debian.org/debian forky/main arm64 python3-biopython arm64 1.86+dfsg-1 [1598 kB] Get: 138 http://deb.debian.org/debian forky/main arm64 python3-more-itertools all 10.8.0-1 [71.7 kB] Get: 139 http://deb.debian.org/debian forky/main arm64 python3-typing-extensions all 4.15.0-1 [92.4 kB] Get: 140 http://deb.debian.org/debian forky/main arm64 python3-typeguard all 4.4.4-1 [37.1 kB] Get: 141 http://deb.debian.org/debian forky/main arm64 python3-inflect all 7.5.0-1 [33.0 kB] Get: 142 http://deb.debian.org/debian forky/main arm64 python3-iniconfig all 2.1.0-1 [7432 B] Get: 143 http://deb.debian.org/debian forky/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 144 http://deb.debian.org/debian forky/main arm64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 145 http://deb.debian.org/debian forky/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 146 http://deb.debian.org/debian forky/main arm64 python3-zipp all 3.23.0-1 [11.0 kB] Get: 147 http://deb.debian.org/debian forky/main arm64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 148 http://deb.debian.org/debian forky/main arm64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 149 http://deb.debian.org/debian forky/main arm64 python3-packaging all 25.0-1 [56.6 kB] Get: 150 http://deb.debian.org/debian forky/main arm64 python3-pluggy all 1.6.0-1 [27.1 kB] Get: 151 http://deb.debian.org/debian forky/main arm64 python3-pysam arm64 0.23.0+ds-1+b1 [3417 kB] Get: 152 http://deb.debian.org/debian forky/main arm64 python3-pybedtools arm64 0.10.0-5 [12.1 MB] Get: 153 http://deb.debian.org/debian forky/main arm64 python3-pyfaidx all 0.8.1.3-2 [29.1 kB] Get: 154 http://deb.debian.org/debian forky/main arm64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get: 155 http://deb.debian.org/debian forky/main arm64 python3-pytest all 8.4.2-1 [266 kB] Fetched 76.9 MB in 1s (139 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19971 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.3-1_arm64.deb ... Unpacking libexpat1:arm64 (2.7.3-1) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../liblocale-gettext-perl_1.07-7+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package libpython3.13-minimal:arm64. Preparing to unpack .../libpython3.13-minimal_3.13.9-1_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.9-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.9-1_arm64.deb ... Unpacking python3.13-minimal (3.13.9-1) ... Setting up libpython3.13-minimal:arm64 (3.13.9-1) ... Setting up libexpat1:arm64 (2.7.3-1) ... Setting up python3.13-minimal (3.13.9-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20320 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.7-1_arm64.deb ... Unpacking python3-minimal (3.13.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_14.0.0_all.deb ... Unpacking media-types (14.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.5_all.deb ... Unpacking netbase (6.5) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025b-5_all.deb ... Unpacking tzdata (2025b-5) ... Selecting previously unselected package libffi8:arm64. Preparing to unpack .../4-libffi8_3.5.2-2_arm64.deb ... Unpacking libffi8:arm64 (3.5.2-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.3-3_all.deb ... Unpacking readline-common (8.3-3) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../6-libreadline8t64_8.3-3_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.9-1_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.9-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.9-1_arm64.deb ... Unpacking python3.13 (3.13.9-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../9-libpython3-stdlib_3.13.7-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.13.7-1) ... Setting up python3-minimal (3.13.7-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21335 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.7-1_arm64.deb ... Unpacking python3 (3.13.7-1) ... Selecting previously unselected package python3-numpy-dev:arm64. Preparing to unpack .../001-python3-numpy-dev_1%3a2.3.3+ds-3_arm64.deb ... Unpacking python3-numpy-dev:arm64 (1:2.3.3+ds-3) ... Selecting previously unselected package libblas3:arm64. Preparing to unpack .../002-libblas3_3.12.1-7_arm64.deb ... Unpacking libblas3:arm64 (3.12.1-7) ... Selecting previously unselected package libgfortran5:arm64. Preparing to unpack .../003-libgfortran5_15.2.0-7_arm64.deb ... Unpacking libgfortran5:arm64 (15.2.0-7) ... Selecting previously unselected package liblapack3:arm64. Preparing to unpack .../004-liblapack3_3.12.1-7_arm64.deb ... Unpacking liblapack3:arm64 (3.12.1-7) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../005-python3-numpy_1%3a2.3.3+ds-3_arm64.deb ... Unpacking python3-numpy (1:2.3.3+ds-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../006-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../007-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../008-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../009-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../010-gettext-base_0.23.1-2+b1_arm64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../011-libuchardet0_0.0.8-2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../012-groff-base_1.23.0-9_arm64.deb ... Unpacking groff-base (1.23.0-9) ... 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Setting up libfontenc1:arm64 (1:1.1.8-1+b2) ... Setting up autotools-dev (20240727.1) ... Setting up libblas3:arm64 (3.12.1-7) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libjpeg62-turbo:arm64 (1:2.1.5-4) ... Setting up libx11-data (2:1.8.12-1) ... Setting up libsvtav1enc2:arm64 (2.3.0+dfsg-1) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:arm64 (1.0.16-3) ... Setting up libimagequant0:arm64 (4.4.0-3) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:arm64 (1.6.50-1) ... Setting up python3-numpy-dev:arm64 (1:2.3.3+ds-3) ... Setting up autopoint (0.23.1-2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libgav1-1:arm64 (0.19.0-3+b1) ... Setting up libk5crypto3:arm64 (1.21.3-5) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-10) ... 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Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:arm64 (1.18.4-1+b1) ... Setting up python3-pygments (2.18.0+dfsg-2) ... Setting up python3-packaging (25.0-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libraqm0:arm64 (0.10.3-1) ... Setting up python3-typing-extensions (4.15.0-1) ... Setting up python3-numpy (1:2.3.3+ds-3) ... Setting up python3-pluggy (1.6.0-1) ... Setting up python3-argcomplete (3.6.2-1) ... Setting up libngtcp2-crypto-gnutls8:arm64 (1.16.0-1) ... Setting up dh-python (6.20250414) ... Setting up python3-more-itertools (10.8.0-1) ... Setting up python3-pyfaidx (0.8.1.3-2) ... Setting up python3-iniconfig (2.1.0-1) ... Setting up python3-argh (0.31.3-1) ... Setting up python3-cairo (1.27.0-2) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up python3-charset-normalizer (3.4.3-1) ... Setting up python3-pytest (8.4.2-1) ... 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Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.37.1.2-1). Solving dependencies... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/reproducible-path/python-gffutils-0.13/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../python-gffutils_0.13-3_source.changes dpkg-buildpackage: info: source package python-gffutils dpkg-buildpackage: info: source version 0.13-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Alexandre Detiste dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py clean /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running clean removing '/build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build' (and everything under it) 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.13' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py config /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/python-gffutils-0.13' dh_auto_build I: pybuild base:311: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running build running build_py creating /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/helpers.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/feature.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/version.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/pybedtools_integration.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/parser.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/merge_criteria.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/iterators.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/interface.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/inspect.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/gffwriter.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/exceptions.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/create.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/convert.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/constants.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/biopython_integration.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/bins.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/attributes.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/__init__.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils creating /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/scripts copying gffutils/scripts/gffutils-flybase-convert.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/scripts creating /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/test_1.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/test_merge_all.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/test_merge.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/test_iterators.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/test_issues.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/test_cli.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/test_biopython_integration.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/synth_test_base.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/performance_evaluation.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/parser_test.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/helpers_test.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/feature_test.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/expected.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/conftest.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/attr_test_cases.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/__init__.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test creating /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/wormbase_gff2_alt.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/wormbase_gff2.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/unsanitized.gff -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/synthetic.gff3 -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/sharr.gtf -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/random-chr.gff -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/nonascii -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/ncbi_gff3.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/mouse_extra_comma.gff3 -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/keyval_sep_in_attrs.gff -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/keep-order-test.gtf -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/jgi_gff2.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/issue_197.gff -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/issue174.gtf -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/issue167.gff -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/intro_docs_example.gff -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/hybrid1.gff3 -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/gms2_example.gff3 -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/glimmer_nokeyval.gff3 -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/gff_example1.gff3.gz -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/gff_example1.gff3 -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/gencode.vM8.chromsizes.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/gencode.vM8.5000_transcript_ids.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/gencode.vM8.5000_gene_ids.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/gencode-v19.gtf -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/ensembl_gtf.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/download-large-annotation-files.sh -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/dmel-all-no-analysis-r5.49_50k_lines.gff -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/dm6-chr2L.fa.fai -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/dm6-chr2L.fa -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/c_elegans_WS199_shortened_gff.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/c_elegans_WS199_dna_shortened.fa -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/c_elegans_WS199_ann_gff.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.chromsizes.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.5000_transcript_ids.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.5000_gene_ids.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/FBgn0031208.gtf.db -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/FBgn0031208.gtf -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/FBgn0031208.gff -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/F3-unique-3.v2.gff -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data running build_scripts creating build/scripts-3.13 copying and adjusting gffutils/scripts/gffutils-cli -> build/scripts-3.13 changing mode of build/scripts-3.13/gffutils-cli from 644 to 755 PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ help2man --version-string=0.13 --no-info \ --name="Command line interface for python-gffutils." \ gffutils-cli > debian/gffutils-cli.1 PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ help2man --version-string=0.13 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_fetch \- Fetch IDs") \ 'gffutils-cli fetch' > debian/gffutils-cli-fetch.1 PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ help2man --version-string=0.13 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_children \- Fetch children from the database according to ID") \ 'gffutils-cli children' > debian/gffutils-cli-children.1 PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ help2man --version-string=0.13 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_parents \- Fetch parents from the database according to ID") \ 'gffutils-cli parents' > debian/gffutils-cli-parents.1 PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ help2man --version-string=0.13 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_region \- Returns features within provided genomic coordinates") \ 'gffutils-cli region' > debian/gffutils-cli-region.1 PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ help2man --version-string=0.13 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_create \- Create a database") \ 'gffutils-cli create' > debian/gffutils-cli-create.1 PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ help2man --version-string=0.13 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_common \- Identify child features in common") \ 'gffutils-cli common' > debian/gffutils-cli-common.1 PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ help2man --version-string=0.13 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_clean \- Perform various QC operations to clean a GFF or GTF file") \ 'gffutils-cli clean' > debian/gffutils-cli-clean.1 PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ help2man --version-string=0.13 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_sanitize \- Sanitize a GFF file") \ 'gffutils-cli sanitize' > debian/gffutils-cli-sanitize.1 PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ help2man --version-string=0.13 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_rmdups \- Remove duplicates from a GFF file") \ 'gffutils-cli rmdups' > debian/gffutils-cli-rmdups.1 make[1]: Leaving directory '/build/reproducible-path/python-gffutils-0.13' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/python-gffutils-0.13' PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games dh_auto_test I: pybuild base:311: cd /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build; python3.13 -m pytest --doctest-modules -m 'not slow' ============================= test session starts ============================== platform linux -- Python 3.13.9, pytest-8.4.2, pluggy-1.6.0 rootdir: /build/reproducible-path/python-gffutils-0.13 plugins: typeguard-4.4.4 collected 112 items gffutils/attributes.py . [ 0%] gffutils/pybedtools_integration.py . [ 1%] gffutils/test/feature_test.py ........... [ 11%] gffutils/test/helpers_test.py .. [ 13%] gffutils/test/parser_test.py .................. [ 29%] gffutils/test/test_1.py ......................s........... [ 59%] gffutils/test/test_biopython_integration.py . [ 60%] gffutils/test/test_cli.py . [ 61%] gffutils/test/test_issues.py ........................ [ 83%] gffutils/test/test_iterators.py .... [ 86%] gffutils/test/test_merge.py ......... [ 94%] gffutils/test/test_merge_all.py ...... [100%] =============================== warnings summary =============================== gffutils/test/performance_evaluation.py:190 /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/performance_evaluation.py:190: PytestUnknownMarkWarning: Unknown pytest.mark.slow - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html @pytest.mark.slow gffutils/test/performance_evaluation.py:208 /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/performance_evaluation.py:208: PytestUnknownMarkWarning: Unknown pytest.mark.slow - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html @pytest.mark.slow .pybuild/cpython3_3.13_gffutils/build/gffutils/test/parser_test.py::test_parser_from_string /usr/lib/python3/dist-packages/_pytest/python.py:161: PytestReturnNotNoneWarning: Test functions should return None, but .pybuild/cpython3_3.13_gffutils/build/gffutils/test/parser_test.py::test_parser_from_string returned . Did you mean to use `assert` instead of `return`? See https://docs.pytest.org/en/stable/how-to/assert.html#return-not-none for more information. warnings.warn( .pybuild/cpython3_3.13_gffutils/build/gffutils/test/parser_test.py::test_inconsistent_dialect .pybuild/cpython3_3.13_gffutils/build/gffutils/test/test_1.py::test_disable_infer .pybuild/cpython3_3.13_gffutils/build/gffutils/test/test_issues.py::test_pr_172 /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/create.py:770: UserWarning: It appears you have a gene feature in your GTF file. You may want to use the `disable_infer_genes=True` option to speed up database creation warnings.warn( .pybuild/cpython3_3.13_gffutils/build/gffutils/test/test_1.py::test_disable_infer /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/create.py:763: UserWarning: It appears you have a transcript feature in your GTF file. You may want to use the `disable_infer_transcripts=True` option to speed up database creation warnings.warn( -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ================== 111 passed, 1 skipped, 7 warnings in 1.98s ================== I: pybuild pybuild:334: find . -name tmp.db -delete make[1]: Leaving directory '/build/reproducible-path/python-gffutils-0.13' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/python3-gffutils/ -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running build_scripts running install_lib creating /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/issue_213.db -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/tmp.db.bak -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages creating /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils creating /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/pybedtools_integration.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/inspect.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/convert.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/biopython_integration.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/iterators.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/merge_criteria.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/interface.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/feature.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/attributes.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/exceptions.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/parser.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/gffwriter.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/helpers.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/bins.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/version.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/constants.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/create.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ creating /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test creating /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/test_merge_all.cpython-313-pytest-8.4.2.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/test_merge.cpython-313-pytest-8.4.2.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/test_iterators.cpython-313-pytest-8.4.2.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/test_issues.cpython-313-pytest-8.4.2.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/test_cli.cpython-313-pytest-8.4.2.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/test_biopython_integration.cpython-313-pytest-8.4.2.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/test_1.cpython-313-pytest-8.4.2.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/synth_test_base.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/performance_evaluation.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/parser_test.cpython-313-pytest-8.4.2.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/helpers_test.cpython-313-pytest-8.4.2.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/feature_test.cpython-313-pytest-8.4.2.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/expected.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/attr_test_cases.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/conftest.cpython-313-pytest-8.4.2.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ creating /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/FBgn0031208.gtf.db -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/F3-unique-3.v2.gff -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/FBgn0031208.gff -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/FBgn0031208.gtf -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.5000_gene_ids.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.5000_transcript_ids.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.chromsizes.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/c_elegans_WS199_ann_gff.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/c_elegans_WS199_dna_shortened.fa -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/c_elegans_WS199_shortened_gff.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/dm6-chr2L.fa -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/dm6-chr2L.fa.fai -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/dmel-all-no-analysis-r5.49_50k_lines.gff -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/download-large-annotation-files.sh -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/ensembl_gtf.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/gencode-v19.gtf -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/gencode.vM8.5000_gene_ids.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/gencode.vM8.5000_transcript_ids.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/gencode.vM8.chromsizes.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/gff_example1.gff3 -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/gff_example1.gff3.gz -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/glimmer_nokeyval.gff3 -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/gms2_example.gff3 -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/hybrid1.gff3 -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/intro_docs_example.gff -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/issue167.gff -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/issue174.gtf -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/issue_197.gff -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/jgi_gff2.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/keep-order-test.gtf -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/keyval_sep_in_attrs.gff -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/mouse_extra_comma.gff3 -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/ncbi_gff3.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/nonascii -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/random-chr.gff -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/sharr.gtf -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/synthetic.gff3 -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/unsanitized.gff -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/wormbase_gff2.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/wormbase_gff2_alt.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__init__.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/attr_test_cases.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/conftest.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/expected.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/feature_test.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/helpers_test.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/parser_test.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/performance_evaluation.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/synth_test_base.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/test_biopython_integration.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/test_cli.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/test_issues.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/test_iterators.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/test_merge.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/test_merge_all.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/test_1.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test creating /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/scripts creating /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/scripts/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/scripts/__pycache__/gffutils-flybase-convert.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/scripts/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/scripts/gffutils-flybase-convert.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/scripts copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__init__.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/attributes.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/bins.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/biopython_integration.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/constants.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/convert.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/create.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/exceptions.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/gffwriter.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/inspect.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/interface.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/iterators.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/merge_criteria.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/parser.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/pybedtools_integration.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/version.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/feature.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/helpers.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/attr_test_cases.py to attr_test_cases.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/conftest.py to conftest.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/expected.py to expected.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/feature_test.py to feature_test.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/helpers_test.py to helpers_test.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/parser_test.py to parser_test.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/performance_evaluation.py to performance_evaluation.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/synth_test_base.py to synth_test_base.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/test_biopython_integration.py to test_biopython_integration.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/test_cli.py to test_cli.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/test_issues.py to test_issues.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/test_iterators.py to test_iterators.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/test_merge.py to test_merge.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/test_merge_all.py to test_merge_all.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/test_1.py to test_1.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/scripts/gffutils-flybase-convert.py to gffutils-flybase-convert.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/attributes.py to attributes.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/bins.py to bins.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/biopython_integration.py to biopython_integration.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/constants.py to constants.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/convert.py to convert.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/create.py to create.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/exceptions.py to exceptions.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/gffwriter.py to gffwriter.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/inspect.py to inspect.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/interface.py to interface.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/iterators.py to iterators.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/merge_criteria.py to merge_criteria.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/parser.py to parser.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/pybedtools_integration.py to pybedtools_integration.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/version.py to version.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/feature.py to feature.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/helpers.py to helpers.cpython-313.pyc running install_egg_info running egg_info creating gffutils.egg-info writing gffutils.egg-info/PKG-INFO writing dependency_links to gffutils.egg-info/dependency_links.txt writing requirements to gffutils.egg-info/requires.txt writing top-level names to gffutils.egg-info/top_level.txt writing manifest file 'gffutils.egg-info/SOURCES.txt' reading manifest file 'gffutils.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*.rst' under directory 'docs/source' warning: no files found matching '*.py' under directory 'docs/source' warning: no files found matching '*' under directory 'docs/source/images' warning: no files found matching 'docs/Makefile' warning: no files found matching 'docs/make.bat' warning: no files found matching 'gffutils/test/data/__init__.py' warning: no files found matching 'gffutils/test/data/t.py' adding license file 'LICENSE' writing manifest file 'gffutils.egg-info/SOURCES.txt' Copying gffutils.egg-info to /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils-0.13.egg-info Skipping SOURCES.txt running install_scripts creating /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/bin copying build/scripts-3.13/gffutils-cli -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/bin changing mode of /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/bin/gffutils-cli to 755 debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/python-gffutils-0.13' dh_install find debian -name "*.bak" -delete find debian -name "issue_*.db" -delete make[1]: Leaving directory '/build/reproducible-path/python-gffutils-0.13' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild I: dh_python3 tools:114: replacing shebang in debian/python3-gffutils/usr/bin/gffutils-cli 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_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-gffutils' in '../python3-gffutils_0.13-3_all.deb'. dpkg-genbuildinfo --build=binary -O../python-gffutils_0.13-3_arm64.buildinfo dpkg-genchanges --build=binary -O../python-gffutils_0.13-3_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1698365 and its subdirectories I: Current time: Sat Nov 1 02:10:02 -12 2025 I: pbuilder-time-stamp: 1762006202 Sat Nov 1 14:10:02 UTC 2025 I: Signing ./b1/python-gffutils_0.13-3_arm64.buildinfo as python-gffutils_0.13-3_arm64.buildinfo.asc Sat Nov 1 14:10:02 UTC 2025 I: Signed ./b1/python-gffutils_0.13-3_arm64.buildinfo as ./b1/python-gffutils_0.13-3_arm64.buildinfo.asc Sat Nov 1 14:10:02 UTC 2025 - build #1 for python-gffutils/forky/arm64 on codethink04-arm64 done. Starting cleanup. All cleanup done. Sat Nov 1 14:10:02 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-fJ1GIyuC, removing. /srv/reproducible-results/rbuild-debian/r-b-build.p5Ol6mnr: total 16 drwxrwxr-x 2 jenkins jenkins 4096 Nov 1 14:10 b1 drwxrwxr-x 2 jenkins jenkins 4096 Nov 1 14:08 b2 -rw-rw-r-- 1 jenkins jenkins 2331 Aug 23 17:27 python-gffutils_0.13-3.dsc -rw------- 1 jenkins jenkins 3487 Nov 1 14:08 rbuildlog.kdDUpWp /srv/reproducible-results/rbuild-debian/r-b-build.p5Ol6mnr/b1: total 1188 -rw-r--r-- 1 jenkins jenkins 124294 Nov 1 14:10 build.log -rw-r--r-- 1 jenkins jenkins 5460 Nov 1 14:10 python-gffutils_0.13-3.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2331 Nov 1 14:10 python-gffutils_0.13-3.dsc -rw-r--r-- 1 jenkins jenkins 8404 Nov 1 14:10 python-gffutils_0.13-3_arm64.buildinfo -rw-rw-r-- 1 jenkins jenkins 9286 Nov 1 14:10 python-gffutils_0.13-3_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1137 Nov 1 14:10 python-gffutils_0.13-3_arm64.changes -rw-r--r-- 1 jenkins jenkins 1282 Nov 1 14:10 python-gffutils_0.13-3_source.changes -rw-r--r-- 1 jenkins jenkins 1040840 Nov 1 14:10 python3-gffutils_0.13-3_all.deb /srv/reproducible-results/rbuild-debian/r-b-build.p5Ol6mnr/b2: total 0 Sat Nov 1 14:10:03 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Nov 1 02:08:36 -12 2025 I: pbuilder-time-stamp: 1762006116 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [python-gffutils_0.13-3.dsc] I: copying [./python-gffutils_0.13.orig.tar.gz] I: copying [./python-gffutils_0.13-3.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./python-gffutils_0.13-3.dsc: no acceptable signature found dpkg-source: info: extracting python-gffutils in python-gffutils-0.13 dpkg-source: info: unpacking python-gffutils_0.13.orig.tar.gz dpkg-source: info: unpacking python-gffutils_0.13-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying python3 dpkg-source: info: applying fix-version.patch dpkg-source: info: applying pr235.patch dpkg-source: info: applying pytest8.4.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1698365/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='3ba4072e2ae845ec8735b330ca0151fd' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1698365' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.p5Ol6mnr/pbuilderrc_VXr4 --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.p5Ol6mnr/b1 --logfile b1/build.log python-gffutils_0.13-3.dsc' SUDO_GID='109' SUDO_HOME='/var/lib/jenkins' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1698365/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, bedtools, python3-all, python3-setuptools, python3-argcomplete, python3-argh, python3-pyfaidx, python3-pytest, python3-biopython, python3-pybedtools, help2man dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19971 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on bedtools; however: Package bedtools is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-argcomplete; however: Package python3-argcomplete is not installed. pbuilder-satisfydepends-dummy depends on python3-argh; however: Package python3-argh is not installed. pbuilder-satisfydepends-dummy depends on python3-pyfaidx; however: Package python3-pyfaidx is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-pybedtools; however: Package python3-pybedtools is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bedtools{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libabsl20240722{a} libaom3{a} libarchive-zip-perl{a} libavif16{a} libblas3{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libcurl3t64-gnutls{a} libdav1d7{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgfortran5{a} libglib2.0-0t64{a} libgnutls30t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhts3t64{a} libhtscodecs2{a} libidn2-0{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblcms2-2{a} libldap2{a} liblerc4{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libopenjp2-7{a} libp11-kit0{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libraqm0{a} librav1e0.8{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libssh2-1t64{a} libsvtav1enc2{a} libtasn1-6{a} libtiff6{a} libtool{a} libuchardet0{a} libunistring5{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2-16{a} libxrender1{a} libyuv0{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-all{a} python3-argcomplete{a} python3-argh{a} python3-autocommand{a} python3-biopython{a} python3-cairo{a} python3-charset-normalizer{a} python3-freetype{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-numpy-dev{a} python3-packaging{a} python3-pil{a} python3-pkg-resources{a} python3-pluggy{a} python3-pybedtools{a} python3-pyfaidx{a} python3-pygments{a} python3-pysam{a} python3-pytest{a} python3-reportlab{a} python3-rlpycairo{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} tzdata{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl fonts-dejavu-extra krb5-locales libarchive-cpio-perl libglib2.0-data libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx ncbi-blast+ publicsuffix python-biopython-doc python3-olefile shared-mime-info wget xdg-user-dirs 0 packages upgraded, 155 newly installed, 0 to remove and 0 not upgraded. Need to get 76.9 MB of archives. After unpacking 273 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main arm64 libexpat1 arm64 2.7.3-1 [96.5 kB] Get: 2 http://deb.debian.org/debian forky/main arm64 liblocale-gettext-perl arm64 1.07-7+b1 [15.2 kB] Get: 3 http://deb.debian.org/debian forky/main arm64 libpython3.13-minimal arm64 3.13.9-1 [858 kB] Get: 4 http://deb.debian.org/debian forky/main arm64 python3.13-minimal arm64 3.13.9-1 [2061 kB] Get: 5 http://deb.debian.org/debian forky/main arm64 python3-minimal arm64 3.13.7-1 [27.2 kB] Get: 6 http://deb.debian.org/debian forky/main arm64 media-types all 14.0.0 [30.8 kB] Get: 7 http://deb.debian.org/debian forky/main arm64 netbase all 6.5 [12.4 kB] Get: 8 http://deb.debian.org/debian forky/main arm64 tzdata all 2025b-5 [260 kB] Get: 9 http://deb.debian.org/debian forky/main arm64 libffi8 arm64 3.5.2-2 [21.5 kB] Get: 10 http://deb.debian.org/debian forky/main arm64 readline-common all 8.3-3 [74.8 kB] Get: 11 http://deb.debian.org/debian forky/main arm64 libreadline8t64 arm64 8.3-3 [169 kB] Get: 12 http://deb.debian.org/debian forky/main arm64 libpython3.13-stdlib arm64 3.13.9-1 [1900 kB] Get: 13 http://deb.debian.org/debian forky/main arm64 python3.13 arm64 3.13.9-1 [764 kB] Get: 14 http://deb.debian.org/debian forky/main arm64 libpython3-stdlib arm64 3.13.7-1 [10.2 kB] Get: 15 http://deb.debian.org/debian forky/main arm64 python3 arm64 3.13.7-1 [28.3 kB] Get: 16 http://deb.debian.org/debian forky/main arm64 python3-numpy-dev arm64 1:2.3.3+ds-3 [135 kB] Get: 17 http://deb.debian.org/debian forky/main arm64 libblas3 arm64 3.12.1-7 [135 kB] Get: 18 http://deb.debian.org/debian forky/main arm64 libgfortran5 arm64 15.2.0-7 [371 kB] Get: 19 http://deb.debian.org/debian forky/main arm64 liblapack3 arm64 3.12.1-7 [1846 kB] Get: 20 http://deb.debian.org/debian forky/main arm64 python3-numpy arm64 1:2.3.3+ds-3 [3589 kB] Get: 21 http://deb.debian.org/debian forky/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get: 22 http://deb.debian.org/debian forky/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 23 http://deb.debian.org/debian forky/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 24 http://deb.debian.org/debian forky/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 25 http://deb.debian.org/debian forky/main arm64 gettext-base arm64 0.23.1-2+b1 [241 kB] Get: 26 http://deb.debian.org/debian forky/main arm64 libuchardet0 arm64 0.0.8-2 [69.0 kB] Get: 27 http://deb.debian.org/debian forky/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 28 http://deb.debian.org/debian forky/main arm64 bsdextrautils arm64 2.41.2-4 [97.3 kB] Get: 29 http://deb.debian.org/debian forky/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 30 http://deb.debian.org/debian forky/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 31 http://deb.debian.org/debian forky/main arm64 m4 arm64 1.4.20-2 [315 kB] Get: 32 http://deb.debian.org/debian forky/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 33 http://deb.debian.org/debian forky/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 34 http://deb.debian.org/debian forky/main arm64 automake all 1:1.18.1-2 [877 kB] Get: 35 http://deb.debian.org/debian forky/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 36 http://deb.debian.org/debian forky/main arm64 bedtools arm64 2.31.1+dfsg-2+b1 [601 kB] Get: 37 http://deb.debian.org/debian forky/main arm64 libdebhelper-perl all 13.28 [92.4 kB] Get: 38 http://deb.debian.org/debian forky/main arm64 libtool all 2.5.4-7 [540 kB] Get: 39 http://deb.debian.org/debian forky/main arm64 dh-autoreconf all 21 [12.2 kB] Get: 40 http://deb.debian.org/debian forky/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 41 http://deb.debian.org/debian forky/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 42 http://deb.debian.org/debian forky/main arm64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 43 http://deb.debian.org/debian forky/main arm64 libelf1t64 arm64 0.193-3 [189 kB] Get: 44 http://deb.debian.org/debian forky/main arm64 dwz arm64 0.16-2 [100 kB] Get: 45 http://deb.debian.org/debian forky/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 46 http://deb.debian.org/debian forky/main arm64 libxml2-16 arm64 2.14.6+dfsg-0.1 [601 kB] Get: 47 http://deb.debian.org/debian forky/main arm64 gettext arm64 0.23.1-2+b1 [1612 kB] Get: 48 http://deb.debian.org/debian forky/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 49 http://deb.debian.org/debian forky/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 50 http://deb.debian.org/debian forky/main arm64 debhelper all 13.28 [941 kB] Get: 51 http://deb.debian.org/debian forky/main arm64 dh-python all 6.20250414 [116 kB] Get: 52 http://deb.debian.org/debian forky/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 53 http://deb.debian.org/debian forky/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 54 http://deb.debian.org/debian forky/main arm64 libfontenc1 arm64 1:1.1.8-1+b2 [22.5 kB] Get: 55 http://deb.debian.org/debian forky/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 56 http://deb.debian.org/debian forky/main arm64 libpng16-16t64 arm64 1.6.50-1 [275 kB] Get: 57 http://deb.debian.org/debian forky/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 58 http://deb.debian.org/debian forky/main arm64 x11-common all 1:7.7+26 [217 kB] Get: 59 http://deb.debian.org/debian forky/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 60 http://deb.debian.org/debian forky/main arm64 xfonts-utils arm64 1:7.7+7 [89.3 kB] Get: 61 http://deb.debian.org/debian forky/main arm64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 62 http://deb.debian.org/debian forky/main arm64 fontconfig-config arm64 2.15.0-2.4 [318 kB] Get: 63 http://deb.debian.org/debian forky/main arm64 help2man arm64 1.49.3+b1 [198 kB] Get: 64 http://deb.debian.org/debian forky/main arm64 libabsl20240722 arm64 20240722.0-4 [452 kB] Get: 65 http://deb.debian.org/debian forky/main arm64 libaom3 arm64 3.13.1-2 [1632 kB] Get: 66 http://deb.debian.org/debian forky/main arm64 libdav1d7 arm64 1.5.1-1 [252 kB] Get: 67 http://deb.debian.org/debian forky/main arm64 libgav1-1 arm64 0.19.0-3+b1 [491 kB] Get: 68 http://deb.debian.org/debian forky/main arm64 librav1e0.8 arm64 0.8.1-5 [688 kB] Get: 69 http://deb.debian.org/debian forky/main arm64 libsvtav1enc2 arm64 2.3.0+dfsg-1 [1558 kB] Get: 70 http://deb.debian.org/debian forky/main arm64 libjpeg62-turbo arm64 1:2.1.5-4 [173 kB] Get: 71 http://deb.debian.org/debian forky/main arm64 libyuv0 arm64 0.0.1919.20250919-1 [138 kB] Get: 72 http://deb.debian.org/debian forky/main arm64 libavif16 arm64 1.3.0-1+b1 [127 kB] Get: 73 http://deb.debian.org/debian forky/main arm64 libfontconfig1 arm64 2.15.0-2.4 [387 kB] Get: 74 http://deb.debian.org/debian forky/main arm64 libpixman-1-0 arm64 0.46.4-1 [174 kB] Get: 75 http://deb.debian.org/debian forky/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 76 http://deb.debian.org/debian forky/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 77 http://deb.debian.org/debian forky/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 78 http://deb.debian.org/debian forky/main arm64 libx11-data all 2:1.8.12-1 [343 kB] Get: 79 http://deb.debian.org/debian forky/main arm64 libx11-6 arm64 2:1.8.12-1 [795 kB] Get: 80 http://deb.debian.org/debian forky/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 81 http://deb.debian.org/debian forky/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 82 http://deb.debian.org/debian forky/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB] Get: 83 http://deb.debian.org/debian forky/main arm64 libxrender1 arm64 1:0.9.12-1 [27.0 kB] Get: 84 http://deb.debian.org/debian forky/main arm64 libcairo2 arm64 1.18.4-1+b1 [483 kB] Get: 85 http://deb.debian.org/debian forky/main arm64 libcom-err2 arm64 1.47.2-3+b3 [24.9 kB] Get: 86 http://deb.debian.org/debian forky/main arm64 libnghttp3-9 arm64 1.12.0-1 [63.6 kB] Get: 87 http://deb.debian.org/debian forky/main arm64 libngtcp2-16 arm64 1.16.0-1 [123 kB] Get: 88 http://deb.debian.org/debian forky/main arm64 libidn2-0 arm64 2.3.8-4 [108 kB] Get: 89 http://deb.debian.org/debian forky/main arm64 libp11-kit0 arm64 0.25.9-2 [420 kB] Get: 90 http://deb.debian.org/debian forky/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 91 http://deb.debian.org/debian forky/main arm64 libgnutls30t64 arm64 3.8.10-3 [1384 kB] Get: 92 http://deb.debian.org/debian forky/main arm64 libkrb5support0 arm64 1.21.3-5 [32.4 kB] Get: 93 http://deb.debian.org/debian forky/main arm64 libk5crypto3 arm64 1.21.3-5 [81.2 kB] Get: 94 http://deb.debian.org/debian forky/main arm64 libkeyutils1 arm64 1.6.3-6 [9716 B] Get: 95 http://deb.debian.org/debian forky/main arm64 libkrb5-3 arm64 1.21.3-5 [308 kB] Get: 96 http://deb.debian.org/debian forky/main arm64 libgssapi-krb5-2 arm64 1.21.3-5 [127 kB] Get: 97 http://deb.debian.org/debian forky/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-10 [19.8 kB] Get: 98 http://deb.debian.org/debian forky/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-10 [55.0 kB] Get: 99 http://deb.debian.org/debian forky/main arm64 libldap2 arm64 2.6.10+dfsg-1 [179 kB] Get: 100 http://deb.debian.org/debian forky/main arm64 libnghttp2-14 arm64 1.64.0-1.1+b1 [71.7 kB] Get: 101 http://deb.debian.org/debian forky/main arm64 libngtcp2-crypto-gnutls8 arm64 1.16.0-1 [23.8 kB] Get: 102 http://deb.debian.org/debian forky/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 103 http://deb.debian.org/debian forky/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-3 [56.3 kB] Get: 104 http://deb.debian.org/debian forky/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 105 http://deb.debian.org/debian forky/main arm64 libcurl3t64-gnutls arm64 8.17.0~rc3-1 [362 kB] Get: 106 http://deb.debian.org/debian forky/main arm64 libdeflate0 arm64 1.23-2 [42.4 kB] Get: 107 http://deb.debian.org/debian forky/main arm64 libfribidi0 arm64 1.0.16-3 [26.5 kB] Get: 108 http://deb.debian.org/debian forky/main arm64 libglib2.0-0t64 arm64 2.86.1-1 [1436 kB] Get: 109 http://deb.debian.org/debian forky/main arm64 libgraphite2-3 arm64 1.3.14-11 [70.8 kB] Get: 110 http://deb.debian.org/debian forky/main arm64 libharfbuzz0b arm64 12.1.0-1 [486 kB] Get: 111 http://deb.debian.org/debian forky/main arm64 libhtscodecs2 arm64 1.6.1-2 [74.7 kB] Get: 112 http://deb.debian.org/debian forky/main arm64 libhts3t64 arm64 1.22.1+ds2-1 [434 kB] Get: 113 http://deb.debian.org/debian forky/main arm64 libimagequant0 arm64 4.4.0-3 [216 kB] Get: 114 http://deb.debian.org/debian forky/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 115 http://deb.debian.org/debian forky/main arm64 liblcms2-2 arm64 2.16-2 [151 kB] Get: 116 http://deb.debian.org/debian forky/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 117 http://deb.debian.org/debian forky/main arm64 libopenjp2-7 arm64 2.5.3-2.1 [189 kB] Get: 118 http://deb.debian.org/debian forky/main arm64 libraqm0 arm64 0.10.3-1 [13.6 kB] Get: 119 http://deb.debian.org/debian forky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [114 kB] Get: 120 http://deb.debian.org/debian forky/main arm64 libwebp7 arm64 1.5.0-0.1 [271 kB] Get: 121 http://deb.debian.org/debian forky/main arm64 libtiff6 arm64 4.7.1-1 [334 kB] Get: 122 http://deb.debian.org/debian forky/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [113 kB] Get: 123 http://deb.debian.org/debian forky/main arm64 libwebpmux3 arm64 1.5.0-0.1 [125 kB] Get: 124 http://deb.debian.org/debian forky/main arm64 python3-all arm64 3.13.7-1 [1044 B] Get: 125 http://deb.debian.org/debian forky/main arm64 python3-argcomplete all 3.6.2-1 [40.9 kB] Get: 126 http://deb.debian.org/debian forky/main arm64 python3-argh all 0.31.3-1 [26.6 kB] Get: 127 http://deb.debian.org/debian forky/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 128 http://deb.debian.org/debian forky/main arm64 python3-charset-normalizer arm64 3.4.3-1 [123 kB] Get: 129 http://deb.debian.org/debian forky/main arm64 python3-pil arm64 11.3.0-1 [507 kB] Get: 130 http://deb.debian.org/debian forky/main arm64 python3-cairo arm64 1.27.0-2 [114 kB] Get: 131 http://deb.debian.org/debian forky/main arm64 python3-freetype all 2.5.1-2 [89.4 kB] Get: 132 http://deb.debian.org/debian forky/main arm64 python3-rlpycairo all 0.3.0-4 [10.1 kB] Get: 133 http://deb.debian.org/debian forky/main arm64 python3-reportlab all 4.4.4-2 [1170 kB] Get: 134 http://deb.debian.org/debian forky/main arm64 sgml-base all 1.31+nmu1 [10.9 kB] Get: 135 http://deb.debian.org/debian forky/main arm64 xml-core all 0.19 [20.1 kB] Get: 136 http://deb.debian.org/debian forky/main arm64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 137 http://deb.debian.org/debian forky/main arm64 python3-biopython arm64 1.86+dfsg-1 [1598 kB] Get: 138 http://deb.debian.org/debian forky/main arm64 python3-more-itertools all 10.8.0-1 [71.7 kB] Get: 139 http://deb.debian.org/debian forky/main arm64 python3-typing-extensions all 4.15.0-1 [92.4 kB] Get: 140 http://deb.debian.org/debian forky/main arm64 python3-typeguard all 4.4.4-1 [37.1 kB] Get: 141 http://deb.debian.org/debian forky/main arm64 python3-inflect all 7.5.0-1 [33.0 kB] Get: 142 http://deb.debian.org/debian forky/main arm64 python3-iniconfig all 2.1.0-1 [7432 B] Get: 143 http://deb.debian.org/debian forky/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 144 http://deb.debian.org/debian forky/main arm64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 145 http://deb.debian.org/debian forky/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 146 http://deb.debian.org/debian forky/main arm64 python3-zipp all 3.23.0-1 [11.0 kB] Get: 147 http://deb.debian.org/debian forky/main arm64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 148 http://deb.debian.org/debian forky/main arm64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 149 http://deb.debian.org/debian forky/main arm64 python3-packaging all 25.0-1 [56.6 kB] Get: 150 http://deb.debian.org/debian forky/main arm64 python3-pluggy all 1.6.0-1 [27.1 kB] Get: 151 http://deb.debian.org/debian forky/main arm64 python3-pysam arm64 0.23.0+ds-1+b1 [3417 kB] Get: 152 http://deb.debian.org/debian forky/main arm64 python3-pybedtools arm64 0.10.0-5 [12.1 MB] Get: 153 http://deb.debian.org/debian forky/main arm64 python3-pyfaidx all 0.8.1.3-2 [29.1 kB] Get: 154 http://deb.debian.org/debian forky/main arm64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get: 155 http://deb.debian.org/debian forky/main arm64 python3-pytest all 8.4.2-1 [266 kB] Fetched 76.9 MB in 1s (139 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19971 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.3-1_arm64.deb ... Unpacking libexpat1:arm64 (2.7.3-1) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../liblocale-gettext-perl_1.07-7+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package libpython3.13-minimal:arm64. Preparing to unpack .../libpython3.13-minimal_3.13.9-1_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.9-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.9-1_arm64.deb ... Unpacking python3.13-minimal (3.13.9-1) ... Setting up libpython3.13-minimal:arm64 (3.13.9-1) ... Setting up libexpat1:arm64 (2.7.3-1) ... Setting up python3.13-minimal (3.13.9-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.9-1_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.9-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.9-1_arm64.deb ... Unpacking python3.13 (3.13.9-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../9-libpython3-stdlib_3.13.7-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.13.7-1) ... Setting up python3-minimal (3.13.7-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21335 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.7-1_arm64.deb ... Unpacking python3 (3.13.7-1) ... Selecting previously unselected package python3-numpy-dev:arm64. Preparing to unpack .../001-python3-numpy-dev_1%3a2.3.3+ds-3_arm64.deb ... Unpacking python3-numpy-dev:arm64 (1:2.3.3+ds-3) ... Selecting previously unselected package libblas3:arm64. Preparing to unpack .../002-libblas3_3.12.1-7_arm64.deb ... Unpacking libblas3:arm64 (3.12.1-7) ... Selecting previously unselected package libgfortran5:arm64. Preparing to unpack .../003-libgfortran5_15.2.0-7_arm64.deb ... Unpacking libgfortran5:arm64 (15.2.0-7) ... Selecting previously unselected package liblapack3:arm64. Preparing to unpack .../004-liblapack3_3.12.1-7_arm64.deb ... Unpacking liblapack3:arm64 (3.12.1-7) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../005-python3-numpy_1%3a2.3.3+ds-3_arm64.deb ... Unpacking python3-numpy (1:2.3.3+ds-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../006-sensible-utils_0.0.26_all.deb ... 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Selecting previously unselected package x11-common. Preparing to unpack .../043-x11-common_1%3a7.7+26_all.deb ... Unpacking x11-common (1:7.7+26) ... Selecting previously unselected package xfonts-encodings. Preparing to unpack .../044-xfonts-encodings_1%3a1.0.4-2.2_all.deb ... Unpacking xfonts-encodings (1:1.0.4-2.2) ... Selecting previously unselected package xfonts-utils. Preparing to unpack .../045-xfonts-utils_1%3a7.7+7_arm64.deb ... Unpacking xfonts-utils (1:7.7+7) ... Selecting previously unselected package fonts-urw-base35. Preparing to unpack .../046-fonts-urw-base35_20200910-8_all.deb ... Unpacking fonts-urw-base35 (20200910-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../047-fontconfig-config_2.15.0-2.4_arm64.deb ... Unpacking fontconfig-config (2.15.0-2.4) ... Selecting previously unselected package help2man. Preparing to unpack .../048-help2man_1.49.3+b1_arm64.deb ... Unpacking help2man (1.49.3+b1) ... 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Unpacking python3-pytest (8.4.2-1) ... Setting up libhtscodecs2:arm64 (1.6.1-2) ... Setting up media-types (14.0.0) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libgraphite2-3:arm64 (1.3.14-11) ... Setting up liblcms2-2:arm64 (2.16-2) ... Setting up libpixman-1-0:arm64 (0.46.4-1) ... Setting up libsharpyuv0:arm64 (1.5.0-0.1) ... Setting up libaom3:arm64 (3.13.1-2) ... Setting up libxau6:arm64 (1:1.0.11-1) ... Setting up libxdmcp6:arm64 (1:1.1.5-1) ... Setting up libkeyutils1:arm64 (1.6.3-6) ... Setting up libxcb1:arm64 (1.17.0-2+b1) ... Setting up liblerc4:arm64 (4.0.0+ds-5) ... Setting up bsdextrautils (2.41.2-4) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libxcb-render0:arm64 (1.17.0-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:arm64 (2.14.6+dfsg-0.1) ... Setting up libdebhelper-perl (13.28) ... Setting up libbrotli1:arm64 (1.1.0-2+b7) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up x11-common (1:7.7+26) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libnghttp2-14:arm64 (1.64.0-1.1+b1) ... Setting up libdeflate0:arm64 (1.23-2) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-2) ... Setting up libxcb-shm0:arm64 (1.17.0-2+b1) ... Setting up libcom-err2:arm64 (1.47.2-3+b3) ... Setting up file (1:5.46-5) ... Setting up libabsl20240722:arm64 (20240722.0-4) ... Setting up libjbig0:arm64 (2.1-6.1+b2) ... Setting up libelf1t64:arm64 (0.193-3) ... Setting up libkrb5support0:arm64 (1.21.3-5) ... Setting up librav1e0.8:arm64 (0.8.1-5) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-10) ... Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Nov 1 14:08:55 UTC 2025. Universal Time is now: Sat Nov 1 14:08:55 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:arm64 (1:1.1.8-1+b2) ... Setting up autotools-dev (20240727.1) ... Setting up libblas3:arm64 (3.12.1-7) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libjpeg62-turbo:arm64 (1:2.1.5-4) ... Setting up libx11-data (2:1.8.12-1) ... Setting up libsvtav1enc2:arm64 (2.3.0+dfsg-1) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:arm64 (1.0.16-3) ... Setting up libimagequant0:arm64 (4.4.0-3) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:arm64 (1.6.50-1) ... Setting up python3-numpy-dev:arm64 (1:2.3.3+ds-3) ... Setting up autopoint (0.23.1-2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libgav1-1:arm64 (0.19.0-3+b1) ... Setting up libk5crypto3:arm64 (1.21.3-5) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-10) ... Setting up libgfortran5:arm64 (15.2.0-7) ... Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:arm64 (1.12.0-1) ... Setting up libwebp7:arm64 (1.5.0-0.1) ... Setting up libffi8:arm64 (3.5.2-2) ... Setting up dwz (0.16-2) ... Setting up libdav1d7:arm64 (1.5.1-1) ... Setting up sensible-utils (0.0.26) ... Setting up libtiff6:arm64 (4.7.1-1) ... Setting up libuchardet0:arm64 (0.0.8-2) ... Setting up libtasn1-6:arm64 (4.20.0-2) ... Setting up libopenjp2-7:arm64 (2.5.3-2.1) ... Setting up libx11-6:arm64 (2:1.8.12-1) ... Setting up netbase (6.5) ... Setting up libngtcp2-16:arm64 (1.16.0-1) ... Setting up sgml-base (1.31+nmu1) ... Setting up libkrb5-3:arm64 (1.21.3-5) ... Setting up libssh2-1t64:arm64 (1.11.1-1) ... Setting up libwebpmux3:arm64 (1.5.0-0.1) ... Setting up libyuv0:arm64 (0.0.1919.20250919-1) ... Setting up readline-common (8.3-3) ... Setting up bedtools (2.31.1+dfsg-2+b1) ... Setting up libldap2:arm64 (2.6.10+dfsg-1) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up automake (1:1.18.1-2) ... update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up libavif16:arm64 (1.3.0-1+b1) ... Setting up liblapack3:arm64 (3.12.1-7) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.23.1-2+b1) ... Setting up libxrender1:arm64 (1:0.9.12-1) ... Setting up libtool (2.5.4-7) ... Setting up fontconfig-config (2.15.0-2.4) ... Setting up libwebpdemux2:arm64 (1.5.0-0.1) ... Setting up libxext6:arm64 (2:1.3.4-1+b3) ... Setting up libidn2-0:arm64 (2.3.8-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3+b1) ... Setting up dh-autoreconf (21) ... Setting up libglib2.0-0t64:arm64 (2.86.1-1) ... No schema files found: doing nothing. Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up libp11-kit0:arm64 (0.25.9-2) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-5) ... Setting up libreadline8t64:arm64 (8.3-3) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up xml-core (0.19) ... Setting up libharfbuzz0b:arm64 (12.1.0-1) ... Setting up libfontconfig1:arm64 (2.15.0-2.4) ... Setting up libpython3.13-stdlib:arm64 (3.13.9-1) ... Setting up libpython3-stdlib:arm64 (3.13.7-1) ... Setting up libgnutls30t64:arm64 (3.8.10-3) ... Setting up python3.13 (3.13.9-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:arm64 (0.21.2-1.1+b1) ... Setting up python3 (3.13.7-1) ... Setting up python3-zipp (3.23.0-1) ... Setting up python3-freetype (2.5.1-2) ... Setting up xfonts-utils (1:7.7+7) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:arm64 (1.18.4-1+b1) ... Setting up python3-pygments (2.18.0+dfsg-2) ... Setting up python3-packaging (25.0-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libraqm0:arm64 (0.10.3-1) ... Setting up python3-typing-extensions (4.15.0-1) ... Setting up python3-numpy (1:2.3.3+ds-3) ... Setting up python3-pluggy (1.6.0-1) ... Setting up python3-argcomplete (3.6.2-1) ... Setting up libngtcp2-crypto-gnutls8:arm64 (1.16.0-1) ... Setting up dh-python (6.20250414) ... Setting up python3-more-itertools (10.8.0-1) ... Setting up python3-pyfaidx (0.8.1.3-2) ... Setting up python3-iniconfig (2.1.0-1) ... Setting up python3-argh (0.31.3-1) ... Setting up python3-cairo (1.27.0-2) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up python3-charset-normalizer (3.4.3-1) ... Setting up python3-pytest (8.4.2-1) ... Setting up python3-typeguard (4.4.4-1) ... Setting up libcurl3t64-gnutls:arm64 (8.17.0~rc3-1) ... Setting up python3-all (3.13.7-1) ... Setting up debhelper (13.28) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up python3-pil:arm64 (11.3.0-1) ... Setting up python3-inflect (7.5.0-1) ... Setting up python3-rlpycairo (0.3.0-4) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-reportlab (4.4.4-2) ... Setting up libhts3t64:arm64 (1.22.1+ds2-1) ... Setting up python3-pkg-resources (78.1.1-0.1) ... Setting up python3-pysam (0.23.0+ds-1+b1) ... Setting up python3-setuptools (78.1.1-0.1) ... Setting up python3-pybedtools (0.10.0-5) ... Processing triggers for libc-bin (2.41-12) ... Processing triggers for sgml-base (1.31+nmu1) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.86+dfsg-1) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.37.1.2-1). Solving dependencies... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/reproducible-path/python-gffutils-0.13/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../python-gffutils_0.13-3_source.changes dpkg-buildpackage: info: source package python-gffutils dpkg-buildpackage: info: source version 0.13-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Alexandre Detiste dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py clean /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running clean removing '/build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build' (and everything under it) 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.13' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py config /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/python-gffutils-0.13' dh_auto_build I: pybuild base:311: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running build running build_py creating /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/helpers.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/feature.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/version.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/pybedtools_integration.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/parser.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/merge_criteria.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/iterators.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/interface.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/inspect.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/gffwriter.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/exceptions.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/create.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/convert.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/constants.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/biopython_integration.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/bins.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/attributes.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/__init__.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils creating /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/scripts copying gffutils/scripts/gffutils-flybase-convert.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/scripts creating /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/test_1.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/test_merge_all.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/test_merge.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/test_iterators.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/test_issues.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/test_cli.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/test_biopython_integration.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/synth_test_base.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/performance_evaluation.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/parser_test.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/helpers_test.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/feature_test.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/expected.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/conftest.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/attr_test_cases.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/__init__.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test creating /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/wormbase_gff2_alt.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/wormbase_gff2.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/unsanitized.gff -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/synthetic.gff3 -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/sharr.gtf -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/random-chr.gff -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/nonascii -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/ncbi_gff3.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/mouse_extra_comma.gff3 -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/keyval_sep_in_attrs.gff -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/keep-order-test.gtf -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/jgi_gff2.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/issue_197.gff -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/issue174.gtf -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/issue167.gff -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/intro_docs_example.gff -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/hybrid1.gff3 -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/gms2_example.gff3 -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/glimmer_nokeyval.gff3 -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/gff_example1.gff3.gz -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/gff_example1.gff3 -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/gencode.vM8.chromsizes.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/gencode.vM8.5000_transcript_ids.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/gencode.vM8.5000_gene_ids.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/gencode-v19.gtf -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/ensembl_gtf.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/download-large-annotation-files.sh -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/dmel-all-no-analysis-r5.49_50k_lines.gff -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/dm6-chr2L.fa.fai -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/dm6-chr2L.fa -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/c_elegans_WS199_shortened_gff.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/c_elegans_WS199_dna_shortened.fa -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/c_elegans_WS199_ann_gff.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.chromsizes.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.5000_transcript_ids.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.5000_gene_ids.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/FBgn0031208.gtf.db -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/FBgn0031208.gtf -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/FBgn0031208.gff -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/F3-unique-3.v2.gff -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data running build_scripts creating build/scripts-3.13 copying and adjusting gffutils/scripts/gffutils-cli -> build/scripts-3.13 changing mode of build/scripts-3.13/gffutils-cli from 644 to 755 PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ help2man --version-string=0.13 --no-info \ --name="Command line interface for python-gffutils." \ gffutils-cli > debian/gffutils-cli.1 PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ help2man --version-string=0.13 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_fetch \- Fetch IDs") \ 'gffutils-cli fetch' > debian/gffutils-cli-fetch.1 PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ help2man --version-string=0.13 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_children \- Fetch children from the database according to ID") \ 'gffutils-cli children' > debian/gffutils-cli-children.1 PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ help2man --version-string=0.13 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_parents \- Fetch parents from the database according to ID") \ 'gffutils-cli parents' > debian/gffutils-cli-parents.1 PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ help2man --version-string=0.13 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_region \- Returns features within provided genomic coordinates") \ 'gffutils-cli region' > debian/gffutils-cli-region.1 PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ help2man --version-string=0.13 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_create \- Create a database") \ 'gffutils-cli create' > debian/gffutils-cli-create.1 PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ help2man --version-string=0.13 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_common \- Identify child features in common") \ 'gffutils-cli common' > debian/gffutils-cli-common.1 PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ help2man --version-string=0.13 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_clean \- Perform various QC operations to clean a GFF or GTF file") \ 'gffutils-cli clean' > debian/gffutils-cli-clean.1 PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ help2man --version-string=0.13 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_sanitize \- Sanitize a GFF file") \ 'gffutils-cli sanitize' > debian/gffutils-cli-sanitize.1 PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ help2man --version-string=0.13 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_rmdups \- Remove duplicates from a GFF file") \ 'gffutils-cli rmdups' > debian/gffutils-cli-rmdups.1 make[1]: Leaving directory '/build/reproducible-path/python-gffutils-0.13' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/python-gffutils-0.13' PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games dh_auto_test I: pybuild base:311: cd /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build; python3.13 -m pytest --doctest-modules -m 'not slow' ============================= test session starts ============================== platform linux -- Python 3.13.9, pytest-8.4.2, pluggy-1.6.0 rootdir: /build/reproducible-path/python-gffutils-0.13 plugins: typeguard-4.4.4 collected 112 items gffutils/attributes.py . [ 0%] gffutils/pybedtools_integration.py . [ 1%] gffutils/test/feature_test.py ........... [ 11%] gffutils/test/helpers_test.py .. [ 13%] gffutils/test/parser_test.py .................. [ 29%] gffutils/test/test_1.py ......................s........... [ 59%] gffutils/test/test_biopython_integration.py . [ 60%] gffutils/test/test_cli.py . [ 61%] gffutils/test/test_issues.py ........................ [ 83%] gffutils/test/test_iterators.py .... [ 86%] gffutils/test/test_merge.py ......... [ 94%] gffutils/test/test_merge_all.py ...... [100%] =============================== warnings summary =============================== gffutils/test/performance_evaluation.py:190 /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/performance_evaluation.py:190: PytestUnknownMarkWarning: Unknown pytest.mark.slow - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html @pytest.mark.slow gffutils/test/performance_evaluation.py:208 /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/performance_evaluation.py:208: PytestUnknownMarkWarning: Unknown pytest.mark.slow - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html @pytest.mark.slow .pybuild/cpython3_3.13_gffutils/build/gffutils/test/parser_test.py::test_parser_from_string /usr/lib/python3/dist-packages/_pytest/python.py:161: PytestReturnNotNoneWarning: Test functions should return None, but .pybuild/cpython3_3.13_gffutils/build/gffutils/test/parser_test.py::test_parser_from_string returned . Did you mean to use `assert` instead of `return`? See https://docs.pytest.org/en/stable/how-to/assert.html#return-not-none for more information. warnings.warn( .pybuild/cpython3_3.13_gffutils/build/gffutils/test/parser_test.py::test_inconsistent_dialect .pybuild/cpython3_3.13_gffutils/build/gffutils/test/test_1.py::test_disable_infer .pybuild/cpython3_3.13_gffutils/build/gffutils/test/test_issues.py::test_pr_172 /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/create.py:770: UserWarning: It appears you have a gene feature in your GTF file. You may want to use the `disable_infer_genes=True` option to speed up database creation warnings.warn( .pybuild/cpython3_3.13_gffutils/build/gffutils/test/test_1.py::test_disable_infer /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/create.py:763: UserWarning: It appears you have a transcript feature in your GTF file. You may want to use the `disable_infer_transcripts=True` option to speed up database creation warnings.warn( -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ================== 111 passed, 1 skipped, 7 warnings in 1.98s ================== I: pybuild pybuild:334: find . -name tmp.db -delete make[1]: Leaving directory '/build/reproducible-path/python-gffutils-0.13' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/python3-gffutils/ -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running build_scripts running install_lib creating /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/issue_213.db -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/tmp.db.bak -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages creating /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils creating /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/pybedtools_integration.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/inspect.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/convert.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/biopython_integration.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/iterators.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/merge_criteria.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/interface.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/feature.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/attributes.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/exceptions.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/parser.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/gffwriter.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/helpers.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/bins.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/version.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/constants.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/create.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ creating /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test creating /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/test_merge_all.cpython-313-pytest-8.4.2.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/test_merge.cpython-313-pytest-8.4.2.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/test_iterators.cpython-313-pytest-8.4.2.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/test_issues.cpython-313-pytest-8.4.2.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/test_cli.cpython-313-pytest-8.4.2.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/test_biopython_integration.cpython-313-pytest-8.4.2.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/test_1.cpython-313-pytest-8.4.2.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/synth_test_base.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/performance_evaluation.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/parser_test.cpython-313-pytest-8.4.2.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/helpers_test.cpython-313-pytest-8.4.2.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/feature_test.cpython-313-pytest-8.4.2.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/expected.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/attr_test_cases.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/conftest.cpython-313-pytest-8.4.2.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ creating /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/FBgn0031208.gtf.db -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/F3-unique-3.v2.gff -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/FBgn0031208.gff -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/FBgn0031208.gtf -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.5000_gene_ids.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.5000_transcript_ids.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.chromsizes.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/c_elegans_WS199_ann_gff.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/c_elegans_WS199_dna_shortened.fa -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/c_elegans_WS199_shortened_gff.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/dm6-chr2L.fa -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/dm6-chr2L.fa.fai -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/dmel-all-no-analysis-r5.49_50k_lines.gff -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/download-large-annotation-files.sh -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/ensembl_gtf.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/gencode-v19.gtf -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/gencode.vM8.5000_gene_ids.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/gencode.vM8.5000_transcript_ids.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/gencode.vM8.chromsizes.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/gff_example1.gff3 -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/gff_example1.gff3.gz -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/glimmer_nokeyval.gff3 -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/gms2_example.gff3 -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/hybrid1.gff3 -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/intro_docs_example.gff -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/issue167.gff -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/issue174.gtf -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/issue_197.gff -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/jgi_gff2.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/keep-order-test.gtf -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/keyval_sep_in_attrs.gff -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/mouse_extra_comma.gff3 -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/ncbi_gff3.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/nonascii -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/random-chr.gff -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/sharr.gtf -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/synthetic.gff3 -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/unsanitized.gff -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/wormbase_gff2.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/wormbase_gff2_alt.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__init__.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/attr_test_cases.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/conftest.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/expected.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/feature_test.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/helpers_test.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/parser_test.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/performance_evaluation.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/synth_test_base.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/test_biopython_integration.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/test_cli.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/test_issues.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/test_iterators.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/test_merge.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/test_merge_all.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/test_1.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test creating /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/scripts creating /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/scripts/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/scripts/__pycache__/gffutils-flybase-convert.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/scripts/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/scripts/gffutils-flybase-convert.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/scripts copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__init__.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/attributes.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/bins.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/biopython_integration.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/constants.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/convert.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/create.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/exceptions.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/gffwriter.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/inspect.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/interface.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/iterators.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/merge_criteria.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/parser.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/pybedtools_integration.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/version.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/feature.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/helpers.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/attr_test_cases.py to attr_test_cases.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/conftest.py to conftest.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/expected.py to expected.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/feature_test.py to feature_test.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/helpers_test.py to helpers_test.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/parser_test.py to parser_test.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/performance_evaluation.py to performance_evaluation.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/synth_test_base.py to synth_test_base.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/test_biopython_integration.py to test_biopython_integration.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/test_cli.py to test_cli.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/test_issues.py to test_issues.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/test_iterators.py to test_iterators.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/test_merge.py to test_merge.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/test_merge_all.py to test_merge_all.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/test_1.py to test_1.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/scripts/gffutils-flybase-convert.py to gffutils-flybase-convert.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/attributes.py to attributes.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/bins.py to bins.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/biopython_integration.py to biopython_integration.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/constants.py to constants.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/convert.py to convert.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/create.py to create.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/exceptions.py to exceptions.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/gffwriter.py to gffwriter.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/inspect.py to inspect.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/interface.py to interface.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/iterators.py to iterators.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/merge_criteria.py to merge_criteria.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/parser.py to parser.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/pybedtools_integration.py to pybedtools_integration.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/version.py to version.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/feature.py to feature.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/helpers.py to helpers.cpython-313.pyc running install_egg_info running egg_info creating gffutils.egg-info writing gffutils.egg-info/PKG-INFO writing dependency_links to gffutils.egg-info/dependency_links.txt writing requirements to gffutils.egg-info/requires.txt writing top-level names to gffutils.egg-info/top_level.txt writing manifest file 'gffutils.egg-info/SOURCES.txt' reading manifest file 'gffutils.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*.rst' under directory 'docs/source' warning: no files found matching '*.py' under directory 'docs/source' warning: no files found matching '*' under directory 'docs/source/images' warning: no files found matching 'docs/Makefile' warning: no files found matching 'docs/make.bat' warning: no files found matching 'gffutils/test/data/__init__.py' warning: no files found matching 'gffutils/test/data/t.py' adding license file 'LICENSE' writing manifest file 'gffutils.egg-info/SOURCES.txt' Copying gffutils.egg-info to /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils-0.13.egg-info Skipping SOURCES.txt running install_scripts creating /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/bin copying build/scripts-3.13/gffutils-cli -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/bin changing mode of /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/bin/gffutils-cli to 755 debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/python-gffutils-0.13' dh_install find debian -name "*.bak" -delete find debian -name "issue_*.db" -delete make[1]: Leaving directory '/build/reproducible-path/python-gffutils-0.13' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild I: dh_python3 tools:114: replacing shebang in debian/python3-gffutils/usr/bin/gffutils-cli 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_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-gffutils' in '../python3-gffutils_0.13-3_all.deb'. dpkg-genbuildinfo --build=binary -O../python-gffutils_0.13-3_arm64.buildinfo dpkg-genchanges --build=binary -O../python-gffutils_0.13-3_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1698365 and its subdirectories I: Current time: Sat Nov 1 02:10:02 -12 2025 I: pbuilder-time-stamp: 1762006202 Sat Nov 1 14:10:03 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Sat Nov 1 14:10:03 UTC 2025 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Sat Nov 1 14:10:03 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Sat Nov 1 14:10:03 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-FyZ4oJ' ==================================================================================== Fri Dec 4 20:33:04 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink03-arm64, called using "2 python-gffutils forky /srv/reproducible-results/rbuild-debian/r-b-build.p5Ol6mnr 0.13-3" as arguments. Fri Dec 4 20:33:04 UTC 2026 - actually running "reproducible_build.sh" (md5sum bcb6fe1b50cf4e8eedacd0971a9eb63f) as "/tmp/jenkins-script-vkwBF0tZ" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Dec 4 20:33:04 UTC 2026 I: Downloading source for forky/python-gffutils=0.13-3 Reading package lists... NOTICE: 'python-gffutils' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/python-gffutils.git Please use: git clone https://salsa.debian.org/med-team/python-gffutils.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1568 kB of source archives. Get:1 http://deb.debian.org/debian forky/main python-gffutils 0.13-3 (dsc) [2331 B] Get:2 http://deb.debian.org/debian forky/main python-gffutils 0.13-3 (tar) [1560 kB] Get:3 http://deb.debian.org/debian forky/main python-gffutils 0.13-3 (diff) [5460 B] Fetched 1568 kB in 0s (80.2 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'python-gffutils' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/python-gffutils.git Please use: git clone https://salsa.debian.org/med-team/python-gffutils.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1568 kB of source archives. Get:1 http://deb.debian.org/debian forky/main python-gffutils 0.13-3 (dsc) [2331 B] Get:2 http://deb.debian.org/debian forky/main python-gffutils 0.13-3 (tar) [1560 kB] Get:3 http://deb.debian.org/debian forky/main python-gffutils 0.13-3 (diff) [5460 B] Fetched 1568 kB in 0s (80.2 MB/s) Download complete and in download only mode ============================================================================= Re-Building python-gffutils in forky on arm64 on codethink03-arm64 now. Date: Fri Dec 4 20:33:05 GMT 2026 Date UTC: Fri Dec 4 20:33:05 UTC 2026 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.p5Ol6mnr + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.p5Ol6mnr/pbuilderrc_0XXy + case ${ARCH} in + case $ARCH in + locale=nl_BE + language=nl + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' python-gffutils = debian-installer -o python-gffutils = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' python-gffutils = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.p5Ol6mnr/pbuilderrc_0XXy --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.p5Ol6mnr/b2 --logfile b2/build.log python-gffutils_0.13-3.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Sat Dec 5 10:33:05 +14 2026 I: pbuilder-time-stamp: 1796416385 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [python-gffutils_0.13-3.dsc] I: copying [./python-gffutils_0.13.orig.tar.gz] I: copying [./python-gffutils_0.13-3.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./python-gffutils_0.13-3.dsc: no acceptable signature found dpkg-source: info: extracting python-gffutils in python-gffutils-0.13 dpkg-source: info: unpacking python-gffutils_0.13.orig.tar.gz dpkg-source: info: unpacking python-gffutils_0.13-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying python3 dpkg-source: info: applying fix-version.patch dpkg-source: info: applying pr235.patch dpkg-source: info: applying pytest8.4.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3374847/tmp/hooks/D01_modify_environment starting debug: Running on codethink03-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Dec 4 20:33 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/3374847/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3374847/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.3.3(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 nocheck' DIRSTACK=() DISTRIBUTION=forky EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=a80bd8c36a8342b5abbe2fa860f368f4 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=3374847 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.p5Ol6mnr/pbuilderrc_0XXy --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.p5Ol6mnr/b2 --logfile b2/build.log python-gffutils_0.13-3.dsc' SUDO_GID=109 SUDO_HOME=/var/lib/jenkins SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3374847/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, bedtools, python3-all, python3-setuptools, python3-argcomplete, python3-argh, python3-pyfaidx, python3-pytest, python3-biopython, python3-pybedtools, help2man dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19964 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on bedtools; however: Package bedtools is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-argcomplete; however: Package python3-argcomplete is not installed. pbuilder-satisfydepends-dummy depends on python3-argh; however: Package python3-argh is not installed. pbuilder-satisfydepends-dummy depends on python3-pyfaidx; however: Package python3-pyfaidx is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-pybedtools; however: Package python3-pybedtools is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bedtools{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libabsl20240722{a} libaom3{a} libarchive-zip-perl{a} libavif16{a} libblas3{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libcurl3t64-gnutls{a} libdav1d7{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgfortran5{a} libglib2.0-0t64{a} libgnutls30t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhts3t64{a} libhtscodecs2{a} libidn2-0{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblcms2-2{a} libldap2{a} liblerc4{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libopenjp2-7{a} libp11-kit0{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libraqm0{a} librav1e0.8{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libssh2-1t64{a} libsvtav1enc2{a} libtasn1-6{a} libtiff6{a} libtool{a} libuchardet0{a} libunistring5{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2-16{a} libxrender1{a} libyuv0{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-all{a} python3-argcomplete{a} python3-argh{a} python3-autocommand{a} python3-biopython{a} python3-cairo{a} python3-charset-normalizer{a} python3-freetype{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-numpy-dev{a} python3-packaging{a} python3-pil{a} python3-pkg-resources{a} python3-pluggy{a} python3-pybedtools{a} python3-pyfaidx{a} python3-pygments{a} python3-pysam{a} python3-pytest{a} python3-reportlab{a} python3-rlpycairo{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} tzdata{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl fonts-dejavu-extra krb5-locales libarchive-cpio-perl libglib2.0-data libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx ncbi-blast+ publicsuffix python-biopython-doc python3-olefile shared-mime-info wget xdg-user-dirs 0 packages upgraded, 155 newly installed, 0 to remove and 0 not upgraded. Need to get 76.9 MB of archives. After unpacking 273 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main arm64 libexpat1 arm64 2.7.3-1 [96.5 kB] Get: 2 http://deb.debian.org/debian forky/main arm64 liblocale-gettext-perl arm64 1.07-7+b1 [15.2 kB] Get: 3 http://deb.debian.org/debian forky/main arm64 libpython3.13-minimal arm64 3.13.9-1 [858 kB] Get: 4 http://deb.debian.org/debian forky/main arm64 python3.13-minimal arm64 3.13.9-1 [2061 kB] Get: 5 http://deb.debian.org/debian forky/main arm64 python3-minimal arm64 3.13.7-1 [27.2 kB] Get: 6 http://deb.debian.org/debian forky/main arm64 media-types all 14.0.0 [30.8 kB] Get: 7 http://deb.debian.org/debian forky/main arm64 netbase all 6.5 [12.4 kB] Get: 8 http://deb.debian.org/debian forky/main arm64 tzdata all 2025b-5 [260 kB] Get: 9 http://deb.debian.org/debian forky/main arm64 libffi8 arm64 3.5.2-2 [21.5 kB] Get: 10 http://deb.debian.org/debian forky/main arm64 readline-common all 8.3-3 [74.8 kB] Get: 11 http://deb.debian.org/debian forky/main arm64 libreadline8t64 arm64 8.3-3 [169 kB] Get: 12 http://deb.debian.org/debian forky/main arm64 libpython3.13-stdlib arm64 3.13.9-1 [1900 kB] Get: 13 http://deb.debian.org/debian forky/main arm64 python3.13 arm64 3.13.9-1 [764 kB] Get: 14 http://deb.debian.org/debian forky/main arm64 libpython3-stdlib arm64 3.13.7-1 [10.2 kB] Get: 15 http://deb.debian.org/debian forky/main arm64 python3 arm64 3.13.7-1 [28.3 kB] Get: 16 http://deb.debian.org/debian forky/main arm64 python3-numpy-dev arm64 1:2.3.3+ds-3 [135 kB] Get: 17 http://deb.debian.org/debian forky/main arm64 libblas3 arm64 3.12.1-7 [135 kB] Get: 18 http://deb.debian.org/debian forky/main arm64 libgfortran5 arm64 15.2.0-7 [371 kB] Get: 19 http://deb.debian.org/debian forky/main arm64 liblapack3 arm64 3.12.1-7 [1846 kB] Get: 20 http://deb.debian.org/debian forky/main arm64 python3-numpy arm64 1:2.3.3+ds-3 [3589 kB] Get: 21 http://deb.debian.org/debian forky/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get: 22 http://deb.debian.org/debian forky/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 23 http://deb.debian.org/debian forky/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 24 http://deb.debian.org/debian forky/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 25 http://deb.debian.org/debian forky/main arm64 gettext-base arm64 0.23.1-2+b1 [241 kB] Get: 26 http://deb.debian.org/debian forky/main arm64 libuchardet0 arm64 0.0.8-2 [69.0 kB] Get: 27 http://deb.debian.org/debian forky/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 28 http://deb.debian.org/debian forky/main arm64 bsdextrautils arm64 2.41.2-4 [97.3 kB] Get: 29 http://deb.debian.org/debian forky/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 30 http://deb.debian.org/debian forky/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 31 http://deb.debian.org/debian forky/main arm64 m4 arm64 1.4.20-2 [315 kB] Get: 32 http://deb.debian.org/debian forky/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 33 http://deb.debian.org/debian forky/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 34 http://deb.debian.org/debian forky/main arm64 automake all 1:1.18.1-2 [877 kB] Get: 35 http://deb.debian.org/debian forky/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 36 http://deb.debian.org/debian forky/main arm64 bedtools arm64 2.31.1+dfsg-2+b1 [601 kB] Get: 37 http://deb.debian.org/debian forky/main arm64 libdebhelper-perl all 13.28 [92.4 kB] Get: 38 http://deb.debian.org/debian forky/main arm64 libtool all 2.5.4-7 [540 kB] Get: 39 http://deb.debian.org/debian forky/main arm64 dh-autoreconf all 21 [12.2 kB] Get: 40 http://deb.debian.org/debian forky/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 41 http://deb.debian.org/debian forky/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 42 http://deb.debian.org/debian forky/main arm64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 43 http://deb.debian.org/debian forky/main arm64 libelf1t64 arm64 0.193-3 [189 kB] Get: 44 http://deb.debian.org/debian forky/main arm64 dwz arm64 0.16-2 [100 kB] Get: 45 http://deb.debian.org/debian forky/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 46 http://deb.debian.org/debian forky/main arm64 libxml2-16 arm64 2.14.6+dfsg-0.1 [601 kB] Get: 47 http://deb.debian.org/debian forky/main arm64 gettext arm64 0.23.1-2+b1 [1612 kB] Get: 48 http://deb.debian.org/debian forky/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 49 http://deb.debian.org/debian forky/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 50 http://deb.debian.org/debian forky/main arm64 debhelper all 13.28 [941 kB] Get: 51 http://deb.debian.org/debian forky/main arm64 dh-python all 6.20250414 [116 kB] Get: 52 http://deb.debian.org/debian forky/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 53 http://deb.debian.org/debian forky/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 54 http://deb.debian.org/debian forky/main arm64 libfontenc1 arm64 1:1.1.8-1+b2 [22.5 kB] Get: 55 http://deb.debian.org/debian forky/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 56 http://deb.debian.org/debian forky/main arm64 libpng16-16t64 arm64 1.6.50-1 [275 kB] Get: 57 http://deb.debian.org/debian forky/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 58 http://deb.debian.org/debian forky/main arm64 x11-common all 1:7.7+26 [217 kB] Get: 59 http://deb.debian.org/debian forky/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 60 http://deb.debian.org/debian forky/main arm64 xfonts-utils arm64 1:7.7+7 [89.3 kB] Get: 61 http://deb.debian.org/debian forky/main arm64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 62 http://deb.debian.org/debian forky/main arm64 fontconfig-config arm64 2.15.0-2.4 [318 kB] Get: 63 http://deb.debian.org/debian forky/main arm64 help2man arm64 1.49.3+b1 [198 kB] Get: 64 http://deb.debian.org/debian forky/main arm64 libabsl20240722 arm64 20240722.0-4 [452 kB] Get: 65 http://deb.debian.org/debian forky/main arm64 libaom3 arm64 3.13.1-2 [1632 kB] Get: 66 http://deb.debian.org/debian forky/main arm64 libdav1d7 arm64 1.5.1-1 [252 kB] Get: 67 http://deb.debian.org/debian forky/main arm64 libgav1-1 arm64 0.19.0-3+b1 [491 kB] Get: 68 http://deb.debian.org/debian forky/main arm64 librav1e0.8 arm64 0.8.1-5 [688 kB] Get: 69 http://deb.debian.org/debian forky/main arm64 libsvtav1enc2 arm64 2.3.0+dfsg-1 [1558 kB] Get: 70 http://deb.debian.org/debian forky/main arm64 libjpeg62-turbo arm64 1:2.1.5-4 [173 kB] Get: 71 http://deb.debian.org/debian forky/main arm64 libyuv0 arm64 0.0.1919.20250919-1 [138 kB] Get: 72 http://deb.debian.org/debian forky/main arm64 libavif16 arm64 1.3.0-1+b1 [127 kB] Get: 73 http://deb.debian.org/debian forky/main arm64 libfontconfig1 arm64 2.15.0-2.4 [387 kB] Get: 74 http://deb.debian.org/debian forky/main arm64 libpixman-1-0 arm64 0.46.4-1 [174 kB] Get: 75 http://deb.debian.org/debian forky/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 76 http://deb.debian.org/debian forky/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 77 http://deb.debian.org/debian forky/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 78 http://deb.debian.org/debian forky/main arm64 libx11-data all 2:1.8.12-1 [343 kB] Get: 79 http://deb.debian.org/debian forky/main arm64 libx11-6 arm64 2:1.8.12-1 [795 kB] Get: 80 http://deb.debian.org/debian forky/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 81 http://deb.debian.org/debian forky/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 82 http://deb.debian.org/debian forky/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB] Get: 83 http://deb.debian.org/debian forky/main arm64 libxrender1 arm64 1:0.9.12-1 [27.0 kB] Get: 84 http://deb.debian.org/debian forky/main arm64 libcairo2 arm64 1.18.4-1+b1 [483 kB] Get: 85 http://deb.debian.org/debian forky/main arm64 libcom-err2 arm64 1.47.2-3+b3 [24.9 kB] Get: 86 http://deb.debian.org/debian forky/main arm64 libnghttp3-9 arm64 1.12.0-1 [63.6 kB] Get: 87 http://deb.debian.org/debian forky/main arm64 libngtcp2-16 arm64 1.16.0-1 [123 kB] Get: 88 http://deb.debian.org/debian forky/main arm64 libidn2-0 arm64 2.3.8-4 [108 kB] Get: 89 http://deb.debian.org/debian forky/main arm64 libp11-kit0 arm64 0.25.9-2 [420 kB] Get: 90 http://deb.debian.org/debian forky/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 91 http://deb.debian.org/debian forky/main arm64 libgnutls30t64 arm64 3.8.10-3 [1384 kB] Get: 92 http://deb.debian.org/debian forky/main arm64 libkrb5support0 arm64 1.21.3-5 [32.4 kB] Get: 93 http://deb.debian.org/debian forky/main arm64 libk5crypto3 arm64 1.21.3-5 [81.2 kB] Get: 94 http://deb.debian.org/debian forky/main arm64 libkeyutils1 arm64 1.6.3-6 [9716 B] Get: 95 http://deb.debian.org/debian forky/main arm64 libkrb5-3 arm64 1.21.3-5 [308 kB] Get: 96 http://deb.debian.org/debian forky/main arm64 libgssapi-krb5-2 arm64 1.21.3-5 [127 kB] Get: 97 http://deb.debian.org/debian forky/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-10 [19.8 kB] Get: 98 http://deb.debian.org/debian forky/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-10 [55.0 kB] Get: 99 http://deb.debian.org/debian forky/main arm64 libldap2 arm64 2.6.10+dfsg-1 [179 kB] Get: 100 http://deb.debian.org/debian forky/main arm64 libnghttp2-14 arm64 1.64.0-1.1+b1 [71.7 kB] Get: 101 http://deb.debian.org/debian forky/main arm64 libngtcp2-crypto-gnutls8 arm64 1.16.0-1 [23.8 kB] Get: 102 http://deb.debian.org/debian forky/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 103 http://deb.debian.org/debian forky/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-3 [56.3 kB] Get: 104 http://deb.debian.org/debian forky/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 105 http://deb.debian.org/debian forky/main arm64 libcurl3t64-gnutls arm64 8.17.0~rc3-1 [362 kB] Get: 106 http://deb.debian.org/debian forky/main arm64 libdeflate0 arm64 1.23-2 [42.4 kB] Get: 107 http://deb.debian.org/debian forky/main arm64 libfribidi0 arm64 1.0.16-3 [26.5 kB] Get: 108 http://deb.debian.org/debian forky/main arm64 libglib2.0-0t64 arm64 2.86.1-1 [1436 kB] Get: 109 http://deb.debian.org/debian forky/main arm64 libgraphite2-3 arm64 1.3.14-11 [70.8 kB] Get: 110 http://deb.debian.org/debian forky/main arm64 libharfbuzz0b arm64 12.1.0-1 [486 kB] Get: 111 http://deb.debian.org/debian forky/main arm64 libhtscodecs2 arm64 1.6.1-2 [74.7 kB] Get: 112 http://deb.debian.org/debian forky/main arm64 libhts3t64 arm64 1.22.1+ds2-1 [434 kB] Get: 113 http://deb.debian.org/debian forky/main arm64 libimagequant0 arm64 4.4.0-3 [216 kB] Get: 114 http://deb.debian.org/debian forky/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 115 http://deb.debian.org/debian forky/main arm64 liblcms2-2 arm64 2.16-2 [151 kB] Get: 116 http://deb.debian.org/debian forky/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 117 http://deb.debian.org/debian forky/main arm64 libopenjp2-7 arm64 2.5.3-2.1 [189 kB] Get: 118 http://deb.debian.org/debian forky/main arm64 libraqm0 arm64 0.10.3-1 [13.6 kB] Get: 119 http://deb.debian.org/debian forky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [114 kB] Get: 120 http://deb.debian.org/debian forky/main arm64 libwebp7 arm64 1.5.0-0.1 [271 kB] Get: 121 http://deb.debian.org/debian forky/main arm64 libtiff6 arm64 4.7.1-1 [334 kB] Get: 122 http://deb.debian.org/debian forky/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [113 kB] Get: 123 http://deb.debian.org/debian forky/main arm64 libwebpmux3 arm64 1.5.0-0.1 [125 kB] Get: 124 http://deb.debian.org/debian forky/main arm64 python3-all arm64 3.13.7-1 [1044 B] Get: 125 http://deb.debian.org/debian forky/main arm64 python3-argcomplete all 3.6.2-1 [40.9 kB] Get: 126 http://deb.debian.org/debian forky/main arm64 python3-argh all 0.31.3-1 [26.6 kB] Get: 127 http://deb.debian.org/debian forky/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 128 http://deb.debian.org/debian forky/main arm64 python3-charset-normalizer arm64 3.4.3-1 [123 kB] Get: 129 http://deb.debian.org/debian forky/main arm64 python3-pil arm64 11.3.0-1 [507 kB] Get: 130 http://deb.debian.org/debian forky/main arm64 python3-cairo arm64 1.27.0-2 [114 kB] Get: 131 http://deb.debian.org/debian forky/main arm64 python3-freetype all 2.5.1-2 [89.4 kB] Get: 132 http://deb.debian.org/debian forky/main arm64 python3-rlpycairo all 0.3.0-4 [10.1 kB] Get: 133 http://deb.debian.org/debian forky/main arm64 python3-reportlab all 4.4.4-2 [1170 kB] Get: 134 http://deb.debian.org/debian forky/main arm64 sgml-base all 1.31+nmu1 [10.9 kB] Get: 135 http://deb.debian.org/debian forky/main arm64 xml-core all 0.19 [20.1 kB] Get: 136 http://deb.debian.org/debian forky/main arm64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 137 http://deb.debian.org/debian forky/main arm64 python3-biopython arm64 1.86+dfsg-1 [1598 kB] Get: 138 http://deb.debian.org/debian forky/main arm64 python3-more-itertools all 10.8.0-1 [71.7 kB] Get: 139 http://deb.debian.org/debian forky/main arm64 python3-typing-extensions all 4.15.0-1 [92.4 kB] Get: 140 http://deb.debian.org/debian forky/main arm64 python3-typeguard all 4.4.4-1 [37.1 kB] Get: 141 http://deb.debian.org/debian forky/main arm64 python3-inflect all 7.5.0-1 [33.0 kB] Get: 142 http://deb.debian.org/debian forky/main arm64 python3-iniconfig all 2.1.0-1 [7432 B] Get: 143 http://deb.debian.org/debian forky/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 144 http://deb.debian.org/debian forky/main arm64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 145 http://deb.debian.org/debian forky/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 146 http://deb.debian.org/debian forky/main arm64 python3-zipp all 3.23.0-1 [11.0 kB] Get: 147 http://deb.debian.org/debian forky/main arm64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 148 http://deb.debian.org/debian forky/main arm64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 149 http://deb.debian.org/debian forky/main arm64 python3-packaging all 25.0-1 [56.6 kB] Get: 150 http://deb.debian.org/debian forky/main arm64 python3-pluggy all 1.6.0-1 [27.1 kB] Get: 151 http://deb.debian.org/debian forky/main arm64 python3-pysam arm64 0.23.0+ds-1+b1 [3417 kB] Get: 152 http://deb.debian.org/debian forky/main arm64 python3-pybedtools arm64 0.10.0-5 [12.1 MB] Get: 153 http://deb.debian.org/debian forky/main arm64 python3-pyfaidx all 0.8.1.3-2 [29.1 kB] Get: 154 http://deb.debian.org/debian forky/main arm64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get: 155 http://deb.debian.org/debian forky/main arm64 python3-pytest all 8.4.2-1 [266 kB] Fetched 76.9 MB in 0s (230 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19964 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.3-1_arm64.deb ... Unpacking libexpat1:arm64 (2.7.3-1) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../liblocale-gettext-perl_1.07-7+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... 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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.9-1_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.9-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.9-1_arm64.deb ... Unpacking python3.13 (3.13.9-1) ... 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Unpacking python3-pytest (8.4.2-1) ... Setting up libhtscodecs2:arm64 (1.6.1-2) ... Setting up media-types (14.0.0) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libgraphite2-3:arm64 (1.3.14-11) ... Setting up liblcms2-2:arm64 (2.16-2) ... Setting up libpixman-1-0:arm64 (0.46.4-1) ... Setting up libsharpyuv0:arm64 (1.5.0-0.1) ... Setting up libaom3:arm64 (3.13.1-2) ... Setting up libxau6:arm64 (1:1.0.11-1) ... Setting up libxdmcp6:arm64 (1:1.1.5-1) ... Setting up libkeyutils1:arm64 (1.6.3-6) ... Setting up libxcb1:arm64 (1.17.0-2+b1) ... Setting up liblerc4:arm64 (4.0.0+ds-5) ... Setting up bsdextrautils (2.41.2-4) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libxcb-render0:arm64 (1.17.0-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:arm64 (2.14.6+dfsg-0.1) ... Setting up libdebhelper-perl (13.28) ... Setting up libbrotli1:arm64 (1.1.0-2+b7) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up x11-common (1:7.7+26) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libnghttp2-14:arm64 (1.64.0-1.1+b1) ... Setting up libdeflate0:arm64 (1.23-2) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-2) ... Setting up libxcb-shm0:arm64 (1.17.0-2+b1) ... Setting up libcom-err2:arm64 (1.47.2-3+b3) ... Setting up file (1:5.46-5) ... Setting up libabsl20240722:arm64 (20240722.0-4) ... Setting up libjbig0:arm64 (2.1-6.1+b2) ... Setting up libelf1t64:arm64 (0.193-3) ... Setting up libkrb5support0:arm64 (1.21.3-5) ... Setting up librav1e0.8:arm64 (0.8.1-5) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-10) ... Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Dec 4 20:33:27 UTC 2026. Universal Time is now: Fri Dec 4 20:33:27 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:arm64 (1:1.1.8-1+b2) ... Setting up autotools-dev (20240727.1) ... Setting up libblas3:arm64 (3.12.1-7) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libjpeg62-turbo:arm64 (1:2.1.5-4) ... Setting up libx11-data (2:1.8.12-1) ... Setting up libsvtav1enc2:arm64 (2.3.0+dfsg-1) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:arm64 (1.0.16-3) ... Setting up libimagequant0:arm64 (4.4.0-3) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:arm64 (1.6.50-1) ... Setting up python3-numpy-dev:arm64 (1:2.3.3+ds-3) ... Setting up autopoint (0.23.1-2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libgav1-1:arm64 (0.19.0-3+b1) ... Setting up libk5crypto3:arm64 (1.21.3-5) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-10) ... Setting up libgfortran5:arm64 (15.2.0-7) ... Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:arm64 (1.12.0-1) ... Setting up libwebp7:arm64 (1.5.0-0.1) ... Setting up libffi8:arm64 (3.5.2-2) ... Setting up dwz (0.16-2) ... Setting up libdav1d7:arm64 (1.5.1-1) ... Setting up sensible-utils (0.0.26) ... Setting up libtiff6:arm64 (4.7.1-1) ... Setting up libuchardet0:arm64 (0.0.8-2) ... Setting up libtasn1-6:arm64 (4.20.0-2) ... Setting up libopenjp2-7:arm64 (2.5.3-2.1) ... Setting up libx11-6:arm64 (2:1.8.12-1) ... Setting up netbase (6.5) ... Setting up libngtcp2-16:arm64 (1.16.0-1) ... Setting up sgml-base (1.31+nmu1) ... Setting up libkrb5-3:arm64 (1.21.3-5) ... Setting up libssh2-1t64:arm64 (1.11.1-1) ... Setting up libwebpmux3:arm64 (1.5.0-0.1) ... Setting up libyuv0:arm64 (0.0.1919.20250919-1) ... Setting up readline-common (8.3-3) ... Setting up bedtools (2.31.1+dfsg-2+b1) ... Setting up libldap2:arm64 (2.6.10+dfsg-1) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up automake (1:1.18.1-2) ... update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up libavif16:arm64 (1.3.0-1+b1) ... Setting up liblapack3:arm64 (3.12.1-7) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.23.1-2+b1) ... Setting up libxrender1:arm64 (1:0.9.12-1) ... Setting up libtool (2.5.4-7) ... Setting up fontconfig-config (2.15.0-2.4) ... Setting up libwebpdemux2:arm64 (1.5.0-0.1) ... Setting up libxext6:arm64 (2:1.3.4-1+b3) ... Setting up libidn2-0:arm64 (2.3.8-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3+b1) ... Setting up dh-autoreconf (21) ... Setting up libglib2.0-0t64:arm64 (2.86.1-1) ... No schema files found: doing nothing. Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up libp11-kit0:arm64 (0.25.9-2) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-5) ... Setting up libreadline8t64:arm64 (8.3-3) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up xml-core (0.19) ... Setting up libharfbuzz0b:arm64 (12.1.0-1) ... Setting up libfontconfig1:arm64 (2.15.0-2.4) ... Setting up libpython3.13-stdlib:arm64 (3.13.9-1) ... Setting up libpython3-stdlib:arm64 (3.13.7-1) ... Setting up libgnutls30t64:arm64 (3.8.10-3) ... Setting up python3.13 (3.13.9-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:arm64 (0.21.2-1.1+b1) ... Setting up python3 (3.13.7-1) ... Setting up python3-zipp (3.23.0-1) ... Setting up python3-freetype (2.5.1-2) ... Setting up xfonts-utils (1:7.7+7) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:arm64 (1.18.4-1+b1) ... Setting up python3-pygments (2.18.0+dfsg-2) ... Setting up python3-packaging (25.0-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libraqm0:arm64 (0.10.3-1) ... Setting up python3-typing-extensions (4.15.0-1) ... Setting up python3-numpy (1:2.3.3+ds-3) ... Setting up python3-pluggy (1.6.0-1) ... Setting up python3-argcomplete (3.6.2-1) ... Setting up libngtcp2-crypto-gnutls8:arm64 (1.16.0-1) ... Setting up dh-python (6.20250414) ... Setting up python3-more-itertools (10.8.0-1) ... Setting up python3-pyfaidx (0.8.1.3-2) ... Setting up python3-iniconfig (2.1.0-1) ... Setting up python3-argh (0.31.3-1) ... Setting up python3-cairo (1.27.0-2) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up python3-charset-normalizer (3.4.3-1) ... Setting up python3-pytest (8.4.2-1) ... Setting up python3-typeguard (4.4.4-1) ... Setting up libcurl3t64-gnutls:arm64 (8.17.0~rc3-1) ... Setting up python3-all (3.13.7-1) ... Setting up debhelper (13.28) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up python3-pil:arm64 (11.3.0-1) ... Setting up python3-inflect (7.5.0-1) ... Setting up python3-rlpycairo (0.3.0-4) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-reportlab (4.4.4-2) ... Setting up libhts3t64:arm64 (1.22.1+ds2-1) ... Setting up python3-pkg-resources (78.1.1-0.1) ... Setting up python3-pysam (0.23.0+ds-1+b1) ... Setting up python3-setuptools (78.1.1-0.1) ... Setting up python3-pybedtools (0.10.0-5) ... Processing triggers for libc-bin (2.41-12) ... Processing triggers for sgml-base (1.31+nmu1) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.86+dfsg-1) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.37.1.2-1). Solving dependencies... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/3374847/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for forky I: user script /srv/workspace/pbuilder/3374847/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/python-gffutils-0.13/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../python-gffutils_0.13-3_source.changes dpkg-buildpackage: info: source package python-gffutils dpkg-buildpackage: info: source version 0.13-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Alexandre Detiste dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py clean /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running clean removing '/build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build' (and everything under it) 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.13' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py config /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/python-gffutils-0.13' dh_auto_build I: pybuild base:311: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running build running build_py creating /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/helpers.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/feature.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/version.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/pybedtools_integration.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/parser.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/merge_criteria.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/iterators.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/interface.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/inspect.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/gffwriter.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/exceptions.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/create.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/convert.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/constants.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/biopython_integration.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/bins.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/attributes.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils copying gffutils/__init__.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils creating /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/scripts copying gffutils/scripts/gffutils-flybase-convert.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/scripts creating /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/test_1.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/test_merge_all.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/test_merge.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/test_iterators.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/test_issues.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/test_cli.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/test_biopython_integration.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/synth_test_base.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/performance_evaluation.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/parser_test.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/helpers_test.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/feature_test.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/expected.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/conftest.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/attr_test_cases.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test copying gffutils/test/__init__.py -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test creating /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/wormbase_gff2_alt.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/wormbase_gff2.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/unsanitized.gff -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/synthetic.gff3 -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/sharr.gtf -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/random-chr.gff -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/nonascii -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/ncbi_gff3.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/mouse_extra_comma.gff3 -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/keyval_sep_in_attrs.gff -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/keep-order-test.gtf -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/jgi_gff2.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/issue_197.gff -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/issue174.gtf -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/issue167.gff -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/intro_docs_example.gff -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/hybrid1.gff3 -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/gms2_example.gff3 -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/glimmer_nokeyval.gff3 -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/gff_example1.gff3.gz -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/gff_example1.gff3 -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/gencode.vM8.chromsizes.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/gencode.vM8.5000_transcript_ids.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/gencode.vM8.5000_gene_ids.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/gencode-v19.gtf -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/ensembl_gtf.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/download-large-annotation-files.sh -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/dmel-all-no-analysis-r5.49_50k_lines.gff -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/dm6-chr2L.fa.fai -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/dm6-chr2L.fa -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/c_elegans_WS199_shortened_gff.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/c_elegans_WS199_dna_shortened.fa -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/c_elegans_WS199_ann_gff.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.chromsizes.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.5000_transcript_ids.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.5000_gene_ids.txt -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/FBgn0031208.gtf.db -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/FBgn0031208.gtf -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/FBgn0031208.gff -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data copying gffutils/test/data/F3-unique-3.v2.gff -> /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data running build_scripts creating build/scripts-3.13 copying and adjusting gffutils/scripts/gffutils-cli -> build/scripts-3.13 changing mode of build/scripts-3.13/gffutils-cli from 644 to 755 PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path \ help2man --version-string=0.13 --no-info \ --name="Command line interface for python-gffutils." \ gffutils-cli > debian/gffutils-cli.1 PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path \ help2man --version-string=0.13 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_fetch \- Fetch IDs") \ 'gffutils-cli fetch' > debian/gffutils-cli-fetch.1 PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path \ help2man --version-string=0.13 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_children \- Fetch children from the database according to ID") \ 'gffutils-cli children' > debian/gffutils-cli-children.1 PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path \ help2man --version-string=0.13 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_parents \- Fetch parents from the database according to ID") \ 'gffutils-cli parents' > debian/gffutils-cli-parents.1 PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path \ help2man --version-string=0.13 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_region \- Returns features within provided genomic coordinates") \ 'gffutils-cli region' > debian/gffutils-cli-region.1 PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path \ help2man --version-string=0.13 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_create \- Create a database") \ 'gffutils-cli create' > debian/gffutils-cli-create.1 PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path \ help2man --version-string=0.13 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_common \- Identify child features in common") \ 'gffutils-cli common' > debian/gffutils-cli-common.1 PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path \ help2man --version-string=0.13 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_clean \- Perform various QC operations to clean a GFF or GTF file") \ 'gffutils-cli clean' > debian/gffutils-cli-clean.1 PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path \ help2man --version-string=0.13 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_sanitize \- Sanitize a GFF file") \ 'gffutils-cli sanitize' > debian/gffutils-cli-sanitize.1 PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path \ help2man --version-string=0.13 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_rmdups \- Remove duplicates from a GFF file") \ 'gffutils-cli rmdups' > debian/gffutils-cli-rmdups.1 make[1]: Leaving directory '/build/reproducible-path/python-gffutils-0.13' dh: command-omitted: The call to "debian/rules override_dh_auto_test" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/python3-gffutils/ -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running build_scripts running install_lib creating /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages creating /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils creating /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test creating /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/F3-unique-3.v2.gff -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/FBgn0031208.gff -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/FBgn0031208.gtf -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/FBgn0031208.gtf.db -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.5000_gene_ids.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.5000_transcript_ids.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.chromsizes.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/c_elegans_WS199_ann_gff.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/c_elegans_WS199_dna_shortened.fa -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/c_elegans_WS199_shortened_gff.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/dm6-chr2L.fa -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/dm6-chr2L.fa.fai -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/dmel-all-no-analysis-r5.49_50k_lines.gff -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/download-large-annotation-files.sh -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/ensembl_gtf.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/gencode-v19.gtf -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/gencode.vM8.5000_gene_ids.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/gencode.vM8.5000_transcript_ids.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/gencode.vM8.chromsizes.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/gff_example1.gff3 -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/gff_example1.gff3.gz -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/glimmer_nokeyval.gff3 -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/gms2_example.gff3 -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/hybrid1.gff3 -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/intro_docs_example.gff -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/issue167.gff -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/issue174.gtf -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/issue_197.gff -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/jgi_gff2.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/keep-order-test.gtf -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/keyval_sep_in_attrs.gff -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/mouse_extra_comma.gff3 -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/ncbi_gff3.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/nonascii -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/random-chr.gff -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/sharr.gtf -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/synthetic.gff3 -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/unsanitized.gff -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/wormbase_gff2.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/wormbase_gff2_alt.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__init__.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/attr_test_cases.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/conftest.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/expected.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/feature_test.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/helpers_test.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/parser_test.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/performance_evaluation.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/synth_test_base.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/test_biopython_integration.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/test_cli.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/test_issues.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/test_iterators.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/test_merge.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/test_merge_all.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/test_1.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test creating /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/scripts copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/scripts/gffutils-flybase-convert.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/scripts copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__init__.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/attributes.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/bins.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/biopython_integration.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/constants.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/convert.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/create.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/exceptions.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/gffwriter.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/inspect.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/interface.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/iterators.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/merge_criteria.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/parser.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/pybedtools_integration.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/version.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/feature.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/helpers.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/attr_test_cases.py to attr_test_cases.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/conftest.py to conftest.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/expected.py to expected.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/feature_test.py to feature_test.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/helpers_test.py to helpers_test.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/parser_test.py to parser_test.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/performance_evaluation.py to performance_evaluation.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/synth_test_base.py to synth_test_base.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/test_biopython_integration.py to test_biopython_integration.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/test_cli.py to test_cli.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/test_issues.py to test_issues.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/test_iterators.py to test_iterators.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/test_merge.py to test_merge.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/test_merge_all.py to test_merge_all.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/test_1.py to test_1.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/scripts/gffutils-flybase-convert.py to gffutils-flybase-convert.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/attributes.py to attributes.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/bins.py to bins.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/biopython_integration.py to biopython_integration.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/constants.py to constants.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/convert.py to convert.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/create.py to create.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/exceptions.py to exceptions.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/gffwriter.py to gffwriter.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/inspect.py to inspect.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/interface.py to interface.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/iterators.py to iterators.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/merge_criteria.py to merge_criteria.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/parser.py to parser.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/pybedtools_integration.py to pybedtools_integration.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/version.py to version.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/feature.py to feature.cpython-313.pyc byte-compiling /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/helpers.py to helpers.cpython-313.pyc running install_egg_info running egg_info creating gffutils.egg-info writing gffutils.egg-info/PKG-INFO writing dependency_links to gffutils.egg-info/dependency_links.txt writing requirements to gffutils.egg-info/requires.txt writing top-level names to gffutils.egg-info/top_level.txt writing manifest file 'gffutils.egg-info/SOURCES.txt' reading manifest file 'gffutils.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*.rst' under directory 'docs/source' warning: no files found matching '*.py' under directory 'docs/source' warning: no files found matching '*' under directory 'docs/source/images' warning: no files found matching 'docs/Makefile' warning: no files found matching 'docs/make.bat' warning: no files found matching 'gffutils/test/data/__init__.py' warning: no files found matching 'gffutils/test/data/t.py' adding license file 'LICENSE' writing manifest file 'gffutils.egg-info/SOURCES.txt' Copying gffutils.egg-info to /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils-0.13.egg-info Skipping SOURCES.txt running install_scripts creating /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/bin copying build/scripts-3.13/gffutils-cli -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/bin changing mode of /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/bin/gffutils-cli to 755 debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/python-gffutils-0.13' dh_install find debian -name "*.bak" -delete find debian -name "issue_*.db" -delete make[1]: Leaving directory '/build/reproducible-path/python-gffutils-0.13' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild I: dh_python3 tools:114: replacing shebang in debian/python3-gffutils/usr/bin/gffutils-cli 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_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-gffutils' in '../python3-gffutils_0.13-3_all.deb'. dpkg-genbuildinfo --build=binary -O../python-gffutils_0.13-3_arm64.buildinfo dpkg-genchanges --build=binary -O../python-gffutils_0.13-3_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3374847/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3374847/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3374847 and its subdirectories I: Current time: Sat Dec 5 10:34:59 +14 2026 I: pbuilder-time-stamp: 1796416499 + false + set +x Fri Dec 4 20:34:59 UTC 2026 I: Signing ./b2/python-gffutils_0.13-3_arm64.buildinfo as python-gffutils_0.13-3_arm64.buildinfo.asc Fri Dec 4 20:34:59 UTC 2026 I: Signed ./b2/python-gffutils_0.13-3_arm64.buildinfo as ./b2/python-gffutils_0.13-3_arm64.buildinfo.asc Fri Dec 4 20:34:59 UTC 2026 - build #2 for python-gffutils/forky/arm64 on codethink03-arm64 done. Starting cleanup. All cleanup done. Fri Dec 4 20:34:59 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-vkwBF0tZ, removing. /srv/reproducible-results/rbuild-debian/r-b-build.p5Ol6mnr: total 144 drwxrwxr-x 2 jenkins jenkins 4096 Nov 1 14:10 b1 drwxrwxr-x 2 jenkins jenkins 4096 Nov 1 14:11 b2 -rw-rw-r-- 1 jenkins jenkins 2331 Aug 23 17:27 python-gffutils_0.13-3.dsc -rw------- 1 jenkins jenkins 128082 Nov 1 14:10 rbuildlog.kdDUpWp /srv/reproducible-results/rbuild-debian/r-b-build.p5Ol6mnr/b1: total 1196 -rw-r--r-- 1 jenkins jenkins 124294 Nov 1 14:10 build.log -rw-r--r-- 1 jenkins jenkins 5460 Nov 1 14:10 python-gffutils_0.13-3.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2331 Nov 1 14:10 python-gffutils_0.13-3.dsc -rw-r--r-- 1 jenkins jenkins 8404 Nov 1 14:10 python-gffutils_0.13-3_arm64.buildinfo -rw-rw-r-- 1 jenkins jenkins 9286 Nov 1 14:10 python-gffutils_0.13-3_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1137 Nov 1 14:10 python-gffutils_0.13-3_arm64.changes -rw-r--r-- 1 jenkins jenkins 1282 Nov 1 14:10 python-gffutils_0.13-3_source.changes -rw-r--r-- 1 jenkins jenkins 1040840 Nov 1 14:10 python3-gffutils_0.13-3_all.deb /srv/reproducible-results/rbuild-debian/r-b-build.p5Ol6mnr/b2: total 1176 -rw-rw-r-- 1 jenkins jenkins 111853 Nov 1 14:11 build.log -rw-r--r-- 1 jenkins jenkins 5460 Nov 1 14:11 python-gffutils_0.13-3.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2331 Nov 1 14:11 python-gffutils_0.13-3.dsc -rw-rw-r-- 1 jenkins jenkins 8412 Nov 1 14:11 python-gffutils_0.13-3_arm64.buildinfo -rw-rw-r-- 1 jenkins jenkins 9294 Nov 1 14:11 python-gffutils_0.13-3_arm64.buildinfo.asc -rw-rw-r-- 1 jenkins jenkins 1137 Nov 1 14:11 python-gffutils_0.13-3_arm64.changes -rw-rw-r-- 1 jenkins jenkins 1282 Nov 1 14:11 python-gffutils_0.13-3_source.changes -rw-r--r-- 1 jenkins jenkins 1040620 Nov 1 14:11 python3-gffutils_0.13-3_all.deb Sat Nov 1 14:11:59 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Sat Nov 1 14:12:00 UTC 2025 I: python-gffutils_0.13-3_arm64.changes: Format: 1.8 Date: Sat, 23 Aug 2025 18:55:58 +0200 Source: python-gffutils Binary: python3-gffutils Architecture: all Version: 0.13-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Alexandre Detiste Description: python3-gffutils - Work with GFF and GTF files in a flexible database framework Changes: python-gffutils (0.13-3) unstable; urgency=medium . * Team upload. * Patch test for Pytest 8.4 compatibility Checksums-Sha1: 64d9367e3ca00310979832d26794fb21a22aa075 8404 python-gffutils_0.13-3_arm64.buildinfo 4e5ec15d5e30c0102578ae2bf44da82412cd3d4b 1040840 python3-gffutils_0.13-3_all.deb Checksums-Sha256: b2e7dbfbab778d1e311babe9130f1df574bbcbe3590845133bd4cf65d71b001b 8404 python-gffutils_0.13-3_arm64.buildinfo dd1a3b32420a5d7b6406cda300438195ca24c5cf1770aa1d97b7b14a78f894a8 1040840 python3-gffutils_0.13-3_all.deb Files: 32c270cdd319b6fcf6837f1ae00e37db 8404 science optional python-gffutils_0.13-3_arm64.buildinfo 6e16ba9f0c06f427420dd8f2ac88f2d6 1040840 science optional python3-gffutils_0.13-3_all.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/forky/arm64/python-gffutils_0.13-3.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/forky/arm64/python-gffutils_0.13-3.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/forky/arm64/python-gffutils_0.13-3.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/forky/arm64/python-gffutils_0.13-3.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/forky/arm64/python-gffutils_0.13-3_arm64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/forky/arm64/python-gffutils_0.13-3.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-11-01 14:10:02.976881775 +0000 +++ b2/build.log 2025-11-01 14:11:59.476992034 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Nov 1 02:08:36 -12 2025 -I: pbuilder-time-stamp: 1762006116 +I: Current time: Sat Dec 5 10:33:05 +14 2026 +I: pbuilder-time-stamp: 1796416385 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -27,53 +27,85 @@ dpkg-source: info: applying pytest8.4.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1698365/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3374847/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Dec 4 20:33 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3374847/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3374847/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='arm64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 nocheck' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='3ba4072e2ae845ec8735b330ca0151fd' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='1698365' - PS1='# ' - PS2='> ' + INVOCATION_ID=a80bd8c36a8342b5abbe2fa860f368f4 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3374847 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.p5Ol6mnr/pbuilderrc_VXr4 --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.p5Ol6mnr/b1 --logfile b1/build.log python-gffutils_0.13-3.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.p5Ol6mnr/pbuilderrc_0XXy --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.p5Ol6mnr/b2 --logfile b2/build.log python-gffutils_0.13-3.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1698365/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3374847/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -86,7 +118,7 @@ Depends: debhelper-compat (= 13), dh-sequence-python3, bedtools, python3-all, python3-setuptools, python3-argcomplete, python3-argh, python3-pyfaidx, python3-pytest, python3-biopython, python3-pybedtools, help2man dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. -(Reading database ... 19971 files and directories currently installed.) +(Reading database ... 19964 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: @@ -286,10 +318,10 @@ Get: 153 http://deb.debian.org/debian forky/main arm64 python3-pyfaidx all 0.8.1.3-2 [29.1 kB] Get: 154 http://deb.debian.org/debian forky/main arm64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get: 155 http://deb.debian.org/debian forky/main arm64 python3-pytest all 8.4.2-1 [266 kB] -Fetched 76.9 MB in 1s (139 MB/s) +Fetched 76.9 MB in 0s (230 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:arm64. -(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19971 files and directories currently installed.) +(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19964 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.3-1_arm64.deb ... Unpacking libexpat1:arm64 (2.7.3-1) ... Selecting previously unselected package liblocale-gettext-perl. @@ -305,7 +337,7 @@ Setting up libexpat1:arm64 (2.7.3-1) ... Setting up python3.13-minimal (3.13.9-1) ... Selecting previously unselected package python3-minimal. -(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20320 files and directories currently installed.) +(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20313 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.7-1_arm64.deb ... Unpacking python3-minimal (3.13.7-1) ... Selecting previously unselected package media-types. @@ -341,7 +373,7 @@ Unpacking libpython3-stdlib:arm64 (3.13.7-1) ... Setting up python3-minimal (3.13.7-1) ... Selecting previously unselected package python3. -(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21335 files and directories currently installed.) +(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21328 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.7-1_arm64.deb ... Unpacking python3 (3.13.7-1) ... Selecting previously unselected package python3-numpy-dev:arm64. @@ -804,8 +836,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat Nov 1 14:08:55 UTC 2025. -Universal Time is now: Sat Nov 1 14:08:55 UTC 2025. +Local time is now: Fri Dec 4 20:33:27 UTC 2026. +Universal Time is now: Fri Dec 4 20:33:27 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:arm64 (1:1.1.8-1+b2) ... @@ -945,7 +977,11 @@ Solving dependencies... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/reproducible-path/python-gffutils-0.13/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../python-gffutils_0.13-3_source.changes +I: user script /srv/workspace/pbuilder/3374847/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/3374847/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/python-gffutils-0.13/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../python-gffutils_0.13-3_source.changes dpkg-buildpackage: info: source package python-gffutils dpkg-buildpackage: info: source version 0.13-3 dpkg-buildpackage: info: source distribution unstable @@ -1097,99 +1133,48 @@ creating build/scripts-3.13 copying and adjusting gffutils/scripts/gffutils-cli -> build/scripts-3.13 changing mode of build/scripts-3.13/gffutils-cli from 644 to 755 -PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ +PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path \ help2man --version-string=0.13 --no-info \ --name="Command line interface for python-gffutils." \ gffutils-cli > debian/gffutils-cli.1 -PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ +PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path \ help2man --version-string=0.13 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_fetch \- Fetch IDs") \ 'gffutils-cli fetch' > debian/gffutils-cli-fetch.1 -PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ +PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path \ help2man --version-string=0.13 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_children \- Fetch children from the database according to ID") \ 'gffutils-cli children' > debian/gffutils-cli-children.1 -PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ +PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path \ help2man --version-string=0.13 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_parents \- Fetch parents from the database according to ID") \ 'gffutils-cli parents' > debian/gffutils-cli-parents.1 -PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ +PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path \ help2man --version-string=0.13 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_region \- Returns features within provided genomic coordinates") \ 'gffutils-cli region' > debian/gffutils-cli-region.1 -PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ +PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path \ help2man --version-string=0.13 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_create \- Create a database") \ 'gffutils-cli create' > debian/gffutils-cli-create.1 -PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ +PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path \ help2man --version-string=0.13 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_common \- Identify child features in common") \ 'gffutils-cli common' > debian/gffutils-cli-common.1 -PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ +PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path \ help2man --version-string=0.13 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_clean \- Perform various QC operations to clean a GFF or GTF file") \ 'gffutils-cli clean' > debian/gffutils-cli-clean.1 -PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ +PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path \ help2man --version-string=0.13 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_sanitize \- Sanitize a GFF file") \ 'gffutils-cli sanitize' > debian/gffutils-cli-sanitize.1 -PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ +PYTHONPATH=/build/reproducible-path/python-gffutils-0.13 PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path \ help2man --version-string=0.13 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_rmdups \- Remove duplicates from a GFF file") \ 'gffutils-cli rmdups' > debian/gffutils-cli-rmdups.1 make[1]: Leaving directory '/build/reproducible-path/python-gffutils-0.13' - debian/rules override_dh_auto_test -make[1]: Entering directory '/build/reproducible-path/python-gffutils-0.13' -PATH=/build/reproducible-path/python-gffutils-0.13/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games dh_auto_test -I: pybuild base:311: cd /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build; python3.13 -m pytest --doctest-modules -m 'not slow' -============================= test session starts ============================== -platform linux -- Python 3.13.9, pytest-8.4.2, pluggy-1.6.0 -rootdir: /build/reproducible-path/python-gffutils-0.13 -plugins: typeguard-4.4.4 -collected 112 items - -gffutils/attributes.py . [ 0%] -gffutils/pybedtools_integration.py . [ 1%] -gffutils/test/feature_test.py ........... [ 11%] -gffutils/test/helpers_test.py .. [ 13%] -gffutils/test/parser_test.py .................. [ 29%] -gffutils/test/test_1.py ......................s........... [ 59%] -gffutils/test/test_biopython_integration.py . [ 60%] -gffutils/test/test_cli.py . [ 61%] -gffutils/test/test_issues.py ........................ [ 83%] -gffutils/test/test_iterators.py .... [ 86%] -gffutils/test/test_merge.py ......... [ 94%] -gffutils/test/test_merge_all.py ...... [100%] - -=============================== warnings summary =============================== -gffutils/test/performance_evaluation.py:190 - /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/performance_evaluation.py:190: PytestUnknownMarkWarning: Unknown pytest.mark.slow - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html - @pytest.mark.slow - -gffutils/test/performance_evaluation.py:208 - /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/performance_evaluation.py:208: PytestUnknownMarkWarning: Unknown pytest.mark.slow - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html - @pytest.mark.slow - -.pybuild/cpython3_3.13_gffutils/build/gffutils/test/parser_test.py::test_parser_from_string - /usr/lib/python3/dist-packages/_pytest/python.py:161: PytestReturnNotNoneWarning: Test functions should return None, but .pybuild/cpython3_3.13_gffutils/build/gffutils/test/parser_test.py::test_parser_from_string returned . - Did you mean to use `assert` instead of `return`? - See https://docs.pytest.org/en/stable/how-to/assert.html#return-not-none for more information. - warnings.warn( - -.pybuild/cpython3_3.13_gffutils/build/gffutils/test/parser_test.py::test_inconsistent_dialect -.pybuild/cpython3_3.13_gffutils/build/gffutils/test/test_1.py::test_disable_infer -.pybuild/cpython3_3.13_gffutils/build/gffutils/test/test_issues.py::test_pr_172 - /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/create.py:770: UserWarning: It appears you have a gene feature in your GTF file. You may want to use the `disable_infer_genes=True` option to speed up database creation - warnings.warn( - -.pybuild/cpython3_3.13_gffutils/build/gffutils/test/test_1.py::test_disable_infer - /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/create.py:763: UserWarning: It appears you have a transcript feature in your GTF file. You may want to use the `disable_infer_transcripts=True` option to speed up database creation - warnings.warn( - --- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -================== 111 passed, 1 skipped, 7 warnings in 1.98s ================== -I: pybuild pybuild:334: find . -name tmp.db -delete -make[1]: Leaving directory '/build/reproducible-path/python-gffutils-0.13' +dh: command-omitted: The call to "debian/rules override_dh_auto_test" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild @@ -1227,51 +1212,13 @@ running build_scripts running install_lib creating /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/issue_213.db -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/tmp.db.bak -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages creating /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils -creating /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/pybedtools_integration.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/inspect.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/convert.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/biopython_integration.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/iterators.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/merge_criteria.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/interface.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/feature.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/attributes.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/exceptions.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/parser.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/gffwriter.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/helpers.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/bins.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/version.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/constants.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/create.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/__pycache__ creating /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test -creating /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/test_merge_all.cpython-313-pytest-8.4.2.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/test_merge.cpython-313-pytest-8.4.2.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/test_iterators.cpython-313-pytest-8.4.2.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/test_issues.cpython-313-pytest-8.4.2.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/test_cli.cpython-313-pytest-8.4.2.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/test_biopython_integration.cpython-313-pytest-8.4.2.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/test_1.cpython-313-pytest-8.4.2.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/synth_test_base.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/performance_evaluation.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/parser_test.cpython-313-pytest-8.4.2.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/helpers_test.cpython-313-pytest-8.4.2.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/feature_test.cpython-313-pytest-8.4.2.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/expected.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/attr_test_cases.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/conftest.cpython-313-pytest-8.4.2.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/__pycache__ creating /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/FBgn0031208.gtf.db -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/F3-unique-3.v2.gff -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/FBgn0031208.gff -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/FBgn0031208.gtf -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data +copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/FBgn0031208.gtf.db -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.5000_gene_ids.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.5000_transcript_ids.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.chromsizes.txt -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test/data @@ -1325,8 +1272,6 @@ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/test_merge_all.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/test/test_1.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/test creating /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/scripts -creating /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/scripts/__pycache__ -copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/scripts/__pycache__/gffutils-flybase-convert.cpython-313.pyc -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/scripts/__pycache__ copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/scripts/gffutils-flybase-convert.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils/scripts copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/__init__.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils copying /build/reproducible-path/python-gffutils-0.13/.pybuild/cpython3_3.13_gffutils/build/gffutils/attributes.py -> /build/reproducible-path/python-gffutils-0.13/debian/python3-gffutils/usr/lib/python3.13/dist-packages/gffutils @@ -1437,12 +1382,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3374847/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3374847/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/1698365 and its subdirectories -I: Current time: Sat Nov 1 02:10:02 -12 2025 -I: pbuilder-time-stamp: 1762006202 +I: removing directory /srv/workspace/pbuilder/3374847 and its subdirectories +I: Current time: Sat Dec 5 10:34:59 +14 2026 +I: pbuilder-time-stamp: 1796416499 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/forky/arm64/python-gffutils_0.13-3.diff: 84.8% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/forky/arm64/python-gffutils_0.13-3.diff.gz b2/build.log: 86.1% -- replaced with stdout Compressing the 1st log... b1/build.log: 87.2% -- replaced with stdout Sat Nov 1 14:12:00 UTC 2025 I: diffoscope 307 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_python-gffutils_forky_arm64_1762006320 + touch /var/log/reproducible-builds/diffoscope_stamp_python-gffutils_forky_arm64_1762006320 + RESULT=0 + systemd-run '--description=diffoscope on python-gffutils/0.13-3 in forky/arm64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-arm64_12-127530 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.p5Ol6mnr --run-session -c jenkins-reproducible-forky-diffoscope-248c655b-874a-4f36-8de9-8c87b954562e -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.p5Ol6mnr/dbd-tmp-qI4UYzv ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.p5Ol6mnr/python-gffutils_0.13-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.p5Ol6mnr/python-gffutils_0.13-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.p5Ol6mnr/python-gffutils_0.13-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.p5Ol6mnr/b1/python-gffutils_0.13-3_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.p5Ol6mnr/b2/python-gffutils_0.13-3_arm64.changes' + false + set +x Running as unit: rb-diffoscope-arm64_12-127530.service; invocation ID: 07f340397ad44637ab862290a6f5a81c # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.p5Ol6mnr/python-gffutils_0.13-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.p5Ol6mnr/python-gffutils_0.13-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.p5Ol6mnr/python-gffutils_0.13-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.p5Ol6mnr/b1/python-gffutils_0.13-3_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.p5Ol6mnr/b2/python-gffutils_0.13-3_arm64.changes ## close_archive (total time: 0.000s) 0.000s 4 calls diffoscope.comparators.xz.XzContainer 0.000s 4 calls diffoscope.comparators.tar.TarContainer ## command (total time: 0.202s) 0.154s 6 calls xz 0.040s 6 calls diff 0.004s 11 calls sqlite3 0.002s 1 call cmp 0.002s 1 call cmp (external) 0.001s 12 calls cmp (internal) ## compare_files (cumulative) (total time: 1.806s) 0.473s 1 call abc.DotChangesFile 0.464s 1 call abc.DebFile 0.447s 2 calls abc.XzFile 0.256s 1 call abc.DebDataTarFile 0.134s 1 call abc.Sqlite3Database 0.028s 1 call abc.TarFile 0.005s 1 call abc.Md5sumsFile ## container_extract (total time: 0.208s) 0.155s 6 calls diffoscope.comparators.xz.XzContainer 0.046s 192 calls diffoscope.comparators.deb.DebTarContainer 0.004s 8 calls diffoscope.comparators.deb.DebContainer 0.003s 10 calls diffoscope.comparators.tar.TarContainer ## diff (total time: 0.001s) 0.001s 4 calls linediff ## has_same_content_as (total time: 0.003s) 0.002s 1 call abc.DebDataTarFile 0.000s 4 calls abc.TextFile 0.000s 2 calls abc.Md5sumsFile 0.000s 1 call diffoscope.comparators.binary.FilesystemFile 0.000s 2 calls abc.XzFile 0.000s 1 call abc.DotChangesFile 0.000s 1 call abc.Sqlite3Database 0.000s 1 call abc.TarFile 0.000s 1 call abc.DebFile ## main (total time: 0.769s) 0.758s 2 calls outputs 0.011s 1 call cleanup ## open_archive (total time: 0.000s) 0.000s 6 calls diffoscope.comparators.xz.XzContainer 0.000s 4 calls diffoscope.comparators.tar.TarContainer 0.000s 2 calls diffoscope.comparators.deb.DebContainer 0.000s 2 calls diffoscope.comparators.deb.DebTarContainer ## output (total time: 0.018s) 0.018s 1 call html 0.000s 1 call text 0.000s 1 call json ## recognizes (total time: 0.062s) 0.028s 668 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 0.017s 12 calls diffoscope.comparators.binary.FilesystemFile 0.014s 264 calls diffoscope.comparators.utils.archive.ArchiveMember 0.003s 54 calls diffoscope.comparators.debian.DebControlMember ## specialize (total time: 0.299s) 0.299s 13 calls specialize Finished with result: success Main processes terminated with: code=exited, status=1/FAILURE Service runtime: 999ms CPU time consumed: 911ms Memory peak: 93.7M (swap: 0B) Sat Nov 1 14:12:01 UTC 2025 W: Diffoscope claims the build is reproducible, but there is a diffoscope file. Please investigate. Sat Nov 1 14:12:01 UTC 2025 E: python-gffutils failed to build reproducibly in forky on arm64. Sat Nov 1 14:12:02 UTC 2025 I: https://tests.reproducible-builds.org/debian/forky/arm64/python-gffutils : reproducible ➤ FTBR INSERT 0 1 INSERT 0 1 DELETE 1 [2025-11-01 14:12:02] INFO: Starting at 2025-11-01 14:12:02.450356 [2025-11-01 14:12:02] INFO: Generating the pages of 1 package(s) [2025-11-01 14:12:02] CRITICAL: https://tests.reproducible-builds.org/debian/forky/arm64/python-gffutils didn't produce a buildlog, even though it has been built. [2025-11-01 14:12:02] INFO: Finished at 2025-11-01 14:12:02.778176, took: 0:00:00.327823 Sat Nov 1 14:12:02 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/forky/arm64/python-gffutils.html [2025-11-01 14:12:03] INFO: Starting at 2025-11-01 14:12:03.096221 [2025-11-01 14:12:03] INFO: Scheduling packages in arm64/forky [2025-11-01 14:12:03] INFO: jenkins scheduled in forky/arm64, reason: 'reproducible ➤ FTBR': python-gffutils Transport error: 500 Can't connect to kgb.tincho.org:9418 (Name or service not known) [2025-11-01 14:12:03] INFO: Finished at 2025-11-01 14:12:03.585749, took: 0:00:00.489534 Sat Nov 1 14:12:03 UTC 2025 I: Removing signed python-gffutils_0.13-3_arm64.buildinfo.asc files: removed './b1/python-gffutils_0.13-3_arm64.buildinfo.asc' removed './b2/python-gffutils_0.13-3_arm64.buildinfo.asc' 1762006323 arm64 forky python-gffutils Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/forky/arm64/python-gffutils_0.13-3.rbuild.log: 85.4% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/forky/arm64/python-gffutils_0.13-3.rbuild.log.gz [2025-11-01 14:12:03] INFO: Starting at 2025-11-01 14:12:03.929443 [2025-11-01 14:12:04] INFO: Generating the pages of 1 package(s) [2025-11-01 14:12:04] INFO: Finished at 2025-11-01 14:12:04.240274, took: 0:00:00.310836 All cleanup done. Sat Nov 1 14:12:04 UTC 2025 - total duration: 0h 3m 37s. Sat Nov 1 14:12:04 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-v6p6DqWv, removing. Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 3min 38.646s CPU time consumed: 4.040s Memory peak: 61.8M (swap: 0B)