Fri Oct 25 12:23:44 UTC 2024 I: starting to build pyfastx/trixie/arm64 on jenkins on '2024-10-25 12:23' Fri Oct 25 12:23:44 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_3/61312/console.log Fri Oct 25 12:23:44 UTC 2024 I: Downloading source for trixie/pyfastx=2.1.0-2 --2024-10-25 12:23:44-- 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% 230M=0s 2024-10-25 12:23:44 (230 MB/s) - ‘pyfastx_2.1.0-2.dsc’ saved [2289/2289] Fri Oct 25 12:23:44 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----- Fri Oct 25 12:23:44 UTC 2024 I: Checking whether the package is not for us Fri Oct 25 12:23:44 UTC 2024 I: Starting 1st build on remote node codethink01-arm64.debian.net. Fri Oct 25 12:23:44 UTC 2024 I: Preparing to do remote build '1' on codethink01-arm64.debian.net. Fri Oct 25 12:24:55 UTC 2024 I: Deleting $TMPDIR on codethink01-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Nov 27 06:46:45 -12 2025 I: pbuilder-time-stamp: 1764269205 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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/2706594/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='914b5814f3a54b7c8d7c8b49fd46ee22' 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='2706594' 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.Qcux7ljr/pbuilderrc_FRon --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Qcux7ljr/b1 --logfile b1/build.log pyfastx_2.1.0-2.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink01-arm64 6.1.0-26-cloud-arm64 #1 SMP Debian 6.1.112-1 (2024-09-30) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2706594/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-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 ... 21997 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} 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-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} 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, 84 newly installed, 0 to remove and 0 not upgraded. Need to get 44.1 MB of archives. After unpacking 224 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 libpython3.12-minimal arm64 3.12.6-1 [806 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.3-1 [90.2 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 python3.12-minimal arm64 3.12.6-1 [1935 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.12.6-1 [26.7 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.1-1 [22.8 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B] Get: 12 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3 [78.4 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libnsl2 arm64 1.3.0-3+b2 [37.7 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-5 [159 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libpython3.12-stdlib arm64 3.12.6-1 [1898 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 python3.12 arm64 3.12.6-1 [669 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.2-9 [96.6 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 44 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-2 [188 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-5 [9224 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.1 [630 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.20 [915 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 python3-zipp all 3.20.2-1 [10.3 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 python3-importlib-metadata all 8.5.0-1 [21.0 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 python3-typeguard all 4.3.0-1 [36.5 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 60 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 python3-pkg-resources all 74.1.2-2 [213 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 python3-setuptools all 74.1.2-2 [736 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 dh-python all 6.20240824 [109 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 libblas3 arm64 3.12.0-3 [91.7 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 libexpat1-dev arm64 2.6.3-1 [142 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14.2.0-6 [361 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 libjs-sphinxdoc all 7.4.7-3 [158 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.0-3 [1757 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 libpython3.12t64 arm64 3.12.6-1 [1981 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1 [916 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 libpython3.12-dev arm64 3.12.6-1 [4782 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 libpython3-dev arm64 3.12.6-1 [9952 B] Get: 75 http://deb.debian.org/debian trixie/main arm64 libpython3-all-dev arm64 3.12.6-1 [1064 B] Get: 76 http://deb.debian.org/debian trixie/main arm64 libsqlite3-dev arm64 3.46.1-1 [1058 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 python3-all arm64 3.12.6-1 [1040 B] Get: 78 http://deb.debian.org/debian trixie/main arm64 python3.12-dev arm64 3.12.6-1 [506 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 python3-dev arm64 3.12.6-1 [26.1 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 python3-all-dev arm64 3.12.6-1 [1068 B] Get: 81 http://deb.debian.org/debian trixie/main arm64 python3-numpy arm64 1:1.26.4+ds-11 [3351 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 python3-indexed-gzip arm64 1.8.7-3 [994 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 python3-packaging all 24.1-1 [45.8 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 python3-pyfaidx all 0.8.1.3-1 [29.1 kB] Fetched 44.1 MB in 0s (134 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21997 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.6-1_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.6-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.3-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.6-1_arm64.deb ... Unpacking python3.12-minimal (3.12.6-1) ... Setting up libpython3.12-minimal:arm64 (3.12.6-1) ... Setting up libexpat1:arm64 (2.6.3-1) ... Setting up python3.12-minimal (3.12.6-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 22317 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_arm64.deb ... 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Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.3) ... Selecting previously unselected package libnsl2:arm64. Preparing to unpack .../12-libnsl2_1.3.0-3+b2_arm64.deb ... Unpacking libnsl2:arm64 (1.3.0-3+b2) ... 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:arm64. Preparing to unpack .../14-libreadline8t64_8.2-5_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:arm64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.6-1_arm64.deb ... Unpacking libpython3.12-stdlib:arm64 (3.12.6-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.6-1_arm64.deb ... Unpacking python3.12 (3.12.6-1) ... 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Setting up file (1:5.45-3) ... Setting up libelf1t64:arm64 (0.191-2) ... Setting up libkrb5support0:arm64 (1.21.3-3) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Nov 27 18:47:20 UTC 2025. Universal Time is now: Thu Nov 27 18:47:20 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:arm64 (3.12.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libexpat1-dev:arm64 (2.6.3-1) ... Setting up libsqlite3-dev:arm64 (3.46.1-1) ... Setting up autopoint (0.22.5-2) ... Setting up libk5crypto3:arm64 (1.21.3-3) ... Setting up libgfortran5:arm64 (14.2.0-6) ... Setting up autoconf (2.72-3) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up netbase (6.4) ... Setting up libkrb5-3:arm64 (1.21.3-3) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up readline-common (8.2-5) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up liblapack3:arm64 (3.12.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-3) ... Setting up libjs-sphinxdoc (7.4.7-3) ... Setting up libreadline8t64:arm64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libtirpc3t64:arm64 (1.3.4+ds-1.3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libnsl2:arm64 (1.3.0-3+b2) ... Setting up libpython3.12-stdlib:arm64 (3.12.6-1) ... Setting up python3.12 (3.12.6-1) ... Setting up debhelper (13.20) ... Setting up libpython3.12t64:arm64 (3.12.6-1) ... Setting up libpython3-stdlib:arm64 (3.12.6-1) ... Setting up python3 (3.12.6-1) ... Setting up libpython3.12-dev:arm64 (3.12.6-1) ... Setting up python3-zipp (3.20.2-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-packaging (24.1-1) ... Setting up python3.12-dev (3.12.6-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up libpython3-dev:arm64 (3.12.6-1) ... Setting up python3-importlib-metadata (8.5.0-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-typeguard (4.3.0-1) ... Setting up python3-all (3.12.6-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up libpython3-all-dev:arm64 (3.12.6-1) ... Setting up python3-dev (3.12.6-1) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up python3-all-dev (3.12.6-1) ... Setting up python3-pyfaidx (0.8.1.3-1) ... Setting up python3-setuptools (74.1.2-2) ... Setting up python3-numpy (1:1.26.4+ds-11) ... Setting up python3-indexed-gzip (1.8.7-3) ... Setting up dh-python (6.20240824) ... Processing triggers for libc-bin (2.40-3) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps 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 arm64 debian/rules clean dh clean --buildsystem pybuild --with python3 dh_auto_clean -O--buildsystem=pybuild 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-aarch64' 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: python3.12 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 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 creating build/temp.linux-aarch64-cpython-312 creating build/temp.linux-aarch64-cpython-312/build creating build/temp.linux-aarch64-cpython-312/build/reproducible-path creating build/temp.linux-aarch64-cpython-312/build/reproducible-path/pyfastx-2.1.0 creating build/temp.linux-aarch64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src aarch64-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 -mbranch-protection=standard -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-aarch64-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 aarch64-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 -mbranch-protection=standard -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-aarch64-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; | ^ aarch64-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 -mbranch-protection=standard -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-aarch64-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 aarch64-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 -mbranch-protection=standard -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-aarch64-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 aarch64-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 -mbranch-protection=standard -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-aarch64-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 aarch64-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 -mbranch-protection=standard -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-aarch64-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 aarch64-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 -mbranch-protection=standard -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-aarch64-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 aarch64-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 -mbranch-protection=standard -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-aarch64-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); | ~~~~~~^~~ aarch64-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 -mbranch-protection=standard -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-aarch64-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 aarch64-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 -mbranch-protection=standard -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-aarch64-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; | ^~~~~~~~~ aarch64-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 -mbranch-protection=standard -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-aarch64-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 aarch64-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 -mbranch-protection=standard -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-aarch64-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 aarch64-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 -mbranch-protection=standard -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-aarch64-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 aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/fakeys.o build/temp.linux-aarch64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/fasta.o build/temp.linux-aarch64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/fastq.o build/temp.linux-aarch64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/fastx.o build/temp.linux-aarch64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/fqkeys.o build/temp.linux-aarch64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/index.o build/temp.linux-aarch64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/kseq.o build/temp.linux-aarch64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/module.o build/temp.linux-aarch64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/read.o build/temp.linux-aarch64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/sequence.o build/temp.linux-aarch64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/util.o build/temp.linux-aarch64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/zran.o build/temp.linux-aarch64-cpython-312/build/reproducible-path/pyfastx-2.1.0/src/zran_file_util.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/pyfastx-2.1.0/.pybuild/cpython3_3.12/build/pyfastx.cpython-312-aarch64-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_3.12/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 0.804s 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 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 creating /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib creating /build/reproducible-path/pyfastx-2.1.0/debian/tmp/usr/lib/python3.12 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-aarch64-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 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/python3.12/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 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged 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 'python3-pyfastx-dbgsym' in '../python3-pyfastx-dbgsym_2.1.0-2_arm64.deb'. dpkg-deb: building package 'pyfastx' in '../pyfastx_2.1.0-2_arm64.deb'. dpkg-deb: building package 'python3-pyfastx' in '../python3-pyfastx_2.1.0-2_arm64.deb'. dpkg-genbuildinfo --build=binary -O../pyfastx_2.1.0-2_arm64.buildinfo dpkg-genchanges --build=binary -O../pyfastx_2.1.0-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2706594 and its subdirectories I: Current time: Thu Nov 27 06:47:52 -12 2025 I: pbuilder-time-stamp: 1764269272 Fri Oct 25 12:24:55 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Fri Oct 25 12:24:55 UTC 2024 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Fri Oct 25 12:25:57 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Fri Oct 25 12:25:58 UTC 2024 I: pyfastx_2.1.0-2_arm64.changes: Format: 1.8 Date: Fri, 30 Aug 2024 20:31:18 +0200 Source: pyfastx Binary: pyfastx python3-pyfastx python3-pyfastx-dbgsym Architecture: arm64 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: b19dfc8e3663393449c3974e6a3d87f5a922c1a6 6944 pyfastx_2.1.0-2_arm64.buildinfo d903460f8e5ff859d9ef28a72705eac3a54e0e31 127156 pyfastx_2.1.0-2_arm64.deb f9d6581f7964373e47cd221f44b4432f84b64b68 123544 python3-pyfastx-dbgsym_2.1.0-2_arm64.deb 873866c619abb0e0e2d150ca3260ed4f60043f0a 54620 python3-pyfastx_2.1.0-2_arm64.deb Checksums-Sha256: e8d6af6a83439c7855234e605285a2171ec3101eb0287f9f88b6ef81b34bbea7 6944 pyfastx_2.1.0-2_arm64.buildinfo b85da90ed1d77426b31681e472eb10b7afc82b8a048a4da6928ebfa3802f7d2c 127156 pyfastx_2.1.0-2_arm64.deb 1020d89948ee05361e0175b54e0898633ffef1b6ad6353d235c4268c12559321 123544 python3-pyfastx-dbgsym_2.1.0-2_arm64.deb 2fc7b5429f9dde5c851880e1f1aa2396876e73c841bb77dade9b1a853c671dd9 54620 python3-pyfastx_2.1.0-2_arm64.deb Files: e48596433494b6c383fbc8aca393f0f7 6944 science optional pyfastx_2.1.0-2_arm64.buildinfo b0ef0dcb728f4fa96b32cd4de6c01d4e 127156 science optional pyfastx_2.1.0-2_arm64.deb 06a972e984cd91bf7abd34018d90e6b9 123544 debug optional python3-pyfastx-dbgsym_2.1.0-2_arm64.deb fb414d757befbfac95bccd2126892299 54620 python optional python3-pyfastx_2.1.0-2_arm64.deb Fri Oct 25 12:25:59 UTC 2024 I: diffoscope 281 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_3-61312.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.Qcux7ljr/pyfastx_2.1.0-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.Qcux7ljr/pyfastx_2.1.0-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.Qcux7ljr/pyfastx_2.1.0-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.Qcux7ljr/b1/pyfastx_2.1.0-2_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.Qcux7ljr/b2/pyfastx_2.1.0-2_arm64.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: 0.402s) 0.402s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.022s) 0.022s 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: 751ms CPU time consumed: 751ms Fri Oct 25 12:26:00 UTC 2024 I: diffoscope 281 found no differences in the changes files, and a .buildinfo file also exists. Fri Oct 25 12:26:00 UTC 2024 I: pyfastx from trixie built successfully and reproducibly on arm64. Fri Oct 25 12:26:01 UTC 2024 I: Submitting .buildinfo files to external archives: Fri Oct 25 12:26:01 UTC 2024 I: Submitting 8.0K b1/pyfastx_2.1.0-2_arm64.buildinfo.asc Fri Oct 25 12:26:02 UTC 2024 I: Submitting 8.0K b2/pyfastx_2.1.0-2_arm64.buildinfo.asc Fri Oct 25 12:26:03 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Oct 25 12:26:03 UTC 2024 I: Done submitting .buildinfo files. Fri Oct 25 12:26:03 UTC 2024 I: Removing signed pyfastx_2.1.0-2_arm64.buildinfo.asc files: removed './b1/pyfastx_2.1.0-2_arm64.buildinfo.asc' removed './b2/pyfastx_2.1.0-2_arm64.buildinfo.asc'