Running as unit: rb-build-amd64_2-23817.service ==================================================================================== Thu Nov 21 00:35:22 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_2) on jenkins, called using "ionos5-amd64 ionos1-amd64" as arguments. Thu Nov 21 00:35:22 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-d2sLDUIT" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Nov 21 00:35:22 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos5-amd64.debian.net is marked as down. Thu Nov 21 00:35:22 UTC 2024 - checking via ssh if ionos5-amd64.debian.net is up. removed '/tmp/read-only-fs-test-VgK38j' Thu Nov 21 00:35:23 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Thu Nov 21 00:35:23 UTC 2024 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-Dy2s6I' ok, let's check if pyfastx is building anywhere yet… ok, pyfastx is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of pyfastx in unstable on amd64 on jenkins now. 1st build will be done on ionos5-amd64.debian.net. 2nd build will be done on ionos1-amd64.debian.net. ============================================================================= Thu Nov 21 00:35:36 UTC 2024 I: starting to build pyfastx/unstable/amd64 on jenkins on '2024-11-21 00:35' Thu Nov 21 00:35:36 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_2/23817/console.log 1732149336 amd64 unstable pyfastx Thu Nov 21 00:35:36 UTC 2024 I: Downloading source for unstable/pyfastx=2.1.0-2 --2024-11-21 00:35:37-- http://deb.debian.org/debian/pool/main/p/pyfastx/pyfastx_2.1.0-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2289 (2.2K) [text/prs.lines.tag] Saving to: ‘pyfastx_2.1.0-2.dsc’ 0K .. 100% 238M=0s 2024-11-21 00:35:37 (238 MB/s) - ‘pyfastx_2.1.0-2.dsc’ saved [2289/2289] --2024-11-21 00:35:37-- http://deb.debian.org/debian/pool/main/p/pyfastx/pyfastx_2.1.0-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2289 (2.2K) [text/prs.lines.tag] Saving to: ‘pyfastx_2.1.0-2.dsc’ 0K .. 100% 238M=0s 2024-11-21 00:35:37 (238 MB/s) - ‘pyfastx_2.1.0-2.dsc’ saved [2289/2289] Thu Nov 21 00:35:37 UTC 2024 I: pyfastx_2.1.0-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: pyfastx Binary: pyfastx, python3-pyfastx Architecture: any Version: 2.1.0-2 Maintainer: Debian Med Packaging Team Uploaders: Étienne Mollier Homepage: https://github.com/lmdu/pyfastx Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/pyfastx Vcs-Git: https://salsa.debian.org/med-team/pyfastx.git Testsuite: autopkgtest Testsuite-Triggers: python3-all Build-Depends: debhelper-compat (= 13), dh-python, libsqlite3-dev, zlib1g-dev, python3-all-dev, python3-indexed-gzip, python3-pyfaidx , python3-setuptools Package-List: pyfastx deb science optional arch=any python3-pyfastx deb python optional arch=any Checksums-Sha1: fdc420393162cb5fa05f9cc119a236ac2aacc4e9 230396 pyfastx_2.1.0.orig.tar.xz c8c9fccac2c3f4cb5f1cb762b5a7173e41692110 7412 pyfastx_2.1.0-2.debian.tar.xz Checksums-Sha256: 13af5bba7815829979f75646181db953bf56cc57cf144b6fd72c04ffb63c36b1 230396 pyfastx_2.1.0.orig.tar.xz 424406bffc761eb0181ae8eaa66affe9896ab22c63d3811f00ed9a290a5b9146 7412 pyfastx_2.1.0-2.debian.tar.xz Files: 97e910eb169d9eb8eb0e240627920aec 230396 pyfastx_2.1.0.orig.tar.xz 7bd60ea3fa2936412a8e16c887ba986f 7412 pyfastx_2.1.0-2.debian.tar.xz Dgit: 3ba78ed13356df04198f85a17ecb368144fc4101 debian archive/debian/2.1.0-2 https://git.dgit.debian.org/pyfastx -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmbSFCgUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdq9sBAAiOIyfP+CQPUppRW6Ivg+hOO7wSOr Yc3vQsJwdsNp4mV6NafOXQgfLMkeS97jN6EfGCTh8hX9/nZlI85cCo+SsGtSEqcn xlehqltIHJEcCQ1DLO3DFk1YCbeRGcTOZxHg7+Ux4jhrNH1mFXJ9HIwioRZ4+GHD zMBFuUrvrVsZjWGpZE146zaaJrHenPTDMG2duXiBSPESKBFdcLG83swNqsFHNpED X2zdmppC2hyRWG6fRRxMjj2mgE62HOvH6Fk2Sea1R7VG4Q8GuWH0TLx9RlT+YGZL zbQ5/Df+UKP8CK6DwiP8T8XmHSmMMgPPUzhbYMp6Z03ERA6IeW3DlpEOkQejIoMs oB967Ek6ZYH8eV7y7zxUWqC0Epu9/XWQlqz2u/NoDxQAcvzOVIr21yG9i3ozPZsu pMK+jqApzRtfm+QuywX9C9lA4Za/58KLESJIHyiHYLTxZaJOp+QtI5C+cXa8lsnt ZftLGuai6iYy4xzqric4zEWYfgETMzIkg0XtbMvoHv6q1PiVSeOLZf7bOyy0dBIK 7rsOdexzgs8PPKjfRA8Y+7xIhbeT2EZ/GgBfXk03XNgWK5NPgp1BV9OaE0zY5SYs IyXKsaVnc/EAfN8CrRBBDlZpYhxfpGwuRfHI3ZTVhmittU+iJUiroNDkEe8G4iiK IqqnEb3BcDOLQyw= =Llkl -----END PGP SIGNATURE----- Thu Nov 21 00:35:37 UTC 2024 I: Checking whether the package is not for us Thu Nov 21 00:35:37 UTC 2024 I: Starting 1st build on remote node ionos5-amd64.debian.net. Thu Nov 21 00:35:37 UTC 2024 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Thu Nov 21 00:35:37 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos5-amd64.debian.net is marked as down. Thu Nov 21 00:35:37 UTC 2024 - checking via ssh if ionos5-amd64.debian.net is up. removed '/tmp/read-only-fs-test-eestSH' ==================================================================================== Wed Dec 24 06:58:38 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos5-amd64, called using "1 pyfastx unstable /srv/reproducible-results/rbuild-debian/r-b-build.v7khtA9G 2.1.0-2" as arguments. Wed Dec 24 06:58:38 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-Iea3RESL" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Dec 24 06:58:38 UTC 2025 I: Downloading source for unstable/pyfastx=2.1.0-2 Reading package lists... NOTICE: 'pyfastx' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/pyfastx.git Please use: git clone https://salsa.debian.org/med-team/pyfastx.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 240 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main pyfastx 2.1.0-2 (dsc) [2289 B] Get:2 http://deb.debian.org/debian unstable/main pyfastx 2.1.0-2 (tar) [230 kB] Get:3 http://deb.debian.org/debian unstable/main pyfastx 2.1.0-2 (diff) [7412 B] Fetched 240 kB in 0s (5606 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'pyfastx' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/pyfastx.git Please use: git clone https://salsa.debian.org/med-team/pyfastx.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 240 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main pyfastx 2.1.0-2 (dsc) [2289 B] Get:2 http://deb.debian.org/debian unstable/main pyfastx 2.1.0-2 (tar) [230 kB] Get:3 http://deb.debian.org/debian unstable/main pyfastx 2.1.0-2 (diff) [7412 B] Fetched 240 kB in 0s (5606 kB/s) Download complete and in download only mode ============================================================================= Building pyfastx in unstable on amd64 on ionos5-amd64 now. Date: Wed Dec 24 06:58:38 UTC 2025 Date UTC: Wed Dec 24 06:58:38 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: Tue Dec 23 18:58:38 -12 2025 I: pbuilder-time-stamp: 1766559518 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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 [pyfastx_2.1.0-2.dsc] I: copying [./pyfastx_2.1.0.orig.tar.xz] I: copying [./pyfastx_2.1.0-2.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Aug 30 18:49:12 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./pyfastx_2.1.0-2.dsc: no acceptable signature found dpkg-source: info: extracting pyfastx in pyfastx-2.1.0 dpkg-source: info: unpacking pyfastx_2.1.0.orig.tar.xz dpkg-source: info: unpacking pyfastx_2.1.0-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 0001-t-test_sequence.py.patch dpkg-source: info: applying use_debian_packaged_indexed-gzip.patch dpkg-source: info: applying use_debian_packaged_zlib.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1758472/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='21c16f996d964a44969182c0d65e7cc1' 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='1758472' 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.v7khtA9G/pbuilderrc_dXA6 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.v7khtA9G/b1 --logfile b1/build.log pyfastx_2.1.0-2.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1758472/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: amd64 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-python, libsqlite3-dev, zlib1g-dev, python3-all-dev, python3-indexed-gzip, python3-pyfaidx, python3-setuptools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19966 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-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on libsqlite3-dev; however: Package libsqlite3-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-indexed-gzip; however: Package python3-indexed-gzip is not installed. pbuilder-satisfydepends-dummy depends on python3-pyfaidx; however: Package python3-pyfaidx is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools 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} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libcom-err2{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgssapi-krb5-2{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libmagic-mgc{a} libmagic1t64{a} libnsl2{a} libpipeline1{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libsqlite3-dev{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-all{a} python3-all-dev{a} python3-autocommand{a} python3-dev{a} python3-importlib-metadata{a} python3-indexed-gzip{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-packaging{a} python3-pkg-resources{a} python3-pyfaidx{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common krb5-locales libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx python3-biopython wget 0 packages upgraded, 92 newly installed, 0 to remove and 0 not upgraded. Need to get 61.8 MB of archives. After unpacking 320 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.7-3 [815 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.7-3 [2162 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.12.7-1 [26.8 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024b-3 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1+b1 [23.2 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 12 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.7-3 [1966 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.7-3 [671 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.12.7-1 [9712 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.12.7-1 [27.8 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.0-2 [856 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.0-2 [2038 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-8 [517 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 46 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 python3-importlib-metadata all 8.5.0-1 [21.0 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 62 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 75.2.0-1 [731 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20241024 [109 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-4 [152 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 7.4.7-4 [158 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libpython3.12t64 amd64 3.12.7-3 [2153 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libpython3.12-dev amd64 3.12.7-3 [5124 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.12.7-1 [9976 B] Get: 78 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [1992 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.0-2 [2137 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.0-2 [4994 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libpython3-all-dev amd64 3.12.7-1 [1072 B] Get: 82 http://deb.debian.org/debian unstable/main amd64 libsqlite3-dev amd64 3.46.1-1 [1107 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.0-2 [730 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.12.7-1 [1052 B] Get: 85 http://deb.debian.org/debian unstable/main amd64 python3.12-dev amd64 3.12.7-3 [505 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.12.7-1 [26.1 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.0-2 [504 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 python3-all-dev amd64 3.12.7-1 [1076 B] Get: 89 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:1.26.4+ds-12 [4738 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 python3-indexed-gzip amd64 1.8.7-3+b1 [1499 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 python3-pyfaidx all 0.8.1.3-1 [29.1 kB] Fetched 61.8 MB in 3s (19.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (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 ... 19966 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.7-3_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.7-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.7-3_amd64.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:amd64 (3.12.7-3) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.7-3) ... 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 ... 20286 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.7-1_amd64.deb ... Unpacking python3-minimal (3.12.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-3_all.deb ... Unpacking tzdata (2024b-3) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../05-libcom-err2_1.47.1-1+b1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../07-libkeyutils1_1.6.3-4_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../14-libreadline8t64_8.2-5_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.7-3_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.7-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.7-3_amd64.deb ... Unpacking python3.12 (3.12.7-3) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../17-libpython3-stdlib_3.12.7-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.7-1) ... Setting up python3-minimal (3.12.7-1) ... 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 ... 21348 files and directories currently installed.) Preparing to unpack .../00-python3_3.12.7-1_amd64.deb ... Unpacking python3 (3.12.7-1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../01-libpython3.13-minimal_3.13.0-2_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.0-2) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../02-python3.13-minimal_3.13.0-2_amd64.deb ... Unpacking python3.13-minimal (3.13.0-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../03-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../05-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../06-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. 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Selecting previously unselected package libicu72:amd64. Preparing to unpack .../26-libicu72_72.1-5+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-5+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../27-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../28-gettext_0.22.5-2_amd64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../29-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../30-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../31-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package python3-autocommand. Preparing to unpack .../32-python3-autocommand_2.2.2-3_all.deb ... Unpacking python3-autocommand (2.2.2-3) ... Selecting previously unselected package python3-more-itertools. Preparing to unpack .../33-python3-more-itertools_10.5.0-1_all.deb ... Unpacking python3-more-itertools (10.5.0-1) ... Selecting previously unselected package python3-typing-extensions. Preparing to unpack .../34-python3-typing-extensions_4.12.2-2_all.deb ... Unpacking python3-typing-extensions (4.12.2-2) ... Selecting previously unselected package python3-zipp. Preparing to unpack .../35-python3-zipp_3.21.0-1_all.deb ... Unpacking python3-zipp (3.21.0-1) ... Selecting previously unselected package python3-importlib-metadata. Preparing to unpack .../36-python3-importlib-metadata_8.5.0-1_all.deb ... Unpacking python3-importlib-metadata (8.5.0-1) ... Selecting previously unselected package python3-typeguard. Preparing to unpack .../37-python3-typeguard_4.4.1-1_all.deb ... Unpacking python3-typeguard (4.4.1-1) ... Selecting previously unselected package python3-inflect. Preparing to unpack .../38-python3-inflect_7.3.1-2_all.deb ... Unpacking python3-inflect (7.3.1-2) ... Selecting previously unselected package python3-jaraco.context. Preparing to unpack .../39-python3-jaraco.context_6.0.0-1_all.deb ... Unpacking python3-jaraco.context (6.0.0-1) ... Selecting previously unselected package python3-jaraco.functools. Preparing to unpack .../40-python3-jaraco.functools_4.1.0-1_all.deb ... Unpacking python3-jaraco.functools (4.1.0-1) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../41-python3-pkg-resources_75.2.0-1_all.deb ... Unpacking python3-pkg-resources (75.2.0-1) ... Selecting previously unselected package python3-jaraco.text. Preparing to unpack .../42-python3-jaraco.text_4.0.0-1_all.deb ... Unpacking python3-jaraco.text (4.0.0-1) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../43-python3-setuptools_75.2.0-1_all.deb ... Unpacking python3-setuptools (75.2.0-1) ... Selecting previously unselected package dh-python. Preparing to unpack .../44-dh-python_6.20241024_all.deb ... Unpacking dh-python (6.20241024) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../45-libblas3_3.12.0-4_amd64.deb ... Unpacking libblas3:amd64 (3.12.0-4) ... Selecting previously unselected package libexpat1-dev:amd64. Preparing to unpack .../46-libexpat1-dev_2.6.4-1_amd64.deb ... Unpacking libexpat1-dev:amd64 (2.6.4-1) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../47-libgfortran5_14.2.0-8_amd64.deb ... Unpacking libgfortran5:amd64 (14.2.0-8) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../48-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../49-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../50-libjs-sphinxdoc_7.4.7-4_all.deb ... Unpacking libjs-sphinxdoc (7.4.7-4) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../51-liblapack3_3.12.0-4_amd64.deb ... Unpacking liblapack3:amd64 (3.12.0-4) ... Selecting previously unselected package libpython3.12t64:amd64. Preparing to unpack .../52-libpython3.12t64_3.12.7-3_amd64.deb ... Unpacking libpython3.12t64:amd64 (3.12.7-3) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../53-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Selecting previously unselected package libpython3.12-dev:amd64. 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Setting up libicu72:amd64 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:amd64 (1.47.1-1+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Dec 24 07:00:21 UTC 2025. Universal Time is now: Wed Dec 24 07:00:21 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libpython3.13-minimal:amd64 (3.13.0-2) ... Setting up autotools-dev (20220109.1) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/pyfastx-2.1.0/ && 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 > ../pyfastx_2.1.0-2_source.changes dpkg-buildpackage: info: source package pyfastx dpkg-buildpackage: info: source version 2.1.0-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem pybuild --with python3 dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py clean /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) running clean removing '/build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.13' does not exist -- can't clean it I: pybuild base:311: python3.12 setup.py clean /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) running clean removing '/build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem pybuild --with python3 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/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) running config I: pybuild base:311: python3.12 setup.py config /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) running config debian/rules execute_before_dh_auto_build make[1]: Entering directory '/build/reproducible-path/pyfastx-2.1.0' # Upstream originally vendored these files straight in src/, but # stopped for some reason. We're pulling them instead from the # package python3-indexed-gzip. cp --update=none /usr/lib/python3/dist-packages/indexed_gzip/zran.c src/ cp --update=none /usr/lib/python3/dist-packages/indexed_gzip/zran.h src/ cp --update=none /usr/lib/python3/dist-packages/indexed_gzip/zran_file_util.c src/ cp --update=none /usr/lib/python3/dist-packages/indexed_gzip/zran_file_util.h src/ make[1]: Leaving directory '/build/reproducible-path/pyfastx-2.1.0' dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3.13 setup.py build /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) running build running build_py copying pyfastxcli.py -> /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build running build_ext building 'pyfastx' extension creating build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/fakeys.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/fakeys.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/fasta.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/fasta.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE /build/reproducible-path/pyfastx-2.1.0/src/fasta.c: In function ‘pyfastx_fasta_fetch’: /build/reproducible-path/pyfastx-2.1.0/src/fasta.c:443:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Py_ssize_t’ {aka ‘long int’} [-Wsign-compare] 443 | if (strlen(name) >= self->index->cache_name.m) { | ^~ /build/reproducible-path/pyfastx-2.1.0/src/fasta.c: In function ‘pyfastx_fasta_composition’: /build/reproducible-path/pyfastx-2.1.0/src/fasta.c:1058:13: warning: unused variable ‘i’ [-Wunused-variable] 1058 | int i; | ^ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/fastq.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/fastq.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/fastx.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/fastx.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/fqkeys.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/fqkeys.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/index.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/index.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/kseq.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/kseq.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/module.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/module.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE /build/reproducible-path/pyfastx-2.1.0/src/module.c: In function ‘pyfastx_reverse_complement’: /build/reproducible-path/pyfastx-2.1.0/src/module.c:57:32: warning: passing argument 1 of ‘reverse_complement_seq’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 57 | reverse_complement_seq(s); | ^ In file included from /build/reproducible-path/pyfastx-2.1.0/src/fastq.h:8, from /build/reproducible-path/pyfastx-2.1.0/src/module.c:3: /build/reproducible-path/pyfastx-2.1.0/src/util.h:16:35: note: expected ‘char *’ but argument is of type ‘const char *’ 16 | void reverse_complement_seq(char *seq); | ~~~~~~^~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/read.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/read.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/sequence.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/sequence.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE /build/reproducible-path/pyfastx-2.1.0/src/sequence.c: In function ‘pyfastx_sequence_get_fullseq’: /build/reproducible-path/pyfastx-2.1.0/src/sequence.c:90:32: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Py_ssize_t’ {aka ‘long int’} [-Wsign-compare] 90 | if (strlen(self->name) >= self->index->cache_name.m) { | ^~ /build/reproducible-path/pyfastx-2.1.0/src/sequence.c: In function ‘pyfastx_sequence_subscript’: /build/reproducible-path/pyfastx-2.1.0/src/sequence.c:431:20: warning: variable ‘slice_len’ set but not used [-Wunused-but-set-variable] 431 | Py_ssize_t slice_len; | ^~~~~~~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/util.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/util.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/zran.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/zran.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/zran_file_util.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/zran_file_util.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/fakeys.o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/fasta.o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/fastq.o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/fastx.o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/fqkeys.o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/index.o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/kseq.o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/module.o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/read.o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/sequence.o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/util.o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/zran.o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/zran_file_util.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/pyfastx.cpython-313-x86_64-linux-gnu.so -lsqlite3 I: pybuild base:311: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) running build running build_py copying pyfastxcli.py -> /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build running build_ext building 'pyfastx' extension creating build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/fakeys.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/fakeys.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/fasta.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/fasta.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE /build/reproducible-path/pyfastx-2.1.0/src/fasta.c: In function ‘pyfastx_fasta_fetch’: /build/reproducible-path/pyfastx-2.1.0/src/fasta.c:443:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Py_ssize_t’ {aka ‘long int’} [-Wsign-compare] 443 | if (strlen(name) >= self->index->cache_name.m) { | ^~ /build/reproducible-path/pyfastx-2.1.0/src/fasta.c: In function ‘pyfastx_fasta_composition’: /build/reproducible-path/pyfastx-2.1.0/src/fasta.c:1058:13: warning: unused variable ‘i’ [-Wunused-variable] 1058 | int i; | ^ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/fastq.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/fastq.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/fastx.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/fastx.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/fqkeys.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/fqkeys.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/index.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/index.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/kseq.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/kseq.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/module.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/module.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE /build/reproducible-path/pyfastx-2.1.0/src/module.c: In function ‘pyfastx_reverse_complement’: /build/reproducible-path/pyfastx-2.1.0/src/module.c:57:32: warning: passing argument 1 of ‘reverse_complement_seq’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 57 | reverse_complement_seq(s); | ^ In file included from /build/reproducible-path/pyfastx-2.1.0/src/fastq.h:8, from /build/reproducible-path/pyfastx-2.1.0/src/module.c:3: /build/reproducible-path/pyfastx-2.1.0/src/util.h:16:35: note: expected ‘char *’ but argument is of type ‘const char *’ 16 | void reverse_complement_seq(char *seq); | ~~~~~~^~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/read.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/read.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/sequence.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/sequence.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE /build/reproducible-path/pyfastx-2.1.0/src/sequence.c: In function ‘pyfastx_sequence_get_fullseq’: /build/reproducible-path/pyfastx-2.1.0/src/sequence.c:90:32: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Py_ssize_t’ {aka ‘long int’} [-Wsign-compare] 90 | if (strlen(self->name) >= self->index->cache_name.m) { | ^~ /build/reproducible-path/pyfastx-2.1.0/src/sequence.c: In function ‘pyfastx_sequence_subscript’: /build/reproducible-path/pyfastx-2.1.0/src/sequence.c:431:20: warning: variable ‘slice_len’ set but not used [-Wunused-but-set-variable] 431 | Py_ssize_t slice_len; | ^~~~~~~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/util.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/util.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/zran.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/zran.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/zran_file_util.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/zran_file_util.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/fakeys.o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/fasta.o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/fastq.o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/fastx.o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/fqkeys.o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/index.o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/kseq.o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/module.o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/read.o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/sequence.o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/util.o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/zran.o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/zran_file_util.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/pyfastx.cpython-312-x86_64-linux-gnu.so -lsqlite3 dh_auto_test -O--buildsystem=pybuild I: pybuild pybuild:308: mkdir -pv /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/src && cp -v src/version.h /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/src mkdir: created directory '/build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/src' 'src/version.h' -> '/build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/src/version.h' I: pybuild base:311: cd /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build; python3.13 -m unittest discover -v test_id_exception (tests.test_fakeys.IdentifierTest.test_id_exception) ... ok test_key_identifier (tests.test_fakeys.IdentifierTest.test_key_identifier) ... ok test_key_repr (tests.test_fakeys.IdentifierTest.test_key_repr) ... ok test_key_slice (tests.test_fakeys.IdentifierTest.test_key_slice) ... ok test_keys_filter (tests.test_fakeys.IdentifierTest.test_keys_filter) ... ok test_keys_sort (tests.test_fakeys.IdentifierTest.test_keys_sort) ... ok test_build (tests.test_fasta.FastaTest.test_build) ... ok test_exception (tests.test_fasta.FastaTest.test_exception) ... ok test_fasta (tests.test_fasta.FastaTest.test_fasta) ... ok test_iter_full_name (tests.test_fasta.FastaTest.test_iter_full_name) ... ok test_iter_object (tests.test_fasta.FastaTest.test_iter_object) ... ok test_iter_tuple (tests.test_fasta.FastaTest.test_iter_tuple) ... ok test_iter_upper (tests.test_fasta.FastaTest.test_iter_upper) ... ok test_iter_upper_full_name (tests.test_fasta.FastaTest.test_iter_upper_full_name) ... ok test_key_func (tests.test_fasta.FastaTest.test_key_func) ... ok test_module (tests.test_fasta.FastaTest.test_module) ... ok test_no_upper (tests.test_fasta.FastaTest.test_no_upper) ... ok test_repr (tests.test_fasta.FastaTest.test_repr) ... ok test_seq_fetch (tests.test_fasta.FastaTest.test_seq_fetch) ... ok test_seq_flank (tests.test_fasta.FastaTest.test_seq_flank) ... ok test_seq_type (tests.test_fasta.FastaTest.test_seq_type) ... ok test_statistics (tests.test_fasta.FastaTest.test_statistics) ... ok test_build (tests.test_fastq.FastqTest.test_build) ... ok test_exception (tests.test_fastq.FastqTest.test_exception) ... ok test_fastq (tests.test_fastq.FastqTest.test_fastq) ... ok test_full_name (tests.test_fastq.FastqTest.test_full_name) ... ok test_iter_object (tests.test_fastq.FastqTest.test_iter_object) ... ok test_iter_tuple (tests.test_fastq.FastqTest.test_iter_tuple) ... ok test_negative (tests.test_fastq.FastqTest.test_negative) ... ok test_platform (tests.test_fastq.FastqTest.test_platform) ... ok test_read_len (tests.test_fastq.FastqTest.test_read_len) ... ok test_repr (tests.test_fastq.FastqTest.test_repr) ... ok test_exception (tests.test_fastx.FastxTest.test_exception) ... ok test_fasta_iter (tests.test_fastx.FastxTest.test_fasta_iter) ... ok test_fasta_upper (tests.test_fastx.FastxTest.test_fasta_upper) ... ok test_fastq_iter (tests.test_fastx.FastxTest.test_fastq_iter) ... ok test_fastx_repr (tests.test_fastx.FastxTest.test_fastx_repr) ... ok test_exception (tests.test_fqkeys.FastxTest.test_exception) ... ok test_fastq_key (tests.test_fqkeys.FastxTest.test_fastq_key) ... ok test_read (tests.test_read.ReadTest.test_read) ... ok test_read_description (tests.test_read.ReadTest.test_read_description) ... ok test_read_raw (tests.test_read.ReadTest.test_read_raw) ... ok test_read_seq (tests.test_read.ReadTest.test_read_seq) ... ok test_repr (tests.test_read.ReadTest.test_repr) ... ok test_full_compo (tests.test_sequence.SequenceTest.test_full_compo) ... ok test_seq_by_index (tests.test_sequence.SequenceTest.test_seq_by_index) ... ok test_seq_by_key (tests.test_sequence.SequenceTest.test_seq_by_key) ... ok test_seq_content (tests.test_sequence.SequenceTest.test_seq_content) ... ok test_seq_exception (tests.test_sequence.SequenceTest.test_seq_exception) ... ok test_seq_iter (tests.test_sequence.SequenceTest.test_seq_iter) ... ok test_seq_raw (tests.test_sequence.SequenceTest.test_seq_raw) ... ok test_seq_repr (tests.test_sequence.SequenceTest.test_seq_repr) ... ok test_seq_reverse_complement (tests.test_sequence.SequenceTest.test_seq_reverse_complement) ... ok test_seq_slice (tests.test_sequence.SequenceTest.test_seq_slice) ... ok test_seq_by_index (tests.test_sequence_error.SequenceErrorTest.test_seq_by_index) ... ok test_seq_by_key (tests.test_sequence_error.SequenceErrorTest.test_seq_by_key) ... ok ---------------------------------------------------------------------- Ran 56 tests in 26.148s OK pyfastx: 2.1.0; zlib: 1.3.1; sqlite: 3.46.1; zran: 1.7.0 I: pybuild pybuild:334: rm -rvf /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/src /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/non.fa removed '/build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/src/version.h' removed directory '/build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/src' removed '/build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/non.fa' I: pybuild pybuild:308: mkdir -pv /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/src && cp -v src/version.h /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/src mkdir: created directory '/build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/src' 'src/version.h' -> '/build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/src/version.h' I: pybuild base:311: cd /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build; python3.12 -m unittest discover -v test_id_exception (tests.test_fakeys.IdentifierTest.test_id_exception) ... ok test_key_identifier (tests.test_fakeys.IdentifierTest.test_key_identifier) ... ok test_key_repr (tests.test_fakeys.IdentifierTest.test_key_repr) ... ok test_key_slice (tests.test_fakeys.IdentifierTest.test_key_slice) ... ok test_keys_filter (tests.test_fakeys.IdentifierTest.test_keys_filter) ... ok test_keys_sort (tests.test_fakeys.IdentifierTest.test_keys_sort) ... ok test_build (tests.test_fasta.FastaTest.test_build) ... ok test_exception (tests.test_fasta.FastaTest.test_exception) ... ok test_fasta (tests.test_fasta.FastaTest.test_fasta) ... ok test_iter_full_name (tests.test_fasta.FastaTest.test_iter_full_name) ... ok test_iter_object (tests.test_fasta.FastaTest.test_iter_object) ... ok test_iter_tuple (tests.test_fasta.FastaTest.test_iter_tuple) ... ok test_iter_upper (tests.test_fasta.FastaTest.test_iter_upper) ... ok test_iter_upper_full_name (tests.test_fasta.FastaTest.test_iter_upper_full_name) ... ok test_key_func (tests.test_fasta.FastaTest.test_key_func) ... ok test_module (tests.test_fasta.FastaTest.test_module) ... ok test_no_upper (tests.test_fasta.FastaTest.test_no_upper) ... ok test_repr (tests.test_fasta.FastaTest.test_repr) ... ok test_seq_fetch (tests.test_fasta.FastaTest.test_seq_fetch) ... ok test_seq_flank (tests.test_fasta.FastaTest.test_seq_flank) ... ok test_seq_type (tests.test_fasta.FastaTest.test_seq_type) ... ok test_statistics (tests.test_fasta.FastaTest.test_statistics) ... ok test_build (tests.test_fastq.FastqTest.test_build) ... ok test_exception (tests.test_fastq.FastqTest.test_exception) ... ok test_fastq (tests.test_fastq.FastqTest.test_fastq) ... ok test_full_name (tests.test_fastq.FastqTest.test_full_name) ... ok test_iter_object (tests.test_fastq.FastqTest.test_iter_object) ... ok test_iter_tuple (tests.test_fastq.FastqTest.test_iter_tuple) ... ok test_negative (tests.test_fastq.FastqTest.test_negative) ... ok test_platform (tests.test_fastq.FastqTest.test_platform) ... ok test_read_len (tests.test_fastq.FastqTest.test_read_len) ... ok test_repr (tests.test_fastq.FastqTest.test_repr) ... ok test_exception (tests.test_fastx.FastxTest.test_exception) ... ok test_fasta_iter (tests.test_fastx.FastxTest.test_fasta_iter) ... ok test_fasta_upper (tests.test_fastx.FastxTest.test_fasta_upper) ... ok test_fastq_iter (tests.test_fastx.FastxTest.test_fastq_iter) ... ok test_fastx_repr (tests.test_fastx.FastxTest.test_fastx_repr) ... ok test_exception (tests.test_fqkeys.FastxTest.test_exception) ... ok test_fastq_key (tests.test_fqkeys.FastxTest.test_fastq_key) ... ok test_read (tests.test_read.ReadTest.test_read) ... ok test_read_description (tests.test_read.ReadTest.test_read_description) ... ok test_read_raw (tests.test_read.ReadTest.test_read_raw) ... ok test_read_seq (tests.test_read.ReadTest.test_read_seq) ... ok test_repr (tests.test_read.ReadTest.test_repr) ... ok test_full_compo (tests.test_sequence.SequenceTest.test_full_compo) ... ok test_seq_by_index (tests.test_sequence.SequenceTest.test_seq_by_index) ... ok test_seq_by_key (tests.test_sequence.SequenceTest.test_seq_by_key) ... ok test_seq_content (tests.test_sequence.SequenceTest.test_seq_content) ... ok test_seq_exception (tests.test_sequence.SequenceTest.test_seq_exception) ... ok test_seq_iter (tests.test_sequence.SequenceTest.test_seq_iter) ... ok test_seq_raw (tests.test_sequence.SequenceTest.test_seq_raw) ... ok test_seq_repr (tests.test_sequence.SequenceTest.test_seq_repr) ... ok test_seq_reverse_complement (tests.test_sequence.SequenceTest.test_seq_reverse_complement) ... ok test_seq_slice (tests.test_sequence.SequenceTest.test_seq_slice) ... ok test_seq_by_index (tests.test_sequence_error.SequenceErrorTest.test_seq_by_index) ... ok test_seq_by_key (tests.test_sequence_error.SequenceErrorTest.test_seq_by_key) ... ok ---------------------------------------------------------------------- Ran 56 tests in 19.057s OK pyfastx: 2.1.0; zlib: 1.3.1; sqlite: 3.46.1; zran: 1.7.0 I: pybuild pybuild:334: rm -rvf /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/src /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/non.fa removed '/build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/src/version.h' removed directory '/build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/src' removed '/build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/non.fa' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3.13 setup.py install --root /build/reproducible-path/pyfastx-2.1.0/debian/tmp /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running build_ext running install_lib creating /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.13/dist-packages copying /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/pyfastxcli.py -> /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.13/dist-packages copying /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/pyfastx.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.13/dist-packages byte-compiling /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.13/dist-packages/pyfastxcli.py to pyfastxcli.cpython-313.pyc running install_egg_info running egg_info creating pyfastx.egg-info writing pyfastx.egg-info/PKG-INFO writing dependency_links to pyfastx.egg-info/dependency_links.txt writing entry points to pyfastx.egg-info/entry_points.txt writing top-level names to pyfastx.egg-info/top_level.txt writing manifest file 'pyfastx.egg-info/SOURCES.txt' reading manifest file 'pyfastx.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'pyfastx.egg-info/SOURCES.txt' Copying pyfastx.egg-info to /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.13/dist-packages/pyfastx-2.1.0.egg-info Skipping SOURCES.txt running install_scripts Installing pyfastx script to /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/bin I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/pyfastx-2.1.0/debian/tmp /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running build_ext running install_lib creating /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.12/dist-packages copying /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/pyfastx.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.12/dist-packages copying /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/pyfastxcli.py -> /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.12/dist-packages byte-compiling /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.12/dist-packages/pyfastxcli.py to pyfastxcli.cpython-312.pyc running install_egg_info running egg_info writing pyfastx.egg-info/PKG-INFO writing dependency_links to pyfastx.egg-info/dependency_links.txt writing entry points to pyfastx.egg-info/entry_points.txt writing top-level names to pyfastx.egg-info/top_level.txt reading manifest file 'pyfastx.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'pyfastx.egg-info/SOURCES.txt' Copying pyfastx.egg-info to /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.12/dist-packages/pyfastx-2.1.0.egg-info Skipping SOURCES.txt running install_scripts Installing pyfastx script to /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/bin dh_install -O--buildsystem=pybuild dh_installdocs -O--buildsystem=pybuild debian/rules execute_after_dh_installdocs make[1]: Entering directory '/build/reproducible-path/pyfastx-2.1.0' # Deduplicate changelog entries flagged by lintian. rm debian/pyfastx/usr/share/doc/pyfastx/docs/changelog.rst* cd debian/pyfastx/usr/share/doc/pyfastx/docs \ && ln -s ../changelog.gz changelog.rst.gz make[1]: Leaving directory '/build/reproducible-path/pyfastx-2.1.0' dh_installchangelogs -O--buildsystem=pybuild dh_installexamples -O--buildsystem=pybuild debian/rules execute_after_dh_installexamples make[1]: Entering directory '/build/reproducible-path/pyfastx-2.1.0' # Remove duplicate uncompressed files caused by the nature of the test; # we can get them back during the CLI test. rm debian/pyfastx/usr/share/doc/pyfastx/examples/test.fa rm debian/pyfastx/usr/share/doc/pyfastx/examples/test.fq make[1]: Leaving directory '/build/reproducible-path/pyfastx-2.1.0' dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: package python3-pyfastx: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: Depends field of package pyfastx: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package python3-pyfastx: substitution variable ${python3:Depends} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'pyfastx' in '../pyfastx_2.1.0-2_amd64.deb'. dpkg-deb: building package 'python3-pyfastx' in '../python3-pyfastx_2.1.0-2_amd64.deb'. dpkg-deb: building package 'python3-pyfastx-dbgsym' in '../python3-pyfastx-dbgsym_2.1.0-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../pyfastx_2.1.0-2_amd64.buildinfo dpkg-genchanges --build=binary -O../pyfastx_2.1.0-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) 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/1758472 and its subdirectories I: Current time: Tue Dec 23 19:02:47 -12 2025 I: pbuilder-time-stamp: 1766559767 Wed Dec 24 07:02:47 UTC 2025 I: Signing ./b1/pyfastx_2.1.0-2_amd64.buildinfo as pyfastx_2.1.0-2_amd64.buildinfo.asc Wed Dec 24 07:02:47 UTC 2025 I: Signed ./b1/pyfastx_2.1.0-2_amd64.buildinfo as ./b1/pyfastx_2.1.0-2_amd64.buildinfo.asc Wed Dec 24 07:02:47 UTC 2025 - build #1 for pyfastx/unstable/amd64 on ionos5-amd64 done. Starting cleanup. All cleanup done. Wed Dec 24 07:02:47 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-Iea3RESL, removing. /srv/reproducible-results/rbuild-debian/r-b-build.v7khtA9G: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Nov 21 00:39 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 21 00:35 b2 -rw-r--r-- 1 jenkins jenkins 2289 Aug 30 18:55 pyfastx_2.1.0-2.dsc -rw------- 1 jenkins jenkins 3388 Nov 21 00:35 rbuildlog.fDS12AQ /srv/reproducible-results/rbuild-debian/r-b-build.v7khtA9G/b1: total 548 -rw-r--r-- 1 jenkins jenkins 84334 Nov 21 00:39 build.log -rw-r--r-- 1 jenkins jenkins 7412 Nov 21 00:39 pyfastx_2.1.0-2.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2289 Nov 21 00:39 pyfastx_2.1.0-2.dsc -rw-r--r-- 1 jenkins jenkins 7324 Nov 21 00:39 pyfastx_2.1.0-2_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 8206 Nov 21 00:39 pyfastx_2.1.0-2_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2285 Nov 21 00:39 pyfastx_2.1.0-2_amd64.changes -rw-r--r-- 1 jenkins jenkins 127152 Nov 21 00:39 pyfastx_2.1.0-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 1720 Nov 21 00:39 pyfastx_2.1.0-2_source.changes -rw-r--r-- 1 jenkins jenkins 234472 Nov 21 00:39 python3-pyfastx-dbgsym_2.1.0-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 64596 Nov 21 00:39 python3-pyfastx_2.1.0-2_amd64.deb /srv/reproducible-results/rbuild-debian/r-b-build.v7khtA9G/b2: total 0 Thu Nov 21 00:39:48 UTC 2024 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Dec 23 18:58:38 -12 2025 I: pbuilder-time-stamp: 1766559518 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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 [pyfastx_2.1.0-2.dsc] I: copying [./pyfastx_2.1.0.orig.tar.xz] I: copying [./pyfastx_2.1.0-2.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Aug 30 18:49:12 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./pyfastx_2.1.0-2.dsc: no acceptable signature found dpkg-source: info: extracting pyfastx in pyfastx-2.1.0 dpkg-source: info: unpacking pyfastx_2.1.0.orig.tar.xz dpkg-source: info: unpacking pyfastx_2.1.0-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 0001-t-test_sequence.py.patch dpkg-source: info: applying use_debian_packaged_indexed-gzip.patch dpkg-source: info: applying use_debian_packaged_zlib.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1758472/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='21c16f996d964a44969182c0d65e7cc1' 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='1758472' 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.v7khtA9G/pbuilderrc_dXA6 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.v7khtA9G/b1 --logfile b1/build.log pyfastx_2.1.0-2.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1758472/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: amd64 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-python, libsqlite3-dev, zlib1g-dev, python3-all-dev, python3-indexed-gzip, python3-pyfaidx, python3-setuptools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19966 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-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on libsqlite3-dev; however: Package libsqlite3-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-indexed-gzip; however: Package python3-indexed-gzip is not installed. pbuilder-satisfydepends-dummy depends on python3-pyfaidx; however: Package python3-pyfaidx is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools 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} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libcom-err2{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgssapi-krb5-2{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libmagic-mgc{a} libmagic1t64{a} libnsl2{a} libpipeline1{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libsqlite3-dev{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-all{a} python3-all-dev{a} python3-autocommand{a} python3-dev{a} python3-importlib-metadata{a} python3-indexed-gzip{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-packaging{a} python3-pkg-resources{a} python3-pyfaidx{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common krb5-locales libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx python3-biopython wget 0 packages upgraded, 92 newly installed, 0 to remove and 0 not upgraded. Need to get 61.8 MB of archives. After unpacking 320 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.7-3 [815 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.7-3 [2162 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.12.7-1 [26.8 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024b-3 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1+b1 [23.2 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 12 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.7-3 [1966 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.7-3 [671 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.12.7-1 [9712 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.12.7-1 [27.8 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.0-2 [856 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.0-2 [2038 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-8 [517 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 46 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 python3-importlib-metadata all 8.5.0-1 [21.0 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 62 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 75.2.0-1 [731 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20241024 [109 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-4 [152 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 7.4.7-4 [158 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libpython3.12t64 amd64 3.12.7-3 [2153 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libpython3.12-dev amd64 3.12.7-3 [5124 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.12.7-1 [9976 B] Get: 78 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [1992 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.0-2 [2137 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.0-2 [4994 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libpython3-all-dev amd64 3.12.7-1 [1072 B] Get: 82 http://deb.debian.org/debian unstable/main amd64 libsqlite3-dev amd64 3.46.1-1 [1107 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.0-2 [730 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.12.7-1 [1052 B] Get: 85 http://deb.debian.org/debian unstable/main amd64 python3.12-dev amd64 3.12.7-3 [505 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.12.7-1 [26.1 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.0-2 [504 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 python3-all-dev amd64 3.12.7-1 [1076 B] Get: 89 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:1.26.4+ds-12 [4738 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 python3-indexed-gzip amd64 1.8.7-3+b1 [1499 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 python3-pyfaidx all 0.8.1.3-1 [29.1 kB] Fetched 61.8 MB in 3s (19.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (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 ... 19966 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.7-3_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.7-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.7-3_amd64.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:amd64 (3.12.7-3) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.7-3) ... 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 ... 20286 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.7-1_amd64.deb ... Unpacking python3-minimal (3.12.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-3_all.deb ... Unpacking tzdata (2024b-3) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../05-libcom-err2_1.47.1-1+b1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../07-libkeyutils1_1.6.3-4_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../14-libreadline8t64_8.2-5_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.7-3_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.7-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.7-3_amd64.deb ... Unpacking python3.12 (3.12.7-3) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../17-libpython3-stdlib_3.12.7-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.7-1) ... Setting up python3-minimal (3.12.7-1) ... 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 ... 21348 files and directories currently installed.) Preparing to unpack .../00-python3_3.12.7-1_amd64.deb ... Unpacking python3 (3.12.7-1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../01-libpython3.13-minimal_3.13.0-2_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.0-2) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../02-python3.13-minimal_3.13.0-2_amd64.deb ... Unpacking python3.13-minimal (3.13.0-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../03-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../05-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../06-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/pyfastx-2.1.0/ && 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 > ../pyfastx_2.1.0-2_source.changes dpkg-buildpackage: info: source package pyfastx dpkg-buildpackage: info: source version 2.1.0-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem pybuild --with python3 dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py clean /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) running clean removing '/build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.13' does not exist -- can't clean it I: pybuild base:311: python3.12 setup.py clean /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) running clean removing '/build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem pybuild --with python3 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/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) running config I: pybuild base:311: python3.12 setup.py config /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) running config debian/rules execute_before_dh_auto_build make[1]: Entering directory '/build/reproducible-path/pyfastx-2.1.0' # Upstream originally vendored these files straight in src/, but # stopped for some reason. We're pulling them instead from the # package python3-indexed-gzip. cp --update=none /usr/lib/python3/dist-packages/indexed_gzip/zran.c src/ cp --update=none /usr/lib/python3/dist-packages/indexed_gzip/zran.h src/ cp --update=none /usr/lib/python3/dist-packages/indexed_gzip/zran_file_util.c src/ cp --update=none /usr/lib/python3/dist-packages/indexed_gzip/zran_file_util.h src/ make[1]: Leaving directory '/build/reproducible-path/pyfastx-2.1.0' dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3.13 setup.py build /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) running build running build_py copying pyfastxcli.py -> /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build running build_ext building 'pyfastx' extension creating build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/fakeys.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/fakeys.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/fasta.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/fasta.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE /build/reproducible-path/pyfastx-2.1.0/src/fasta.c: In function ‘pyfastx_fasta_fetch’: /build/reproducible-path/pyfastx-2.1.0/src/fasta.c:443:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Py_ssize_t’ {aka ‘long int’} [-Wsign-compare] 443 | if (strlen(name) >= self->index->cache_name.m) { | ^~ /build/reproducible-path/pyfastx-2.1.0/src/fasta.c: In function ‘pyfastx_fasta_composition’: /build/reproducible-path/pyfastx-2.1.0/src/fasta.c:1058:13: warning: unused variable ‘i’ [-Wunused-variable] 1058 | int i; | ^ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/fastq.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/fastq.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/fastx.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/fastx.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/fqkeys.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/fqkeys.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/index.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/index.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/kseq.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/kseq.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/module.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/module.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE /build/reproducible-path/pyfastx-2.1.0/src/module.c: In function ‘pyfastx_reverse_complement’: /build/reproducible-path/pyfastx-2.1.0/src/module.c:57:32: warning: passing argument 1 of ‘reverse_complement_seq’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 57 | reverse_complement_seq(s); | ^ In file included from /build/reproducible-path/pyfastx-2.1.0/src/fastq.h:8, from /build/reproducible-path/pyfastx-2.1.0/src/module.c:3: /build/reproducible-path/pyfastx-2.1.0/src/util.h:16:35: note: expected ‘char *’ but argument is of type ‘const char *’ 16 | void reverse_complement_seq(char *seq); | ~~~~~~^~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/read.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/read.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/sequence.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/sequence.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE /build/reproducible-path/pyfastx-2.1.0/src/sequence.c: In function ‘pyfastx_sequence_get_fullseq’: /build/reproducible-path/pyfastx-2.1.0/src/sequence.c:90:32: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Py_ssize_t’ {aka ‘long int’} [-Wsign-compare] 90 | if (strlen(self->name) >= self->index->cache_name.m) { | ^~ /build/reproducible-path/pyfastx-2.1.0/src/sequence.c: In function ‘pyfastx_sequence_subscript’: /build/reproducible-path/pyfastx-2.1.0/src/sequence.c:431:20: warning: variable ‘slice_len’ set but not used [-Wunused-but-set-variable] 431 | Py_ssize_t slice_len; | ^~~~~~~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/util.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/util.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/zran.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/zran.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/zran_file_util.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/zran_file_util.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/fakeys.o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/fasta.o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/fastq.o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/fastx.o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/fqkeys.o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/index.o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/kseq.o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/module.o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/read.o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/sequence.o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/util.o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/zran.o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/zran_file_util.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/pyfastx.cpython-313-x86_64-linux-gnu.so -lsqlite3 I: pybuild base:311: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) running build running build_py copying pyfastxcli.py -> /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build running build_ext building 'pyfastx' extension creating build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/fakeys.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/fakeys.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/fasta.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/fasta.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE /build/reproducible-path/pyfastx-2.1.0/src/fasta.c: In function ‘pyfastx_fasta_fetch’: /build/reproducible-path/pyfastx-2.1.0/src/fasta.c:443:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Py_ssize_t’ {aka ‘long int’} [-Wsign-compare] 443 | if (strlen(name) >= self->index->cache_name.m) { | ^~ /build/reproducible-path/pyfastx-2.1.0/src/fasta.c: In function ‘pyfastx_fasta_composition’: /build/reproducible-path/pyfastx-2.1.0/src/fasta.c:1058:13: warning: unused variable ‘i’ [-Wunused-variable] 1058 | int i; | ^ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/fastq.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/fastq.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/fastx.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/fastx.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/fqkeys.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/fqkeys.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/index.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/index.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/kseq.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/kseq.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/module.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/module.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE /build/reproducible-path/pyfastx-2.1.0/src/module.c: In function ‘pyfastx_reverse_complement’: /build/reproducible-path/pyfastx-2.1.0/src/module.c:57:32: warning: passing argument 1 of ‘reverse_complement_seq’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 57 | reverse_complement_seq(s); | ^ In file included from /build/reproducible-path/pyfastx-2.1.0/src/fastq.h:8, from /build/reproducible-path/pyfastx-2.1.0/src/module.c:3: /build/reproducible-path/pyfastx-2.1.0/src/util.h:16:35: note: expected ‘char *’ but argument is of type ‘const char *’ 16 | void reverse_complement_seq(char *seq); | ~~~~~~^~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/read.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/read.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/sequence.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/sequence.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE /build/reproducible-path/pyfastx-2.1.0/src/sequence.c: In function ‘pyfastx_sequence_get_fullseq’: /build/reproducible-path/pyfastx-2.1.0/src/sequence.c:90:32: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Py_ssize_t’ {aka ‘long int’} [-Wsign-compare] 90 | if (strlen(self->name) >= self->index->cache_name.m) { | ^~ /build/reproducible-path/pyfastx-2.1.0/src/sequence.c: In function ‘pyfastx_sequence_subscript’: /build/reproducible-path/pyfastx-2.1.0/src/sequence.c:431:20: warning: variable ‘slice_len’ set but not used [-Wunused-but-set-variable] 431 | Py_ssize_t slice_len; | ^~~~~~~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/util.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/util.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/zran.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/zran.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/zran_file_util.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/zran_file_util.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/fakeys.o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/fasta.o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/fastq.o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/fastx.o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/fqkeys.o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/index.o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/kseq.o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/module.o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/read.o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/sequence.o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/util.o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/zran.o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/zran_file_util.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/pyfastx.cpython-312-x86_64-linux-gnu.so -lsqlite3 dh_auto_test -O--buildsystem=pybuild I: pybuild pybuild:308: mkdir -pv /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/src && cp -v src/version.h /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/src mkdir: created directory '/build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/src' 'src/version.h' -> '/build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/src/version.h' I: pybuild base:311: cd /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build; python3.13 -m unittest discover -v test_id_exception (tests.test_fakeys.IdentifierTest.test_id_exception) ... ok test_key_identifier (tests.test_fakeys.IdentifierTest.test_key_identifier) ... ok test_key_repr (tests.test_fakeys.IdentifierTest.test_key_repr) ... ok test_key_slice (tests.test_fakeys.IdentifierTest.test_key_slice) ... ok test_keys_filter (tests.test_fakeys.IdentifierTest.test_keys_filter) ... ok test_keys_sort (tests.test_fakeys.IdentifierTest.test_keys_sort) ... ok test_build (tests.test_fasta.FastaTest.test_build) ... ok test_exception (tests.test_fasta.FastaTest.test_exception) ... ok test_fasta (tests.test_fasta.FastaTest.test_fasta) ... ok test_iter_full_name (tests.test_fasta.FastaTest.test_iter_full_name) ... ok test_iter_object (tests.test_fasta.FastaTest.test_iter_object) ... ok test_iter_tuple (tests.test_fasta.FastaTest.test_iter_tuple) ... ok test_iter_upper (tests.test_fasta.FastaTest.test_iter_upper) ... ok test_iter_upper_full_name (tests.test_fasta.FastaTest.test_iter_upper_full_name) ... ok test_key_func (tests.test_fasta.FastaTest.test_key_func) ... ok test_module (tests.test_fasta.FastaTest.test_module) ... ok test_no_upper (tests.test_fasta.FastaTest.test_no_upper) ... ok test_repr (tests.test_fasta.FastaTest.test_repr) ... ok test_seq_fetch (tests.test_fasta.FastaTest.test_seq_fetch) ... ok test_seq_flank (tests.test_fasta.FastaTest.test_seq_flank) ... ok test_seq_type (tests.test_fasta.FastaTest.test_seq_type) ... ok test_statistics (tests.test_fasta.FastaTest.test_statistics) ... ok test_build (tests.test_fastq.FastqTest.test_build) ... ok test_exception (tests.test_fastq.FastqTest.test_exception) ... ok test_fastq (tests.test_fastq.FastqTest.test_fastq) ... ok test_full_name (tests.test_fastq.FastqTest.test_full_name) ... ok test_iter_object (tests.test_fastq.FastqTest.test_iter_object) ... ok test_iter_tuple (tests.test_fastq.FastqTest.test_iter_tuple) ... ok test_negative (tests.test_fastq.FastqTest.test_negative) ... ok test_platform (tests.test_fastq.FastqTest.test_platform) ... ok test_read_len (tests.test_fastq.FastqTest.test_read_len) ... ok test_repr (tests.test_fastq.FastqTest.test_repr) ... ok test_exception (tests.test_fastx.FastxTest.test_exception) ... ok test_fasta_iter (tests.test_fastx.FastxTest.test_fasta_iter) ... ok test_fasta_upper (tests.test_fastx.FastxTest.test_fasta_upper) ... ok test_fastq_iter (tests.test_fastx.FastxTest.test_fastq_iter) ... ok test_fastx_repr (tests.test_fastx.FastxTest.test_fastx_repr) ... ok test_exception (tests.test_fqkeys.FastxTest.test_exception) ... ok test_fastq_key (tests.test_fqkeys.FastxTest.test_fastq_key) ... ok test_read (tests.test_read.ReadTest.test_read) ... ok test_read_description (tests.test_read.ReadTest.test_read_description) ... ok test_read_raw (tests.test_read.ReadTest.test_read_raw) ... ok test_read_seq (tests.test_read.ReadTest.test_read_seq) ... ok test_repr (tests.test_read.ReadTest.test_repr) ... ok test_full_compo (tests.test_sequence.SequenceTest.test_full_compo) ... ok test_seq_by_index (tests.test_sequence.SequenceTest.test_seq_by_index) ... ok test_seq_by_key (tests.test_sequence.SequenceTest.test_seq_by_key) ... ok test_seq_content (tests.test_sequence.SequenceTest.test_seq_content) ... ok test_seq_exception (tests.test_sequence.SequenceTest.test_seq_exception) ... ok test_seq_iter (tests.test_sequence.SequenceTest.test_seq_iter) ... ok test_seq_raw (tests.test_sequence.SequenceTest.test_seq_raw) ... ok test_seq_repr (tests.test_sequence.SequenceTest.test_seq_repr) ... ok test_seq_reverse_complement (tests.test_sequence.SequenceTest.test_seq_reverse_complement) ... ok test_seq_slice (tests.test_sequence.SequenceTest.test_seq_slice) ... ok test_seq_by_index (tests.test_sequence_error.SequenceErrorTest.test_seq_by_index) ... ok test_seq_by_key (tests.test_sequence_error.SequenceErrorTest.test_seq_by_key) ... ok ---------------------------------------------------------------------- Ran 56 tests in 26.148s OK pyfastx: 2.1.0; zlib: 1.3.1; sqlite: 3.46.1; zran: 1.7.0 I: pybuild pybuild:334: rm -rvf /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/src /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/non.fa removed '/build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/src/version.h' removed directory '/build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/src' removed '/build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/non.fa' I: pybuild pybuild:308: mkdir -pv /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/src && cp -v src/version.h /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/src mkdir: created directory '/build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/src' 'src/version.h' -> '/build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/src/version.h' I: pybuild base:311: cd /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build; python3.12 -m unittest discover -v test_id_exception (tests.test_fakeys.IdentifierTest.test_id_exception) ... ok test_key_identifier (tests.test_fakeys.IdentifierTest.test_key_identifier) ... ok test_key_repr (tests.test_fakeys.IdentifierTest.test_key_repr) ... ok test_key_slice (tests.test_fakeys.IdentifierTest.test_key_slice) ... ok test_keys_filter (tests.test_fakeys.IdentifierTest.test_keys_filter) ... ok test_keys_sort (tests.test_fakeys.IdentifierTest.test_keys_sort) ... ok test_build (tests.test_fasta.FastaTest.test_build) ... ok test_exception (tests.test_fasta.FastaTest.test_exception) ... ok test_fasta (tests.test_fasta.FastaTest.test_fasta) ... ok test_iter_full_name (tests.test_fasta.FastaTest.test_iter_full_name) ... ok test_iter_object (tests.test_fasta.FastaTest.test_iter_object) ... ok test_iter_tuple (tests.test_fasta.FastaTest.test_iter_tuple) ... ok test_iter_upper (tests.test_fasta.FastaTest.test_iter_upper) ... ok test_iter_upper_full_name (tests.test_fasta.FastaTest.test_iter_upper_full_name) ... ok test_key_func (tests.test_fasta.FastaTest.test_key_func) ... ok test_module (tests.test_fasta.FastaTest.test_module) ... ok test_no_upper (tests.test_fasta.FastaTest.test_no_upper) ... ok test_repr (tests.test_fasta.FastaTest.test_repr) ... ok test_seq_fetch (tests.test_fasta.FastaTest.test_seq_fetch) ... ok test_seq_flank (tests.test_fasta.FastaTest.test_seq_flank) ... ok test_seq_type (tests.test_fasta.FastaTest.test_seq_type) ... ok test_statistics (tests.test_fasta.FastaTest.test_statistics) ... ok test_build (tests.test_fastq.FastqTest.test_build) ... ok test_exception (tests.test_fastq.FastqTest.test_exception) ... ok test_fastq (tests.test_fastq.FastqTest.test_fastq) ... ok test_full_name (tests.test_fastq.FastqTest.test_full_name) ... ok test_iter_object (tests.test_fastq.FastqTest.test_iter_object) ... ok test_iter_tuple (tests.test_fastq.FastqTest.test_iter_tuple) ... ok test_negative (tests.test_fastq.FastqTest.test_negative) ... ok test_platform (tests.test_fastq.FastqTest.test_platform) ... ok test_read_len (tests.test_fastq.FastqTest.test_read_len) ... ok test_repr (tests.test_fastq.FastqTest.test_repr) ... ok test_exception (tests.test_fastx.FastxTest.test_exception) ... ok test_fasta_iter (tests.test_fastx.FastxTest.test_fasta_iter) ... ok test_fasta_upper (tests.test_fastx.FastxTest.test_fasta_upper) ... ok test_fastq_iter (tests.test_fastx.FastxTest.test_fastq_iter) ... ok test_fastx_repr (tests.test_fastx.FastxTest.test_fastx_repr) ... ok test_exception (tests.test_fqkeys.FastxTest.test_exception) ... ok test_fastq_key (tests.test_fqkeys.FastxTest.test_fastq_key) ... ok test_read (tests.test_read.ReadTest.test_read) ... ok test_read_description (tests.test_read.ReadTest.test_read_description) ... ok test_read_raw (tests.test_read.ReadTest.test_read_raw) ... ok test_read_seq (tests.test_read.ReadTest.test_read_seq) ... ok test_repr (tests.test_read.ReadTest.test_repr) ... ok test_full_compo (tests.test_sequence.SequenceTest.test_full_compo) ... ok test_seq_by_index (tests.test_sequence.SequenceTest.test_seq_by_index) ... ok test_seq_by_key (tests.test_sequence.SequenceTest.test_seq_by_key) ... ok test_seq_content (tests.test_sequence.SequenceTest.test_seq_content) ... ok test_seq_exception (tests.test_sequence.SequenceTest.test_seq_exception) ... ok test_seq_iter (tests.test_sequence.SequenceTest.test_seq_iter) ... ok test_seq_raw (tests.test_sequence.SequenceTest.test_seq_raw) ... ok test_seq_repr (tests.test_sequence.SequenceTest.test_seq_repr) ... ok test_seq_reverse_complement (tests.test_sequence.SequenceTest.test_seq_reverse_complement) ... ok test_seq_slice (tests.test_sequence.SequenceTest.test_seq_slice) ... ok test_seq_by_index (tests.test_sequence_error.SequenceErrorTest.test_seq_by_index) ... ok test_seq_by_key (tests.test_sequence_error.SequenceErrorTest.test_seq_by_key) ... ok ---------------------------------------------------------------------- Ran 56 tests in 19.057s OK pyfastx: 2.1.0; zlib: 1.3.1; sqlite: 3.46.1; zran: 1.7.0 I: pybuild pybuild:334: rm -rvf /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/src /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/non.fa removed '/build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/src/version.h' removed directory '/build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/src' removed '/build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/non.fa' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3.13 setup.py install --root /build/reproducible-path/pyfastx-2.1.0/debian/tmp /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running build_ext running install_lib creating /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.13/dist-packages copying /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/pyfastxcli.py -> /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.13/dist-packages copying /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/pyfastx.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.13/dist-packages byte-compiling /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.13/dist-packages/pyfastxcli.py to pyfastxcli.cpython-313.pyc running install_egg_info running egg_info creating pyfastx.egg-info writing pyfastx.egg-info/PKG-INFO writing dependency_links to pyfastx.egg-info/dependency_links.txt writing entry points to pyfastx.egg-info/entry_points.txt writing top-level names to pyfastx.egg-info/top_level.txt writing manifest file 'pyfastx.egg-info/SOURCES.txt' reading manifest file 'pyfastx.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'pyfastx.egg-info/SOURCES.txt' Copying pyfastx.egg-info to /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.13/dist-packages/pyfastx-2.1.0.egg-info Skipping SOURCES.txt running install_scripts Installing pyfastx script to /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/bin I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/pyfastx-2.1.0/debian/tmp /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running build_ext running install_lib creating /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.12/dist-packages copying /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/pyfastx.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.12/dist-packages copying /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/pyfastxcli.py -> /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.12/dist-packages byte-compiling /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.12/dist-packages/pyfastxcli.py to pyfastxcli.cpython-312.pyc running install_egg_info running egg_info writing pyfastx.egg-info/PKG-INFO writing dependency_links to pyfastx.egg-info/dependency_links.txt writing entry points to pyfastx.egg-info/entry_points.txt writing top-level names to pyfastx.egg-info/top_level.txt reading manifest file 'pyfastx.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'pyfastx.egg-info/SOURCES.txt' Copying pyfastx.egg-info to /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.12/dist-packages/pyfastx-2.1.0.egg-info Skipping SOURCES.txt running install_scripts Installing pyfastx script to /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/bin dh_install -O--buildsystem=pybuild dh_installdocs -O--buildsystem=pybuild debian/rules execute_after_dh_installdocs make[1]: Entering directory '/build/reproducible-path/pyfastx-2.1.0' # Deduplicate changelog entries flagged by lintian. rm debian/pyfastx/usr/share/doc/pyfastx/docs/changelog.rst* cd debian/pyfastx/usr/share/doc/pyfastx/docs \ && ln -s ../changelog.gz changelog.rst.gz make[1]: Leaving directory '/build/reproducible-path/pyfastx-2.1.0' dh_installchangelogs -O--buildsystem=pybuild dh_installexamples -O--buildsystem=pybuild debian/rules execute_after_dh_installexamples make[1]: Entering directory '/build/reproducible-path/pyfastx-2.1.0' # Remove duplicate uncompressed files caused by the nature of the test; # we can get them back during the CLI test. rm debian/pyfastx/usr/share/doc/pyfastx/examples/test.fa rm debian/pyfastx/usr/share/doc/pyfastx/examples/test.fq make[1]: Leaving directory '/build/reproducible-path/pyfastx-2.1.0' dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: package python3-pyfastx: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: Depends field of package pyfastx: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package python3-pyfastx: substitution variable ${python3:Depends} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'pyfastx' in '../pyfastx_2.1.0-2_amd64.deb'. dpkg-deb: building package 'python3-pyfastx' in '../python3-pyfastx_2.1.0-2_amd64.deb'. dpkg-deb: building package 'python3-pyfastx-dbgsym' in '../python3-pyfastx-dbgsym_2.1.0-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../pyfastx_2.1.0-2_amd64.buildinfo dpkg-genchanges --build=binary -O../pyfastx_2.1.0-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) 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/1758472 and its subdirectories I: Current time: Tue Dec 23 19:02:47 -12 2025 I: pbuilder-time-stamp: 1766559767 Thu Nov 21 00:39:48 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Thu Nov 21 00:39:48 UTC 2024 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Thu Nov 21 00:39:48 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Thu Nov 21 00:39:48 UTC 2024 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-FpU6vJ' ==================================================================================== Thu Nov 21 00:39:49 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos1-amd64, called using "2 pyfastx unstable /srv/reproducible-results/rbuild-debian/r-b-build.v7khtA9G 2.1.0-2" as arguments. Thu Nov 21 00:39:49 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-fX6DWAQk" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Nov 21 00:39:49 UTC 2024 I: Downloading source for unstable/pyfastx=2.1.0-2 Reading package lists... NOTICE: 'pyfastx' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/pyfastx.git Please use: git clone https://salsa.debian.org/med-team/pyfastx.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 240 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main pyfastx 2.1.0-2 (dsc) [2289 B] Get:2 http://deb.debian.org/debian unstable/main pyfastx 2.1.0-2 (tar) [230 kB] Get:3 http://deb.debian.org/debian unstable/main pyfastx 2.1.0-2 (diff) [7412 B] Fetched 240 kB in 0s (3095 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'pyfastx' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/pyfastx.git Please use: git clone https://salsa.debian.org/med-team/pyfastx.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 240 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main pyfastx 2.1.0-2 (dsc) [2289 B] Get:2 http://deb.debian.org/debian unstable/main pyfastx 2.1.0-2 (tar) [230 kB] Get:3 http://deb.debian.org/debian unstable/main pyfastx 2.1.0-2 (diff) [7412 B] Fetched 240 kB in 0s (3095 kB/s) Download complete and in download only mode ============================================================================= Re-Building pyfastx in unstable on amd64 on ionos1-amd64 now. Date: Thu Nov 21 00:39:50 UTC 2024 Date UTC: Thu Nov 21 00:39:50 UTC 2024 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.v7khtA9G + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.v7khtA9G/pbuilderrc_XK5z + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' pyfastx = debian-installer -o pyfastx = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' pyfastx = u-boot ']' + case "${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.v7khtA9G/pbuilderrc_XK5z --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.v7khtA9G/b2 --logfile b2/build.log pyfastx_2.1.0-2.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: Thu Nov 21 14:39:51 +14 2024 I: pbuilder-time-stamp: 1732149591 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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 [pyfastx_2.1.0-2.dsc] I: copying [./pyfastx_2.1.0.orig.tar.xz] I: copying [./pyfastx_2.1.0-2.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Aug 30 18:49:12 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./pyfastx_2.1.0-2.dsc: no acceptable signature found dpkg-source: info: extracting pyfastx in pyfastx-2.1.0 dpkg-source: info: unpacking pyfastx_2.1.0.orig.tar.xz dpkg-source: info: unpacking pyfastx_2.1.0-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 0001-t-test_sequence.py.patch dpkg-source: info: applying use_debian_packaged_indexed-gzip.patch dpkg-source: info: applying use_debian_packaged_zlib.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3551939/tmp/hooks/D01_modify_environment starting debug: Running on ionos1-amd64. 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 Nov 21 00:40 /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/3551939/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3551939/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]="2" [2]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=3301d2fb2643404ca376f92391dbe9e2 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-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=3551939 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.v7khtA9G/pbuilderrc_XK5z --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.v7khtA9G/b2 --logfile b2/build.log pyfastx_2.1.0-2.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3551939/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: amd64 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-python, libsqlite3-dev, zlib1g-dev, python3-all-dev, python3-indexed-gzip, python3-pyfaidx, python3-setuptools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19966 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-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on libsqlite3-dev; however: Package libsqlite3-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-indexed-gzip; however: Package python3-indexed-gzip is not installed. pbuilder-satisfydepends-dummy depends on python3-pyfaidx; however: Package python3-pyfaidx is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools 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} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libcom-err2{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgssapi-krb5-2{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libmagic-mgc{a} libmagic1t64{a} libnsl2{a} libpipeline1{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libsqlite3-dev{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-all{a} python3-all-dev{a} python3-autocommand{a} python3-dev{a} python3-importlib-metadata{a} python3-indexed-gzip{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-packaging{a} python3-pkg-resources{a} python3-pyfaidx{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common krb5-locales libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx python3-biopython wget 0 packages upgraded, 92 newly installed, 0 to remove and 0 not upgraded. Need to get 61.8 MB of archives. After unpacking 320 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.7-3 [815 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.7-3 [2162 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.12.7-1 [26.8 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024b-3 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1+b1 [23.2 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 12 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.7-3 [1966 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.7-3 [671 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.12.7-1 [9712 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.12.7-1 [27.8 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.0-2 [856 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.0-2 [2038 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-8 [517 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 46 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 python3-importlib-metadata all 8.5.0-1 [21.0 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 62 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 75.2.0-1 [731 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20241024 [109 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-4 [152 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 7.4.7-4 [158 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libpython3.12t64 amd64 3.12.7-3 [2153 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libpython3.12-dev amd64 3.12.7-3 [5124 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.12.7-1 [9976 B] Get: 78 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [1992 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.0-2 [2137 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.0-2 [4994 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libpython3-all-dev amd64 3.12.7-1 [1072 B] Get: 82 http://deb.debian.org/debian unstable/main amd64 libsqlite3-dev amd64 3.46.1-1 [1107 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.0-2 [730 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.12.7-1 [1052 B] Get: 85 http://deb.debian.org/debian unstable/main amd64 python3.12-dev amd64 3.12.7-3 [505 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.12.7-1 [26.1 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.0-2 [504 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 python3-all-dev amd64 3.12.7-1 [1076 B] Get: 89 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:1.26.4+ds-12 [4738 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 python3-indexed-gzip amd64 1.8.7-3+b1 [1499 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 python3-pyfaidx all 0.8.1.3-1 [29.1 kB] Fetched 61.8 MB in 3s (21.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (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 ... 19966 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.7-3_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.7-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.7-3_amd64.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:amd64 (3.12.7-3) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.7-3) ... 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 ... 20286 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.7-1_amd64.deb ... Unpacking python3-minimal (3.12.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-3_all.deb ... Unpacking tzdata (2024b-3) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../05-libcom-err2_1.47.1-1+b1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../07-libkeyutils1_1.6.3-4_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../14-libreadline8t64_8.2-5_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.7-3_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.7-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.7-3_amd64.deb ... Unpacking python3.12 (3.12.7-3) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../17-libpython3-stdlib_3.12.7-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.7-1) ... Setting up python3-minimal (3.12.7-1) ... 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 ... 21348 files and directories currently installed.) Preparing to unpack .../00-python3_3.12.7-1_amd64.deb ... Unpacking python3 (3.12.7-1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../01-libpython3.13-minimal_3.13.0-2_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.0-2) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../02-python3.13-minimal_3.13.0-2_amd64.deb ... Unpacking python3.13-minimal (3.13.0-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../03-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../05-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../06-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../07-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../08-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../09-groff-base_1.23.0-5_amd64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../10-bsdextrautils_2.40.2-11_amd64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../11-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../12-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../15-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../16-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../17-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../18-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../19-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../20-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../21-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../22-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../23-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../24-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../25-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../26-libicu72_72.1-5+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-5+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../27-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../28-gettext_0.22.5-2_amd64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../29-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../30-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../31-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package python3-autocommand. Preparing to unpack .../32-python3-autocommand_2.2.2-3_all.deb ... Unpacking python3-autocommand (2.2.2-3) ... Selecting previously unselected package python3-more-itertools. Preparing to unpack .../33-python3-more-itertools_10.5.0-1_all.deb ... Unpacking python3-more-itertools (10.5.0-1) ... Selecting previously unselected package python3-typing-extensions. Preparing to unpack .../34-python3-typing-extensions_4.12.2-2_all.deb ... Unpacking python3-typing-extensions (4.12.2-2) ... Selecting previously unselected package python3-zipp. Preparing to unpack .../35-python3-zipp_3.21.0-1_all.deb ... Unpacking python3-zipp (3.21.0-1) ... Selecting previously unselected package python3-importlib-metadata. Preparing to unpack .../36-python3-importlib-metadata_8.5.0-1_all.deb ... Unpacking python3-importlib-metadata (8.5.0-1) ... Selecting previously unselected package python3-typeguard. 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Setting up libicu72:amd64 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:amd64 (1.47.1-1+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Nov 21 00:42:34 UTC 2024. Universal Time is now: Thu Nov 21 00:42:34 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libpython3.13-minimal:amd64 (3.13.0-2) ... Setting up autotools-dev (20220109.1) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/3551939/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/3551939/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/pyfastx-2.1.0/ && 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 > ../pyfastx_2.1.0-2_source.changes dpkg-buildpackage: info: source package pyfastx dpkg-buildpackage: info: source version 2.1.0-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem pybuild --with python3 dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py clean /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) running clean removing '/build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.13' does not exist -- can't clean it I: pybuild base:311: python3.12 setup.py clean /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) running clean removing '/build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem pybuild --with python3 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/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) running config I: pybuild base:311: python3.12 setup.py config /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) running config debian/rules execute_before_dh_auto_build make[1]: Entering directory '/build/reproducible-path/pyfastx-2.1.0' # Upstream originally vendored these files straight in src/, but # stopped for some reason. We're pulling them instead from the # package python3-indexed-gzip. cp --update=none /usr/lib/python3/dist-packages/indexed_gzip/zran.c src/ cp --update=none /usr/lib/python3/dist-packages/indexed_gzip/zran.h src/ cp --update=none /usr/lib/python3/dist-packages/indexed_gzip/zran_file_util.c src/ cp --update=none /usr/lib/python3/dist-packages/indexed_gzip/zran_file_util.h src/ make[1]: Leaving directory '/build/reproducible-path/pyfastx-2.1.0' dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3.13 setup.py build /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) running build running build_py copying pyfastxcli.py -> /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build running build_ext building 'pyfastx' extension creating build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/fakeys.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/fakeys.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/fasta.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/fasta.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE /build/reproducible-path/pyfastx-2.1.0/src/fasta.c: In function ‘pyfastx_fasta_fetch’: /build/reproducible-path/pyfastx-2.1.0/src/fasta.c:443:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Py_ssize_t’ {aka ‘long int’} [-Wsign-compare] 443 | if (strlen(name) >= self->index->cache_name.m) { | ^~ /build/reproducible-path/pyfastx-2.1.0/src/fasta.c: In function ‘pyfastx_fasta_composition’: /build/reproducible-path/pyfastx-2.1.0/src/fasta.c:1058:13: warning: unused variable ‘i’ [-Wunused-variable] 1058 | int i; | ^ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/fastq.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/fastq.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/fastx.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/fastx.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/fqkeys.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/fqkeys.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/index.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/index.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/kseq.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/kseq.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/module.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/module.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE /build/reproducible-path/pyfastx-2.1.0/src/module.c: In function ‘pyfastx_reverse_complement’: /build/reproducible-path/pyfastx-2.1.0/src/module.c:57:32: warning: passing argument 1 of ‘reverse_complement_seq’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 57 | reverse_complement_seq(s); | ^ In file included from /build/reproducible-path/pyfastx-2.1.0/src/fastq.h:8, from /build/reproducible-path/pyfastx-2.1.0/src/module.c:3: /build/reproducible-path/pyfastx-2.1.0/src/util.h:16:35: note: expected ‘char *’ but argument is of type ‘const char *’ 16 | void reverse_complement_seq(char *seq); | ~~~~~~^~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/read.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/read.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/sequence.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/sequence.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE /build/reproducible-path/pyfastx-2.1.0/src/sequence.c: In function ‘pyfastx_sequence_get_fullseq’: /build/reproducible-path/pyfastx-2.1.0/src/sequence.c:90:32: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Py_ssize_t’ {aka ‘long int’} [-Wsign-compare] 90 | if (strlen(self->name) >= self->index->cache_name.m) { | ^~ /build/reproducible-path/pyfastx-2.1.0/src/sequence.c: In function ‘pyfastx_sequence_subscript’: /build/reproducible-path/pyfastx-2.1.0/src/sequence.c:431:20: warning: variable ‘slice_len’ set but not used [-Wunused-but-set-variable] 431 | Py_ssize_t slice_len; | ^~~~~~~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/util.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/util.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/zran.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/zran.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c /build/reproducible-path/pyfastx-2.1.0/src/zran_file_util.c -o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/zran_file_util.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/fakeys.o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/fasta.o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/fastq.o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/fastx.o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/fqkeys.o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/index.o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/kseq.o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/module.o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/read.o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/sequence.o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/util.o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/zran.o build/temp.linux-x86_64-cpython-313/build/reproducible-path/pyfastx-2.1.0/src/zran_file_util.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/pyfastx.cpython-313-x86_64-linux-gnu.so -lsqlite3 I: pybuild base:311: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) running build running build_py copying pyfastxcli.py -> /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build running build_ext building 'pyfastx' extension creating build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/fakeys.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/fakeys.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/fasta.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/fasta.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE /build/reproducible-path/pyfastx-2.1.0/src/fasta.c: In function ‘pyfastx_fasta_fetch’: /build/reproducible-path/pyfastx-2.1.0/src/fasta.c:443:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Py_ssize_t’ {aka ‘long int’} [-Wsign-compare] 443 | if (strlen(name) >= self->index->cache_name.m) { | ^~ /build/reproducible-path/pyfastx-2.1.0/src/fasta.c: In function ‘pyfastx_fasta_composition’: /build/reproducible-path/pyfastx-2.1.0/src/fasta.c:1058:13: warning: unused variable ‘i’ [-Wunused-variable] 1058 | int i; | ^ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/fastq.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/fastq.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/fastx.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/fastx.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/fqkeys.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/fqkeys.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/index.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/index.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/kseq.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/kseq.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/module.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/module.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE /build/reproducible-path/pyfastx-2.1.0/src/module.c: In function ‘pyfastx_reverse_complement’: /build/reproducible-path/pyfastx-2.1.0/src/module.c:57:32: warning: passing argument 1 of ‘reverse_complement_seq’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 57 | reverse_complement_seq(s); | ^ In file included from /build/reproducible-path/pyfastx-2.1.0/src/fastq.h:8, from /build/reproducible-path/pyfastx-2.1.0/src/module.c:3: /build/reproducible-path/pyfastx-2.1.0/src/util.h:16:35: note: expected ‘char *’ but argument is of type ‘const char *’ 16 | void reverse_complement_seq(char *seq); | ~~~~~~^~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/read.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/read.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/sequence.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/sequence.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE /build/reproducible-path/pyfastx-2.1.0/src/sequence.c: In function ‘pyfastx_sequence_get_fullseq’: /build/reproducible-path/pyfastx-2.1.0/src/sequence.c:90:32: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Py_ssize_t’ {aka ‘long int’} [-Wsign-compare] 90 | if (strlen(self->name) >= self->index->cache_name.m) { | ^~ /build/reproducible-path/pyfastx-2.1.0/src/sequence.c: In function ‘pyfastx_sequence_subscript’: /build/reproducible-path/pyfastx-2.1.0/src/sequence.c:431:20: warning: variable ‘slice_len’ set but not used [-Wunused-but-set-variable] 431 | Py_ssize_t slice_len; | ^~~~~~~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/util.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/util.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/zran.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/zran.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c /build/reproducible-path/pyfastx-2.1.0/src/zran_file_util.c -o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/zran_file_util.o -Wno-unused-result -D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pyfastx-2.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/fakeys.o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/fasta.o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/fastq.o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/fastx.o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/fqkeys.o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/index.o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/kseq.o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/module.o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/read.o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/sequence.o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/util.o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/zran.o build/temp.linux-x86_64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/zran_file_util.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/pyfastx.cpython-312-x86_64-linux-gnu.so -lsqlite3 dh_auto_test -O--buildsystem=pybuild I: pybuild pybuild:308: mkdir -pv /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/src && cp -v src/version.h /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/src mkdir: created directory '/build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/src' 'src/version.h' -> '/build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/src/version.h' I: pybuild base:311: cd /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build; python3.13 -m unittest discover -v test_id_exception (tests.test_fakeys.IdentifierTest.test_id_exception) ... ok test_key_identifier (tests.test_fakeys.IdentifierTest.test_key_identifier) ... ok test_key_repr (tests.test_fakeys.IdentifierTest.test_key_repr) ... ok test_key_slice (tests.test_fakeys.IdentifierTest.test_key_slice) ... ok test_keys_filter (tests.test_fakeys.IdentifierTest.test_keys_filter) ... ok test_keys_sort (tests.test_fakeys.IdentifierTest.test_keys_sort) ... ok test_build (tests.test_fasta.FastaTest.test_build) ... ok test_exception (tests.test_fasta.FastaTest.test_exception) ... ok test_fasta (tests.test_fasta.FastaTest.test_fasta) ... ok test_iter_full_name (tests.test_fasta.FastaTest.test_iter_full_name) ... ok test_iter_object (tests.test_fasta.FastaTest.test_iter_object) ... ok test_iter_tuple (tests.test_fasta.FastaTest.test_iter_tuple) ... ok test_iter_upper (tests.test_fasta.FastaTest.test_iter_upper) ... ok test_iter_upper_full_name (tests.test_fasta.FastaTest.test_iter_upper_full_name) ... ok test_key_func (tests.test_fasta.FastaTest.test_key_func) ... ok test_module (tests.test_fasta.FastaTest.test_module) ... ok test_no_upper (tests.test_fasta.FastaTest.test_no_upper) ... ok test_repr (tests.test_fasta.FastaTest.test_repr) ... ok test_seq_fetch (tests.test_fasta.FastaTest.test_seq_fetch) ... ok test_seq_flank (tests.test_fasta.FastaTest.test_seq_flank) ... ok test_seq_type (tests.test_fasta.FastaTest.test_seq_type) ... ok test_statistics (tests.test_fasta.FastaTest.test_statistics) ... ok test_build (tests.test_fastq.FastqTest.test_build) ... ok test_exception (tests.test_fastq.FastqTest.test_exception) ... ok test_fastq (tests.test_fastq.FastqTest.test_fastq) ... ok test_full_name (tests.test_fastq.FastqTest.test_full_name) ... ok test_iter_object (tests.test_fastq.FastqTest.test_iter_object) ... ok test_iter_tuple (tests.test_fastq.FastqTest.test_iter_tuple) ... ok test_negative (tests.test_fastq.FastqTest.test_negative) ... ok test_platform (tests.test_fastq.FastqTest.test_platform) ... ok test_read_len (tests.test_fastq.FastqTest.test_read_len) ... ok test_repr (tests.test_fastq.FastqTest.test_repr) ... ok test_exception (tests.test_fastx.FastxTest.test_exception) ... ok test_fasta_iter (tests.test_fastx.FastxTest.test_fasta_iter) ... ok test_fasta_upper (tests.test_fastx.FastxTest.test_fasta_upper) ... ok test_fastq_iter (tests.test_fastx.FastxTest.test_fastq_iter) ... ok test_fastx_repr (tests.test_fastx.FastxTest.test_fastx_repr) ... ok test_exception (tests.test_fqkeys.FastxTest.test_exception) ... ok test_fastq_key (tests.test_fqkeys.FastxTest.test_fastq_key) ... ok test_read (tests.test_read.ReadTest.test_read) ... ok test_read_description (tests.test_read.ReadTest.test_read_description) ... ok test_read_raw (tests.test_read.ReadTest.test_read_raw) ... ok test_read_seq (tests.test_read.ReadTest.test_read_seq) ... ok test_repr (tests.test_read.ReadTest.test_repr) ... ok test_full_compo (tests.test_sequence.SequenceTest.test_full_compo) ... ok test_seq_by_index (tests.test_sequence.SequenceTest.test_seq_by_index) ... ok test_seq_by_key (tests.test_sequence.SequenceTest.test_seq_by_key) ... ok test_seq_content (tests.test_sequence.SequenceTest.test_seq_content) ... ok test_seq_exception (tests.test_sequence.SequenceTest.test_seq_exception) ... ok test_seq_iter (tests.test_sequence.SequenceTest.test_seq_iter) ... ok test_seq_raw (tests.test_sequence.SequenceTest.test_seq_raw) ... ok test_seq_repr (tests.test_sequence.SequenceTest.test_seq_repr) ... ok test_seq_reverse_complement (tests.test_sequence.SequenceTest.test_seq_reverse_complement) ... ok test_seq_slice (tests.test_sequence.SequenceTest.test_seq_slice) ... ok test_seq_by_index (tests.test_sequence_error.SequenceErrorTest.test_seq_by_index) ... ok test_seq_by_key (tests.test_sequence_error.SequenceErrorTest.test_seq_by_key) ... ok ---------------------------------------------------------------------- Ran 56 tests in 9.849s OK pyfastx: 2.1.0; zlib: 1.3.1; sqlite: 3.46.1; zran: 1.7.0 I: pybuild pybuild:334: rm -rvf /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/src /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/non.fa removed '/build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/src/version.h' removed directory '/build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/src' removed '/build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/non.fa' I: pybuild pybuild:308: mkdir -pv /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/src && cp -v src/version.h /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/src mkdir: created directory '/build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/src' 'src/version.h' -> '/build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/src/version.h' I: pybuild base:311: cd /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build; python3.12 -m unittest discover -v test_id_exception (tests.test_fakeys.IdentifierTest.test_id_exception) ... ok test_key_identifier (tests.test_fakeys.IdentifierTest.test_key_identifier) ... ok test_key_repr (tests.test_fakeys.IdentifierTest.test_key_repr) ... ok test_key_slice (tests.test_fakeys.IdentifierTest.test_key_slice) ... ok test_keys_filter (tests.test_fakeys.IdentifierTest.test_keys_filter) ... ok test_keys_sort (tests.test_fakeys.IdentifierTest.test_keys_sort) ... ok test_build (tests.test_fasta.FastaTest.test_build) ... ok test_exception (tests.test_fasta.FastaTest.test_exception) ... ok test_fasta (tests.test_fasta.FastaTest.test_fasta) ... ok test_iter_full_name (tests.test_fasta.FastaTest.test_iter_full_name) ... ok test_iter_object (tests.test_fasta.FastaTest.test_iter_object) ... ok test_iter_tuple (tests.test_fasta.FastaTest.test_iter_tuple) ... ok test_iter_upper (tests.test_fasta.FastaTest.test_iter_upper) ... ok test_iter_upper_full_name (tests.test_fasta.FastaTest.test_iter_upper_full_name) ... ok test_key_func (tests.test_fasta.FastaTest.test_key_func) ... ok test_module (tests.test_fasta.FastaTest.test_module) ... ok test_no_upper (tests.test_fasta.FastaTest.test_no_upper) ... ok test_repr (tests.test_fasta.FastaTest.test_repr) ... ok test_seq_fetch (tests.test_fasta.FastaTest.test_seq_fetch) ... ok test_seq_flank (tests.test_fasta.FastaTest.test_seq_flank) ... ok test_seq_type (tests.test_fasta.FastaTest.test_seq_type) ... ok test_statistics (tests.test_fasta.FastaTest.test_statistics) ... ok test_build (tests.test_fastq.FastqTest.test_build) ... ok test_exception (tests.test_fastq.FastqTest.test_exception) ... ok test_fastq (tests.test_fastq.FastqTest.test_fastq) ... ok test_full_name (tests.test_fastq.FastqTest.test_full_name) ... ok test_iter_object (tests.test_fastq.FastqTest.test_iter_object) ... ok test_iter_tuple (tests.test_fastq.FastqTest.test_iter_tuple) ... ok test_negative (tests.test_fastq.FastqTest.test_negative) ... ok test_platform (tests.test_fastq.FastqTest.test_platform) ... ok test_read_len (tests.test_fastq.FastqTest.test_read_len) ... ok test_repr (tests.test_fastq.FastqTest.test_repr) ... ok test_exception (tests.test_fastx.FastxTest.test_exception) ... ok test_fasta_iter (tests.test_fastx.FastxTest.test_fasta_iter) ... ok test_fasta_upper (tests.test_fastx.FastxTest.test_fasta_upper) ... ok test_fastq_iter (tests.test_fastx.FastxTest.test_fastq_iter) ... ok test_fastx_repr (tests.test_fastx.FastxTest.test_fastx_repr) ... ok test_exception (tests.test_fqkeys.FastxTest.test_exception) ... ok test_fastq_key (tests.test_fqkeys.FastxTest.test_fastq_key) ... ok test_read (tests.test_read.ReadTest.test_read) ... ok test_read_description (tests.test_read.ReadTest.test_read_description) ... ok test_read_raw (tests.test_read.ReadTest.test_read_raw) ... ok test_read_seq (tests.test_read.ReadTest.test_read_seq) ... ok test_repr (tests.test_read.ReadTest.test_repr) ... ok test_full_compo (tests.test_sequence.SequenceTest.test_full_compo) ... ok test_seq_by_index (tests.test_sequence.SequenceTest.test_seq_by_index) ... ok test_seq_by_key (tests.test_sequence.SequenceTest.test_seq_by_key) ... ok test_seq_content (tests.test_sequence.SequenceTest.test_seq_content) ... ok test_seq_exception (tests.test_sequence.SequenceTest.test_seq_exception) ... ok test_seq_iter (tests.test_sequence.SequenceTest.test_seq_iter) ... ok test_seq_raw (tests.test_sequence.SequenceTest.test_seq_raw) ... ok test_seq_repr (tests.test_sequence.SequenceTest.test_seq_repr) ... ok test_seq_reverse_complement (tests.test_sequence.SequenceTest.test_seq_reverse_complement) ... ok test_seq_slice (tests.test_sequence.SequenceTest.test_seq_slice) ... ok test_seq_by_index (tests.test_sequence_error.SequenceErrorTest.test_seq_by_index) ... ok test_seq_by_key (tests.test_sequence_error.SequenceErrorTest.test_seq_by_key) ... ok ---------------------------------------------------------------------- Ran 56 tests in 14.376s OK pyfastx: 2.1.0; zlib: 1.3.1; sqlite: 3.46.1; zran: 1.7.0 I: pybuild pybuild:334: rm -rvf /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/src /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/non.fa removed '/build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/src/version.h' removed directory '/build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/src' removed '/build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/non.fa' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3.13 setup.py install --root /build/reproducible-path/pyfastx-2.1.0/debian/tmp /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running build_ext running install_lib creating /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.13/dist-packages copying /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/pyfastx.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.13/dist-packages copying /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/pyfastxcli.py -> /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.13/dist-packages byte-compiling /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.13/dist-packages/pyfastxcli.py to pyfastxcli.cpython-313.pyc running install_egg_info running egg_info creating pyfastx.egg-info writing pyfastx.egg-info/PKG-INFO writing dependency_links to pyfastx.egg-info/dependency_links.txt writing entry points to pyfastx.egg-info/entry_points.txt writing top-level names to pyfastx.egg-info/top_level.txt writing manifest file 'pyfastx.egg-info/SOURCES.txt' reading manifest file 'pyfastx.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'pyfastx.egg-info/SOURCES.txt' Copying pyfastx.egg-info to /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.13/dist-packages/pyfastx-2.1.0.egg-info Skipping SOURCES.txt running install_scripts Installing pyfastx script to /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/bin I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/pyfastx-2.1.0/debian/tmp /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running build_ext running install_lib creating /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.12/dist-packages copying /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/pyfastxcli.py -> /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.12/dist-packages copying /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/pyfastx.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.12/dist-packages byte-compiling /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.12/dist-packages/pyfastxcli.py to pyfastxcli.cpython-312.pyc running install_egg_info running egg_info writing pyfastx.egg-info/PKG-INFO writing dependency_links to pyfastx.egg-info/dependency_links.txt writing entry points to pyfastx.egg-info/entry_points.txt writing top-level names to pyfastx.egg-info/top_level.txt reading manifest file 'pyfastx.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'pyfastx.egg-info/SOURCES.txt' Copying pyfastx.egg-info to /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.12/dist-packages/pyfastx-2.1.0.egg-info Skipping SOURCES.txt running install_scripts Installing pyfastx script to /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/bin dh_install -O--buildsystem=pybuild dh_installdocs -O--buildsystem=pybuild debian/rules execute_after_dh_installdocs make[1]: Entering directory '/build/reproducible-path/pyfastx-2.1.0' # Deduplicate changelog entries flagged by lintian. rm debian/pyfastx/usr/share/doc/pyfastx/docs/changelog.rst* cd debian/pyfastx/usr/share/doc/pyfastx/docs \ && ln -s ../changelog.gz changelog.rst.gz make[1]: Leaving directory '/build/reproducible-path/pyfastx-2.1.0' dh_installchangelogs -O--buildsystem=pybuild dh_installexamples -O--buildsystem=pybuild debian/rules execute_after_dh_installexamples make[1]: Entering directory '/build/reproducible-path/pyfastx-2.1.0' # Remove duplicate uncompressed files caused by the nature of the test; # we can get them back during the CLI test. rm debian/pyfastx/usr/share/doc/pyfastx/examples/test.fa rm debian/pyfastx/usr/share/doc/pyfastx/examples/test.fq make[1]: Leaving directory '/build/reproducible-path/pyfastx-2.1.0' dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: Depends field of package pyfastx: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package python3-pyfastx: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package python3-pyfastx: substitution variable ${python3:Depends} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-pyfastx-dbgsym' in '../python3-pyfastx-dbgsym_2.1.0-2_amd64.deb'. dpkg-deb: building package 'pyfastx' in '../pyfastx_2.1.0-2_amd64.deb'. dpkg-deb: building package 'python3-pyfastx' in '../python3-pyfastx_2.1.0-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../pyfastx_2.1.0-2_amd64.buildinfo dpkg-genchanges --build=binary -O../pyfastx_2.1.0-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3551939/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3551939/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/3551939 and its subdirectories I: Current time: Thu Nov 21 14:45:16 +14 2024 I: pbuilder-time-stamp: 1732149916 + false + set +x Thu Nov 21 00:45:16 UTC 2024 I: Signing ./b2/pyfastx_2.1.0-2_amd64.buildinfo as pyfastx_2.1.0-2_amd64.buildinfo.asc Thu Nov 21 00:45:16 UTC 2024 I: Signed ./b2/pyfastx_2.1.0-2_amd64.buildinfo as ./b2/pyfastx_2.1.0-2_amd64.buildinfo.asc Thu Nov 21 00:45:16 UTC 2024 - build #2 for pyfastx/unstable/amd64 on ionos1-amd64 done. Starting cleanup. All cleanup done. Thu Nov 21 00:45:16 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-fX6DWAQk, removing. /srv/reproducible-results/rbuild-debian/r-b-build.v7khtA9G: total 104 drwxr-xr-x 2 jenkins jenkins 4096 Nov 21 00:39 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 21 00:45 b2 -rw-r--r-- 1 jenkins jenkins 2289 Aug 30 18:55 pyfastx_2.1.0-2.dsc -rw------- 1 jenkins jenkins 88008 Nov 21 00:39 rbuildlog.fDS12AQ /srv/reproducible-results/rbuild-debian/r-b-build.v7khtA9G/b1: total 564 -rw-r--r-- 1 jenkins jenkins 84334 Nov 21 00:39 build.log -rw-r--r-- 1 jenkins jenkins 7412 Nov 21 00:39 pyfastx_2.1.0-2.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2289 Nov 21 00:39 pyfastx_2.1.0-2.dsc -rw-r--r-- 1 jenkins jenkins 7324 Nov 21 00:39 pyfastx_2.1.0-2_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 8206 Nov 21 00:39 pyfastx_2.1.0-2_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2285 Nov 21 00:39 pyfastx_2.1.0-2_amd64.changes -rw-r--r-- 1 jenkins jenkins 127152 Nov 21 00:39 pyfastx_2.1.0-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 1720 Nov 21 00:39 pyfastx_2.1.0-2_source.changes -rw-r--r-- 1 jenkins jenkins 234472 Nov 21 00:39 python3-pyfastx-dbgsym_2.1.0-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 64596 Nov 21 00:39 python3-pyfastx_2.1.0-2_amd64.deb /srv/reproducible-results/rbuild-debian/r-b-build.v7khtA9G/b2: total 552 -rw-r--r-- 1 jenkins jenkins 86254 Nov 21 00:45 build.log -rw-r--r-- 1 jenkins jenkins 7412 Nov 21 00:45 pyfastx_2.1.0-2.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2289 Nov 21 00:45 pyfastx_2.1.0-2.dsc -rw-r--r-- 1 jenkins jenkins 7315 Nov 21 00:45 pyfastx_2.1.0-2_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 8197 Nov 21 00:45 pyfastx_2.1.0-2_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2285 Nov 21 00:45 pyfastx_2.1.0-2_amd64.changes -rw-r--r-- 1 jenkins jenkins 127152 Nov 21 00:45 pyfastx_2.1.0-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 1720 Nov 21 00:45 pyfastx_2.1.0-2_source.changes -rw-r--r-- 1 jenkins jenkins 234472 Nov 21 00:45 python3-pyfastx-dbgsym_2.1.0-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 64596 Nov 21 00:45 python3-pyfastx_2.1.0-2_amd64.deb Thu Nov 21 00:45:17 UTC 2024 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Thu Nov 21 00:45:17 UTC 2024 I: pyfastx_2.1.0-2_amd64.changes: Format: 1.8 Date: Fri, 30 Aug 2024 20:31:18 +0200 Source: pyfastx Binary: pyfastx python3-pyfastx python3-pyfastx-dbgsym Architecture: amd64 Version: 2.1.0-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: pyfastx - fast random access to sequences from FASTA/Q file - command python3-pyfastx - fast random access to sequences from FASTA/Q file - python3 modul Closes: 1080124 Changes: pyfastx (2.1.0-2) unstable; urgency=medium . * d/rules: make use of indexed-gzip's zran files. * d/zran/: delete: debian's vendored zran is now unnecessary. * d/copyright: remove reference to debian's zran. * d/control: declare compliance to standards version 4.7.0. * use_debian_packaged_indexed-gzip.patch: forwarding not needed. * d/rules: the test suite needs src/version.h. This change also includes a cleanup step that gets rid of a spare non.fa fasta file that clutter the test bed after the run. (Closes: #1080124) * d/rules: use the portable variant of cp -n. Checksums-Sha1: bcc2defe52ded2a01ca012274369284190c4e068 7324 pyfastx_2.1.0-2_amd64.buildinfo b4ba848a587ab06ec1b4884317d7e35195397cbc 127152 pyfastx_2.1.0-2_amd64.deb 8cbbdd2171d4feb528cf386977e58b6402970453 234472 python3-pyfastx-dbgsym_2.1.0-2_amd64.deb f01b08a0ceef2cbb67cc4dc8c68e21721169d7f1 64596 python3-pyfastx_2.1.0-2_amd64.deb Checksums-Sha256: 82955b057413a329381e359985998d04993a49653fc1972f36381d49ddc0262e 7324 pyfastx_2.1.0-2_amd64.buildinfo 16ed491ece8742b917e7bed89c40d066cf004cdcbee2eea1f0fe744deb5079f6 127152 pyfastx_2.1.0-2_amd64.deb daa740f7cc9c3fbda3b94b8f00707623c49696aa8ffbddd5fb7c9df310876b6a 234472 python3-pyfastx-dbgsym_2.1.0-2_amd64.deb e88fc36ac2f99ceb2079a95fd053b6d69797423c13181095f9212f53be83a801 64596 python3-pyfastx_2.1.0-2_amd64.deb Files: 4ed48cfdfae251e472364e07abd7838e 7324 science optional pyfastx_2.1.0-2_amd64.buildinfo 5e3fbbeb9bc630cdde8f9894b6b36183 127152 science optional pyfastx_2.1.0-2_amd64.deb 3d93ecc430c6738c9a29dc99078597c7 234472 debug optional python3-pyfastx-dbgsym_2.1.0-2_amd64.deb 0c7c1dfc6ad70befa1b184bb6be03e31 64596 python optional python3-pyfastx_2.1.0-2_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/pyfastx_2.1.0-2.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/pyfastx_2.1.0-2.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/pyfastx_2.1.0-2.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/pyfastx_2.1.0-2.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/amd64/pyfastx_2.1.0-2_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/pyfastx_2.1.0-2.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2024-11-21 00:39:47.955857616 +0000 +++ b2/build.log 2024-11-21 00:45:17.421004238 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Dec 23 18:58:38 -12 2025 -I: pbuilder-time-stamp: 1766559518 +I: Current time: Thu Nov 21 14:39:51 +14 2024 +I: pbuilder-time-stamp: 1732149591 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -30,52 +30,84 @@ dpkg-source: info: applying use_debian_packaged_zlib.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1758472/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3551939/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +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 Nov 21 00:40 /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/3551939/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3551939/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + 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]="2" [2]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='21c16f996d964a44969182c0d65e7cc1' - 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='1758472' - PS1='# ' - PS2='> ' + INVOCATION_ID=3301d2fb2643404ca376f92391dbe9e2 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-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=3551939 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.v7khtA9G/pbuilderrc_dXA6 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.v7khtA9G/b1 --logfile b1/build.log pyfastx_2.1.0-2.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.v7khtA9G/pbuilderrc_XK5z --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.v7khtA9G/b2 --logfile b2/build.log pyfastx_2.1.0-2.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos5-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1758472/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3551939/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -217,7 +249,7 @@ Get: 90 http://deb.debian.org/debian unstable/main amd64 python3-indexed-gzip amd64 1.8.7-3+b1 [1499 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 python3-pyfaidx all 0.8.1.3-1 [29.1 kB] -Fetched 61.8 MB in 3s (19.8 MB/s) +Fetched 61.8 MB in 3s (21.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (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 ... 19966 files and directories currently installed.) @@ -527,8 +559,8 @@ Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Wed Dec 24 07:00:21 UTC 2025. -Universal Time is now: Wed Dec 24 07:00:21 UTC 2025. +Local time is now: Thu Nov 21 00:42:34 UTC 2024. +Universal Time is now: Thu Nov 21 00:42:34 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libpython3.13-minimal:amd64 (3.13.0-2) ... @@ -616,7 +648,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/pyfastx-2.1.0/ && 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 > ../pyfastx_2.1.0-2_source.changes +I: user script /srv/workspace/pbuilder/3551939/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3551939/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/pyfastx-2.1.0/ && 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 > ../pyfastx_2.1.0-2_source.changes dpkg-buildpackage: info: source package pyfastx dpkg-buildpackage: info: source version 2.1.0-2 dpkg-buildpackage: info: source distribution unstable @@ -825,7 +861,7 @@ test_seq_by_key (tests.test_sequence_error.SequenceErrorTest.test_seq_by_key) ... ok ---------------------------------------------------------------------- -Ran 56 tests in 26.148s +Ran 56 tests in 9.849s OK pyfastx: 2.1.0; zlib: 1.3.1; sqlite: 3.46.1; zran: 1.7.0 @@ -895,7 +931,7 @@ test_seq_by_key (tests.test_sequence_error.SequenceErrorTest.test_seq_by_key) ... ok ---------------------------------------------------------------------- -Ran 56 tests in 19.057s +Ran 56 tests in 14.376s OK pyfastx: 2.1.0; zlib: 1.3.1; sqlite: 3.46.1; zran: 1.7.0 @@ -929,8 +965,8 @@ running build_ext running install_lib creating /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.13/dist-packages -copying /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/pyfastxcli.py -> /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.13/dist-packages copying /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/pyfastx.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.13/dist-packages +copying /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.13/build/pyfastxcli.py -> /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.13/dist-packages byte-compiling /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.13/dist-packages/pyfastxcli.py to pyfastxcli.cpython-313.pyc running install_egg_info running egg_info @@ -970,8 +1006,8 @@ running build_ext running install_lib creating /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.12/dist-packages -copying /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/pyfastx.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.12/dist-packages copying /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/pyfastxcli.py -> /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.12/dist-packages +copying /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/pyfastx.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.12/dist-packages byte-compiling /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.12/dist-packages/pyfastxcli.py to pyfastxcli.cpython-312.pyc running install_egg_info running egg_info @@ -1020,14 +1056,14 @@ dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild -dpkg-gencontrol: warning: package python3-pyfastx: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: Depends field of package pyfastx: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package python3-pyfastx: substitution variable ${python3:Depends} unused, but is defined +dpkg-gencontrol: warning: package python3-pyfastx: substitution variable ${python3:Depends} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild +dpkg-deb: building package 'python3-pyfastx-dbgsym' in '../python3-pyfastx-dbgsym_2.1.0-2_amd64.deb'. dpkg-deb: building package 'pyfastx' in '../pyfastx_2.1.0-2_amd64.deb'. dpkg-deb: building package 'python3-pyfastx' in '../python3-pyfastx_2.1.0-2_amd64.deb'. -dpkg-deb: building package 'python3-pyfastx-dbgsym' in '../python3-pyfastx-dbgsym_2.1.0-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../pyfastx_2.1.0-2_amd64.buildinfo dpkg-genchanges --build=binary -O../pyfastx_2.1.0-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1035,12 +1071,14 @@ 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/3551939/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3551939/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/1758472 and its subdirectories -I: Current time: Tue Dec 23 19:02:47 -12 2025 -I: pbuilder-time-stamp: 1766559767 +I: removing directory /srv/workspace/pbuilder/3551939 and its subdirectories +I: Current time: Thu Nov 21 14:45:16 +14 2024 +I: pbuilder-time-stamp: 1732149916 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/pyfastx_2.1.0-2.diff: 71.1% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/pyfastx_2.1.0-2.diff.gz b2/build.log: 85.6% -- replaced with stdout Compressing the 1st log... b1/build.log: 86.1% -- replaced with stdout Thu Nov 21 00:45:19 UTC 2024 I: diffoscope 283 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_pyfastx_unstable_amd64_1732149919 + touch /var/log/reproducible-builds/diffoscope_stamp_pyfastx_unstable_amd64_1732149919 + RESULT=0 + systemd-run '--description=diffoscope on pyfastx/2.1.0-2 in unstable/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_2-23817 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.v7khtA9G --run-session -c jenkins-reproducible-unstable-diffoscope-75e3d94c-f728-4f33-8323-68a94197d1e5 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.v7khtA9G/dbd-tmp-zKM9Smu ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.v7khtA9G/pyfastx_2.1.0-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.v7khtA9G/pyfastx_2.1.0-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.v7khtA9G/pyfastx_2.1.0-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.v7khtA9G/b1/pyfastx_2.1.0-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.v7khtA9G/b2/pyfastx_2.1.0-2_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_2-23817.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.v7khtA9G/pyfastx_2.1.0-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.v7khtA9G/pyfastx_2.1.0-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.v7khtA9G/pyfastx_2.1.0-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.v7khtA9G/b1/pyfastx_2.1.0-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.v7khtA9G/b2/pyfastx_2.1.0-2_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.410s) 0.410s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.027s) 0.027s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 729ms CPU time consumed: 723ms __ _ _ __ _ _ / _| __ _ ___| |___ __ | '_ \| | | | |_ / _` / __| __\ \/ / | |_) | |_| | _| (_| \__ \ |_ > < | .__/ \__, |_| \__,_|___/\__/_/\_\ |_| |___/ Thu Nov 21 00:45:20 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Thu Nov 21 00:45:20 UTC 2024 I: pyfastx from unstable built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2024-11-21 00:45:20] INFO: Starting at 2024-11-21 00:45:20.958214 [2024-11-21 00:45:21] INFO: Generating the pages of 1 package(s) [2024-11-21 00:45:21] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/amd64/pyfastx didn't produce a buildlog, even though it has been built. [2024-11-21 00:45:21] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/armhf/pyfastx_0.8.4-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/armhf/pyfastx_0.8.4-2.diff.gz is missing [2024-11-21 00:45:21] INFO: Finished at 2024-11-21 00:45:21.270854, took: 0:00:00.312645 Thu Nov 21 00:45:21 UTC 2024 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/pyfastx.html Thu Nov 21 00:45:21 UTC 2024 I: Submitting .buildinfo files to external archives: Thu Nov 21 00:45:21 UTC 2024 I: Submitting 12K b1/pyfastx_2.1.0-2_amd64.buildinfo.asc https://buildinfo.debian.net/bcc2defe52ded2a01ca012274369284190c4e068/pyfastx_2.1.0-2_amd64 Thu Nov 21 00:45:22 UTC 2024 I: Submitting 12K b2/pyfastx_2.1.0-2_amd64.buildinfo.asc https://buildinfo.debian.net/abf42a26c39380eaa88a1fb017c49c1b6845cd90/pyfastx_2.1.0-2_amd64 Thu Nov 21 00:45:22 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Nov 21 00:45:22 UTC 2024 I: Done submitting .buildinfo files. Thu Nov 21 00:45:22 UTC 2024 I: Removing signed pyfastx_2.1.0-2_amd64.buildinfo.asc files: removed './b1/pyfastx_2.1.0-2_amd64.buildinfo.asc' removed './b2/pyfastx_2.1.0-2_amd64.buildinfo.asc' 1732149922 amd64 unstable pyfastx Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/pyfastx_2.1.0-2.rbuild.log: 83.6% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/pyfastx_2.1.0-2.rbuild.log.gz [2024-11-21 00:45:23] INFO: Starting at 2024-11-21 00:45:23.211795 [2024-11-21 00:45:23] INFO: Generating the pages of 1 package(s) [2024-11-21 00:45:23] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/armhf/pyfastx_0.8.4-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/armhf/pyfastx_0.8.4-2.diff.gz is missing [2024-11-21 00:45:23] INFO: Finished at 2024-11-21 00:45:23.502640, took: 0:00:00.290851 All cleanup done. Thu Nov 21 00:45:23 UTC 2024 - total duration: 0h 9m 58s. Thu Nov 21 00:45:23 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-d2sLDUIT, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 10min 737ms CPU time consumed: 7.209s