Running as unit: rb-build-arm64_6-59338.service ==================================================================================== Tue Oct 1 14:33:31 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_6) on jenkins, called using "codethink04-arm64 codethink01-arm64" as arguments. Tue Oct 1 14:33:31 UTC 2024 - actually running "reproducible_build.sh" (md5sum 79f74068471242981be9b3b00196cbfb) as "/tmp/jenkins-script-Ofzvhxqu" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue Oct 1 14:33:31 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Tue Oct 1 14:33:31 UTC 2024 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-SfFKFB' Tue Oct 1 14:33:32 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink01-arm64.debian.net is marked as down. Tue Oct 1 14:33:32 UTC 2024 - checking via ssh if codethink01-arm64.debian.net is up. removed '/tmp/read-only-fs-test-4cUCat' ok, let's check if insilicoseq is building anywhere yet… ok, insilicoseq is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of insilicoseq in trixie on arm64 on jenkins now. 1st build will be done on codethink04-arm64.debian.net. 2nd build will be done on codethink01-arm64.debian.net. ============================================================================= Tue Oct 1 14:33:41 UTC 2024 I: starting to build insilicoseq/trixie/arm64 on jenkins on '2024-10-01 14:33' Tue Oct 1 14:33:41 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_6/59338/console.log 1727793221 arm64 trixie insilicoseq Tue Oct 1 14:33:41 UTC 2024 I: Downloading source for trixie/insilicoseq=2.0.1-1 --2024-10-01 14:33:41-- http://deb.debian.org/debian/pool/main/i/insilicoseq/insilicoseq_2.0.1-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2411 (2.4K) [text/prs.lines.tag] Saving to: ‘insilicoseq_2.0.1-1.dsc’ 0K .. 100% 301M=0s 2024-10-01 14:33:41 (301 MB/s) - ‘insilicoseq_2.0.1-1.dsc’ saved [2411/2411] --2024-10-01 14:33:41-- http://deb.debian.org/debian/pool/main/i/insilicoseq/insilicoseq_2.0.1-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2411 (2.4K) [text/prs.lines.tag] Saving to: ‘insilicoseq_2.0.1-1.dsc’ 0K .. 100% 301M=0s 2024-10-01 14:33:41 (301 MB/s) - ‘insilicoseq_2.0.1-1.dsc’ saved [2411/2411] Tue Oct 1 14:33:41 UTC 2024 I: insilicoseq_2.0.1-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: insilicoseq Binary: insilicoseq Architecture: all Version: 2.0.1-1 Maintainer: Debian Med Packaging Team Uploaders: Sao I Kuan , Étienne Mollier Homepage: https://github.com/HadrienG/InSilicoSeq Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/insilicoseq Vcs-Git: https://salsa.debian.org/med-team/insilicoseq.git Testsuite: autopkgtest, autopkgtest-pkg-python Testsuite-Triggers: python3-all, python3-pytest Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3-setuptools, python3-all, python3-biopython, python3-joblib, python3-numpy, python3-pysam, python3-requests, python3-scipy, python3-pytest Package-List: insilicoseq deb science optional arch=all Checksums-Sha1: 76321048416a39e8b1506124b2bd985a4c006d2c 4591338 insilicoseq_2.0.1.orig.tar.gz bb0f811650bd3b776af3540e4fad53e98ff6acb0 5304 insilicoseq_2.0.1-1.debian.tar.xz Checksums-Sha256: a1b452fbb6781c5c04bad269836893bf8d2103215e8d131c37baa95a74b2cbaa 4591338 insilicoseq_2.0.1.orig.tar.gz 3416563e93abf4b8e8f7b271d8eb388c2f4c65a2a9cbcfd6b392392a3448f60b 5304 insilicoseq_2.0.1-1.debian.tar.xz Files: abf80ebd35fbffd360b15548c42c2e95 4591338 insilicoseq_2.0.1.orig.tar.gz 5e5762210b50edc957be75dc7ab03587 5304 insilicoseq_2.0.1-1.debian.tar.xz Dgit: 795db072c0a639fe120f18f528f1a8de3e536842 debian archive/debian/2.0.1-1 https://git.dgit.debian.org/insilicoseq -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmYo7YIUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdqIQA//TPTkf2xlJEswzyZwaBowNcOEXmJN FKnEgEmDhcQ+ZVev+qORcWuS5emHPgMDgTQugFK6WOWgdwddHLN6UxT+cO0vnazD P181oHtl6iG5xtW58FTXtjfgEpqATZb1V+vggOKRhDrCqQ/abDQCujePqLrtzchb wgdW8ic+fKpe6ZFGJ9ztNl83K4ybEkU/O1mToM071xgMYDLC+tkEjTyPwizeB90C rhtlaqbmHxdgAYtOdWZDSPpncC7w3FtLUOyWwJY/mnAFvdmZM7BMWlDQX+dYL7LH OLubqmInouY8iDbkhstNt9edB+tDj4xlklsgtZshKUEpuSsbHAbSo7U19zS9AYUV ErhVXxd7LWZtLj/NuiMGhB5FY756zk/hbNxUV6VgHP1r/2aXWotUFsnXcaQ1NH+d pXp4hzyvF2zM8ehcn3CKjPkGPtcJwaj259Dy7XbH1U7yVF+UgT79k6nv7+Ri3Sm2 7MTkJ3MmgP9ifJEtmnLOUH658K76xGX0bwOwv8qekhtGlAfkIsKsPTCjvvWo8ZhX fUfnxgZRNO7n3IxrEoDFmosNu//RIhPa6vwDIPRS4XP0vk9Z8WwDWosGmzBqtP9I 8FXFcvEaERaBFwf45XQM/JV9t9d2/EiMaItIPzoaURMehWkl0gZjMnQlm+08Zl5m n77AGxRebwJfQWs= =/2zu -----END PGP SIGNATURE----- Tue Oct 1 14:33:41 UTC 2024 I: Checking whether the package is not for us Tue Oct 1 14:33:41 UTC 2024 I: Starting 1st build on remote node codethink04-arm64.debian.net. Tue Oct 1 14:33:41 UTC 2024 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Tue Oct 1 14:33:41 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Tue Oct 1 14:33:41 UTC 2024 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-b9Mo4e' ==================================================================================== Tue Oct 1 14:33:43 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink04-arm64, called using "1 insilicoseq trixie /srv/reproducible-results/rbuild-debian/r-b-build.Lh7t7LAy 2.0.1-1" as arguments. Tue Oct 1 14:33:43 UTC 2024 - actually running "reproducible_build.sh" (md5sum 79f74068471242981be9b3b00196cbfb) as "/tmp/jenkins-script-2uPO44KB" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue Oct 1 14:33:43 UTC 2024 I: Downloading source for trixie/insilicoseq=2.0.1-1 Reading package lists... NOTICE: 'insilicoseq' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/insilicoseq.git Please use: git clone https://salsa.debian.org/med-team/insilicoseq.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 4599 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main insilicoseq 2.0.1-1 (dsc) [2411 B] Get:2 http://deb.debian.org/debian trixie/main insilicoseq 2.0.1-1 (tar) [4591 kB] Get:3 http://deb.debian.org/debian trixie/main insilicoseq 2.0.1-1 (diff) [5304 B] Fetched 4599 kB in 1s (6822 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'insilicoseq' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/insilicoseq.git Please use: git clone https://salsa.debian.org/med-team/insilicoseq.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 4599 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main insilicoseq 2.0.1-1 (dsc) [2411 B] Get:2 http://deb.debian.org/debian trixie/main insilicoseq 2.0.1-1 (tar) [4591 kB] Get:3 http://deb.debian.org/debian trixie/main insilicoseq 2.0.1-1 (diff) [5304 B] Fetched 4599 kB in 1s (6822 kB/s) Download complete and in download only mode ============================================================================= Building insilicoseq in trixie on arm64 on codethink04-arm64 now. Date: Tue Oct 1 15:33:44 BST 2024 Date UTC: Tue Oct 1 14:33:44 UTC 2024 ============================================================================= 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 Oct 1 02:33:44 -12 2024 I: pbuilder-time-stamp: 1727793224 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 [insilicoseq_2.0.1-1.dsc] I: copying [./insilicoseq_2.0.1.orig.tar.gz] I: copying [./insilicoseq_2.0.1-1.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Apr 24 11:31:14 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 ./insilicoseq_2.0.1-1.dsc: no acceptable signature found dpkg-source: info: extracting insilicoseq in insilicoseq-2.0.1 dpkg-source: info: unpacking insilicoseq_2.0.1.orig.tar.gz dpkg-source: info: unpacking insilicoseq_2.0.1-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no-internet.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3155505/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='a5c93f1b15954144959bbfb8ec035dba' 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='3155505' 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.Lh7t7LAy/pbuilderrc_u6mF --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.Lh7t7LAy/b1 --logfile b1/build.log insilicoseq_2.0.1-1.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 codethink04-arm64 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3155505/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, python3-setuptools, python3-all, python3-biopython, python3-joblib, python3-numpy, python3-pysam, python3-requests, python3-scipy, python3-pytest dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19895 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-joblib; however: Package python3-joblib is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-pysam; however: Package python3-pysam is not installed. pbuilder-satisfydepends-dummy depends on python3-requests; however: Package python3-requests is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest 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} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libcurl3t64-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnsl2{a} libopenjp2-7{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libraqm0{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libssh2-1t64{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxrender1{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} po-debconf{a} procps{a} python3{a} python3-all{a} python3-autocommand{a} python3-biopython{a} python3-cairo{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-decorator{a} python3-freetype{a} python3-idna{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-joblib{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-packaging{a} python3-pil{a} python3-pkg-resources{a} python3-pluggy{a} python3-pysam{a} python3-pytest{a} python3-reportlab{a} python3-requests{a} python3-rlpycairo{a} python3-scipy{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-urllib3{a} python3-zipp{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} tzdata{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-dejavu-extra krb5-locales libarchive-cpio-perl libglib2.0-data libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx ncbi-blast+ psmisc publicsuffix python-biopython-doc python3-olefile python3-psutil python3-pygments python3-simplejson shared-mime-info wget xdg-user-dirs 0 packages upgraded, 148 newly installed, 0 to remove and 0 not upgraded. Need to get 81.6 MB of archives. After unpacking 329 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 sgml-base all 1.31 [15.4 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libproc2-0 arm64 2:4.0.4-5 [61.3 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 procps arm64 2:4.0.4-5 [868 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 openssl arm64 3.3.2-1 [1348 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 ca-certificates all 20240203 [158 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.2-8 [96.6 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 49 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-2 [188 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-5 [9224 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.1 [630 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.20 [915 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 python3-typeguard all 4.3.0-1 [36.5 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 63 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.functools all 4.0.2-1 [11.7 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 python3-pkg-resources all 74.1.2-2 [213 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 python3-zipp all 3.20.2-1 [10.3 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 python3-setuptools all 74.1.2-2 [736 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 dh-python all 6.20240824 [109 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libfontenc1 arm64 1:1.1.8-1 [22.2 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b4 [292 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 libpng16-16t64 arm64 1.6.44-1 [272 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 x11-common all 1:7.7+23.1 [216 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 xfonts-utils arm64 1:7.7+7 [89.3 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 78 http://deb.debian.org/debian trixie/main arm64 fontconfig-config arm64 2.15.0-1.1 [317 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libblas3 arm64 3.12.0-3 [91.7 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 libfontconfig1 arm64 2.15.0-1.1 [385 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 libpixman-1-0 arm64 0.42.2-1+b1 [477 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 libxau6 arm64 1:1.0.9-1+b1 [18.1 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 libxdmcp6 arm64 1:1.1.2-3+b1 [24.3 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 libxcb1 arm64 1.17.0-2 [143 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 libx11-data all 2:1.8.7-1 [328 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 libx11-6 arm64 2:1.8.7-1+b1 [775 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 libxcb-render0 arm64 1.17.0-2 [115 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 libxcb-shm0 arm64 1.17.0-2 [105 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 libxrender1 arm64 1:0.9.10-1.1+b1 [27.0 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 libcairo2 arm64 1.18.2-2 [483 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-3 [174 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.63.0-1 [71.2 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libnghttp3-9 arm64 1.4.0-1 [59.5 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libngtcp2-16 arm64 1.6.0-1 [112 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libngtcp2-crypto-gnutls8 arm64 1.6.0-1 [18.5 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.0-7 [208 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.10.1-1 [329 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.21-1 [42.2 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 libfribidi0 arm64 1.0.15-1 [71.8 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14.2.0-3 [362 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libglib2.0-0t64 arm64 2.82.1-1 [1410 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libgraphite2-3 arm64 1.3.14-2 [69.2 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libharfbuzz0b arm64 9.0.0-1 [441 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libhtscodecs2 arm64 1.6.1-1 [74.6 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libhts3t64 arm64 1.20+ds-1 [416 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 libimagequant0 arm64 2.18.0-1+b1 [34.6 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 libjbig0 arm64 2.1-6.1+b1 [30.4 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo arm64 1:2.1.5-3 [172 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.0-3 [1757 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 liblbfgsb0 arm64 3.0+dfsg.4-1+b1 [25.0 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 liblcms2-2 arm64 2.14-2+b1 [144 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 liblerc4 arm64 4.0.0+ds-4+b1 [142 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 libopenjp2-7 arm64 2.5.0-2+b3 [177 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 libraqm0 arm64 0.10.1-1+b1 [13.7 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [111 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 libwebp7 arm64 1.4.0-0.1 [267 kB] Get: 122 http://deb.debian.org/debian trixie/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 123 http://deb.debian.org/debian trixie/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [110 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 libwebpmux3 arm64 1.4.0-0.1 [122 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 python3-all arm64 3.12.6-1 [1040 B] Get: 126 http://deb.debian.org/debian trixie/main arm64 python3-numpy arm64 1:1.26.4+ds-11 [3351 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 python3-pil arm64 10.4.0-1 [480 kB] Get: 129 http://deb.debian.org/debian trixie/main arm64 python3-cairo arm64 1.26.1-2 [113 kB] Get: 130 http://deb.debian.org/debian trixie/main arm64 python3-freetype all 2.5.1-1 [89.3 kB] Get: 131 http://deb.debian.org/debian trixie/main arm64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 132 http://deb.debian.org/debian trixie/main arm64 python3-reportlab all 4.2.2-1 [1150 kB] Get: 133 http://deb.debian.org/debian trixie/main arm64 xml-core all 0.19 [20.1 kB] Get: 134 http://deb.debian.org/debian trixie/main arm64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 135 http://deb.debian.org/debian trixie/main arm64 python3-biopython arm64 1.83+dfsg1-5 [1597 kB] Get: 136 http://deb.debian.org/debian trixie/main arm64 python3-certifi all 2024.8.30-1 [159 kB] Get: 137 http://deb.debian.org/debian trixie/main arm64 python3-charset-normalizer arm64 3.3.2-4 [110 kB] Get: 138 http://deb.debian.org/debian trixie/main arm64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 139 http://deb.debian.org/debian trixie/main arm64 python3-idna all 3.8-2 [41.6 kB] Get: 140 http://deb.debian.org/debian trixie/main arm64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 141 http://deb.debian.org/debian trixie/main arm64 python3-joblib all 1.3.2-2 [218 kB] Get: 142 http://deb.debian.org/debian trixie/main arm64 python3-packaging all 24.1-1 [45.8 kB] Get: 143 http://deb.debian.org/debian trixie/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 144 http://deb.debian.org/debian trixie/main arm64 python3-pysam arm64 0.22.1+ds-2+b1 [3244 kB] Get: 145 http://deb.debian.org/debian trixie/main arm64 python3-pytest all 8.3.3-1 [249 kB] Get: 146 http://deb.debian.org/debian trixie/main arm64 python3-urllib3 all 2.0.7-2 [111 kB] Get: 147 http://deb.debian.org/debian trixie/main arm64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 148 http://deb.debian.org/debian trixie/main arm64 python3-scipy arm64 1.13.1-5 [15.4 MB] Fetched 81.6 MB in 2s (53.4 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 ... 19895 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 ... 20215 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_arm64.deb ... Unpacking python3-minimal (3.12.6-1) ... 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_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../05-libcom-err2_1.47.1-1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.1-1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../07-libkeyutils1_1.6.3-3_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (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:arm64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3_arm64.deb ... 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) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... 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 ... 21287 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.6-1_arm64.deb ... Unpacking python3 (3.12.6-1) ... 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Setting up libelf1t64:arm64 (0.191-2) ... Setting up libkrb5support0:arm64 (1.21.3-3) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-8) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Oct 1 14:34:35 UTC 2024. Universal Time is now: Tue Oct 1 14:34:35 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:arm64 (1:1.1.8-1) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:arm64 (2.82.1-1) ... No schema files found: doing nothing. 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 libjpeg62-turbo:arm64 (1:2.1.5-3) ... Setting up libx11-data (2:1.8.7-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:arm64 (1.0.15-1) ... 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Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 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/insilicoseq-2.0.1/ && 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 > ../insilicoseq_2.0.1-1_source.changes dpkg-buildpackage: info: source package insilicoseq dpkg-buildpackage: info: source version 2.0.1-1 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 LC_ALL=C.UTF-8 dh clean --buildsystem=pybuild 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: 'tests_require' warnings.warn(msg) running clean removing '/build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/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 LC_ALL=C.UTF-8 dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.12 setup.py config /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) running config 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: 'tests_require' warnings.warn(msg) running build running build_py creating /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss copying iss/version.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss copying iss/util.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss copying iss/modeller.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss copying iss/generator.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss copying iss/download.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss copying iss/bam.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss copying iss/app.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss copying iss/abundance.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss copying iss/__main__.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss copying iss/__init__.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss creating /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test copying iss/test/test_download.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test copying iss/test/test_util.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test copying iss/test/test_modeller.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test copying iss/test/test_generator.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test copying iss/test/test_error_model.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test copying iss/test/test_bam.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test copying iss/test/test_abundance.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test copying iss/test/__init__.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test creating /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/error_models copying iss/error_models/perfect.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/error_models copying iss/error_models/kde.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/error_models copying iss/error_models/basic.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/error_models copying iss/error_models/__init__.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/error_models running egg_info creating InSilicoSeq.egg-info writing InSilicoSeq.egg-info/PKG-INFO writing dependency_links to InSilicoSeq.egg-info/dependency_links.txt writing entry points to InSilicoSeq.egg-info/entry_points.txt writing requirements to InSilicoSeq.egg-info/requires.txt writing top-level names to InSilicoSeq.egg-info/top_level.txt writing manifest file 'InSilicoSeq.egg-info/SOURCES.txt' reading manifest file 'InSilicoSeq.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'InSilicoSeq.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:218: _Warning: Package 'iss.profiles' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'iss.profiles' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'iss.profiles' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'iss.profiles' to be distributed and are already explicitly excluding 'iss.profiles' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) creating /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles copying iss/profiles/HiSeq -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles copying iss/profiles/MiSeq -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles copying iss/profiles/NovaSeq -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles copying iss/profiles/miSeq_0.npz -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles copying iss/profiles/miSeq_20.npz -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles copying iss/profiles/miSeq_24.npz -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles copying iss/profiles/miSeq_28.npz -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles copying iss/profiles/miSeq_32.npz -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles copying iss/profiles/miSeq_36.npz -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles copying iss/profiles/nextSeq.npz -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/insilicoseq-2.0.1' find /build/reproducible-path/insilicoseq-2.0.1 -name read_only.fasta| xargs chmod 0444 PYTHONPATH=/build/reproducible-path/insilicoseq-2.0.1 pytest-3 -v iss ============================= test session starts ============================== platform linux -- Python 3.12.6, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3 cachedir: .pytest_cache rootdir: /build/reproducible-path/insilicoseq-2.0.1 configfile: pyproject.toml plugins: typeguard-4.3.0 collecting ... collected 46 items iss/test/test_abundance.py::test_parsing PASSED [ 2%] iss/test/test_abundance.py::test_parsing_readcounts PASSED [ 4%] iss/test/test_abundance.py::test_parsing_empty PASSED [ 6%] iss/test/test_abundance.py::test_parsing_no_exists PASSED [ 8%] iss/test/test_abundance.py::test_parsing_bad_abundance PASSED [ 10%] iss/test/test_abundance.py::test_cov_calc PASSED [ 13%] iss/test/test_abundance.py::test_distributions PASSED [ 15%] iss/test/test_abundance.py::test_abunance_draft PASSED [ 17%] iss/test/test_abundance.py::test_coverage_scaling PASSED [ 19%] iss/test/test_bam.py::test_read_fail PASSED [ 21%] iss/test/test_bam.py::test_to_model PASSED [ 23%] iss/test/test_download.py::test_ncbi SKIPPED (Test requires Internet.) [ 26%] iss/test/test_error_model.py::test_perfect_phred PASSED [ 28%] iss/test/test_error_model.py::test_basic_phred PASSED [ 30%] iss/test/test_error_model.py::test_kde_phred PASSED [ 32%] iss/test/test_error_model.py::test_introduce_errors PASSED [ 34%] iss/test/test_error_model.py::test_mut_sequence PASSED [ 36%] iss/test/test_error_model.py::test_introduce_indels PASSED [ 39%] iss/test/test_error_model.py::test_adjust_seq_length_extend PASSED [ 41%] iss/test/test_error_model.py::test_introduce_indels_rev PASSED [ 43%] iss/test/test_error_model.py::test_bad_err_mod PASSED [ 45%] iss/test/test_generator.py::test_cleanup_fail PASSED [ 47%] iss/test/test_generator.py::test_simulate_and_save PASSED [ 50%] iss/test/test_generator.py::test_simulate_and_save_short PASSED [ 52%] iss/test/test_generator.py::test_small_input PASSED [ 54%] iss/test/test_generator.py::test_basic PASSED [ 56%] iss/test/test_generator.py::test_kde PASSED [ 58%] iss/test/test_generator.py::test_kde_short PASSED [ 60%] iss/test/test_generator.py::test_amp PASSED [ 63%] iss/test/test_modeller.py::test_kde_qualities PASSED [ 65%] iss/test/test_modeller.py::test_substitutions PASSED [ 67%] iss/test/test_modeller.py::test_indels PASSED [ 69%] iss/test/test_util.py::test_phred_conversions PASSED [ 71%] iss/test/test_util.py::test_rev_comp PASSED [ 73%] iss/test/test_util.py::test_count_records PASSED [ 76%] iss/test/test_util.py::test_count_records_empty PASSED [ 78%] iss/test/test_util.py::test_split_list PASSED [ 80%] iss/test/test_util.py::test_convert_n_reads PASSED [ 82%] iss/test/test_util.py::test_convert_n_reads_bad_not_a_number PASSED [ 84%] iss/test/test_util.py::test_convert_n_reads_bad_suffix PASSED [ 86%] iss/test/test_util.py::test_genome_file_exists PASSED [ 89%] iss/test/test_util.py::test_reservoir PASSED [ 91%] iss/test/test_util.py::test_reservoir_invalid_input PASSED [ 93%] iss/test/test_util.py::test_concatenate PASSED [ 95%] iss/test/test_util.py::test_concatenate_read_only PASSED [ 97%] iss/test/test_util.py::test_compress PASSED [100%] ======================== 45 passed, 1 skipped in 6.85s ========================= make[1]: Leaving directory '/build/reproducible-path/insilicoseq-2.0.1' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/insilicoseq/ -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require' 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 egg_info writing InSilicoSeq.egg-info/PKG-INFO writing dependency_links to InSilicoSeq.egg-info/dependency_links.txt writing entry points to InSilicoSeq.egg-info/entry_points.txt writing requirements to InSilicoSeq.egg-info/requires.txt writing top-level names to InSilicoSeq.egg-info/top_level.txt reading manifest file 'InSilicoSeq.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'InSilicoSeq.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:218: _Warning: Package 'iss.profiles' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'iss.profiles' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'iss.profiles' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'iss.profiles' to be distributed and are already explicitly excluding 'iss.profiles' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) running install_lib creating /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr creating /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib creating /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12 creating /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages creating /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss creating /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/profiles copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles/nextSeq.npz -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/profiles copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles/miSeq_36.npz -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/profiles copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles/miSeq_32.npz -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/profiles copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles/miSeq_28.npz -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/profiles copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles/miSeq_24.npz -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/profiles copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles/miSeq_20.npz -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/profiles copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles/miSeq_0.npz -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/profiles copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles/NovaSeq -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/profiles copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles/MiSeq -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/profiles copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles/HiSeq -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/profiles creating /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/error_models copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/error_models/__init__.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/error_models copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/error_models/basic.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/error_models copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/error_models/kde.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/error_models copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/error_models/perfect.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/error_models creating /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test/__init__.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test/test_abundance.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test/test_bam.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test/test_error_model.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test/test_generator.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test/test_modeller.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test/test_util.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test/test_download.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/__init__.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/__main__.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/abundance.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/app.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/bam.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/download.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/generator.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/modeller.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/util.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/version.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/error_models/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/error_models/basic.py to basic.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/error_models/kde.py to kde.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/error_models/perfect.py to perfect.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test/test_abundance.py to test_abundance.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test/test_bam.py to test_bam.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test/test_error_model.py to test_error_model.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test/test_generator.py to test_generator.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test/test_modeller.py to test_modeller.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test/test_util.py to test_util.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test/test_download.py to test_download.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/__main__.py to __main__.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/abundance.py to abundance.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/app.py to app.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/bam.py to bam.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/download.py to download.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/generator.py to generator.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/modeller.py to modeller.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/util.py to util.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/version.py to version.cpython-312.pyc running install_egg_info Copying InSilicoSeq.egg-info to /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/InSilicoSeq-2.0.1.egg-info Skipping SOURCES.txt running install_scripts Installing iss script to /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/bin dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/insilicoseq-2.0.1' dh_installexamples find debian -name __pycache__ -type d | xargs rm -rf make[1]: Leaving directory '/build/reproducible-path/insilicoseq-2.0.1' dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/insilicoseq-2.0.1' dh_fixperms find debian/ -name read_only.fasta| xargs chmod 0444 make[1]: Leaving directory '/build/reproducible-path/insilicoseq-2.0.1' dh_missing -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: Recommends field of package insilicoseq: substitution variable ${python3:Recommends} used, but is not defined dpkg-gencontrol: warning: Suggests field of package insilicoseq: substitution variable ${python3:Suggests} used, but is not defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'insilicoseq' in '../insilicoseq_2.0.1-1_all.deb'. dpkg-genbuildinfo --build=binary -O../insilicoseq_2.0.1-1_arm64.buildinfo dpkg-genchanges --build=binary -O../insilicoseq_2.0.1-1_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: including full 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/3155505 and its subdirectories I: Current time: Tue Oct 1 02:36:46 -12 2024 I: pbuilder-time-stamp: 1727793406 Tue Oct 1 14:36:46 UTC 2024 I: Signing ./b1/insilicoseq_2.0.1-1_arm64.buildinfo as insilicoseq_2.0.1-1_arm64.buildinfo.asc Tue Oct 1 14:36:46 UTC 2024 I: Signed ./b1/insilicoseq_2.0.1-1_arm64.buildinfo as ./b1/insilicoseq_2.0.1-1_arm64.buildinfo.asc Tue Oct 1 14:36:46 UTC 2024 - build #1 for insilicoseq/trixie/arm64 on codethink04-arm64 done. Starting cleanup. All cleanup done. Tue Oct 1 14:36:46 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-2uPO44KB, removing. /srv/reproducible-results/rbuild-debian/r-b-build.Lh7t7LAy: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Oct 1 14:36 b1 drwxr-xr-x 2 jenkins jenkins 4096 Oct 1 14:33 b2 -rw-r--r-- 1 jenkins jenkins 2411 Apr 24 11:40 insilicoseq_2.0.1-1.dsc -rw------- 1 jenkins jenkins 3544 Oct 1 14:33 rbuildlog.lsaSoAB /srv/reproducible-results/rbuild-debian/r-b-build.Lh7t7LAy/b1: total 8752 -rw-r--r-- 1 jenkins jenkins 89689 Oct 1 14:36 build.log -rw-r--r-- 1 jenkins jenkins 5304 Oct 1 14:36 insilicoseq_2.0.1-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2411 Oct 1 14:36 insilicoseq_2.0.1-1.dsc -rw-r--r-- 1 jenkins jenkins 4234292 Oct 1 14:36 insilicoseq_2.0.1-1_all.deb -rw-r--r-- 1 jenkins jenkins 8432 Oct 1 14:36 insilicoseq_2.0.1-1_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 9314 Oct 1 14:36 insilicoseq_2.0.1-1_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1129 Oct 1 14:36 insilicoseq_2.0.1-1_arm64.changes -rw-r--r-- 1 jenkins jenkins 1556 Oct 1 14:36 insilicoseq_2.0.1-1_source.changes -rw-r--r-- 1 jenkins jenkins 4591338 Oct 1 14:36 insilicoseq_2.0.1.orig.tar.gz /srv/reproducible-results/rbuild-debian/r-b-build.Lh7t7LAy/b2: total 0 Tue Oct 1 14:36:48 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Oct 1 02:33:44 -12 2024 I: pbuilder-time-stamp: 1727793224 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 [insilicoseq_2.0.1-1.dsc] I: copying [./insilicoseq_2.0.1.orig.tar.gz] I: copying [./insilicoseq_2.0.1-1.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Apr 24 11:31:14 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 ./insilicoseq_2.0.1-1.dsc: no acceptable signature found dpkg-source: info: extracting insilicoseq in insilicoseq-2.0.1 dpkg-source: info: unpacking insilicoseq_2.0.1.orig.tar.gz dpkg-source: info: unpacking insilicoseq_2.0.1-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no-internet.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3155505/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='a5c93f1b15954144959bbfb8ec035dba' 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='3155505' 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.Lh7t7LAy/pbuilderrc_u6mF --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.Lh7t7LAy/b1 --logfile b1/build.log insilicoseq_2.0.1-1.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 codethink04-arm64 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3155505/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, python3-setuptools, python3-all, python3-biopython, python3-joblib, python3-numpy, python3-pysam, python3-requests, python3-scipy, python3-pytest dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19895 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-joblib; however: Package python3-joblib is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-pysam; however: Package python3-pysam is not installed. pbuilder-satisfydepends-dummy depends on python3-requests; however: Package python3-requests is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest 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} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libcurl3t64-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnsl2{a} libopenjp2-7{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libraqm0{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libssh2-1t64{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxrender1{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} po-debconf{a} procps{a} python3{a} python3-all{a} python3-autocommand{a} python3-biopython{a} python3-cairo{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-decorator{a} python3-freetype{a} python3-idna{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-joblib{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-packaging{a} python3-pil{a} python3-pkg-resources{a} python3-pluggy{a} python3-pysam{a} python3-pytest{a} python3-reportlab{a} python3-requests{a} python3-rlpycairo{a} python3-scipy{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-urllib3{a} python3-zipp{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} tzdata{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-dejavu-extra krb5-locales libarchive-cpio-perl libglib2.0-data libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx ncbi-blast+ psmisc publicsuffix python-biopython-doc python3-olefile python3-psutil python3-pygments python3-simplejson shared-mime-info wget xdg-user-dirs 0 packages upgraded, 148 newly installed, 0 to remove and 0 not upgraded. Need to get 81.6 MB of archives. After unpacking 329 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 sgml-base all 1.31 [15.4 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libproc2-0 arm64 2:4.0.4-5 [61.3 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 procps arm64 2:4.0.4-5 [868 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 openssl arm64 3.3.2-1 [1348 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 ca-certificates all 20240203 [158 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.2-8 [96.6 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 49 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-2 [188 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-5 [9224 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.1 [630 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.20 [915 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 python3-typeguard all 4.3.0-1 [36.5 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 63 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.functools all 4.0.2-1 [11.7 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 python3-pkg-resources all 74.1.2-2 [213 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 python3-zipp all 3.20.2-1 [10.3 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 python3-setuptools all 74.1.2-2 [736 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 dh-python all 6.20240824 [109 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libfontenc1 arm64 1:1.1.8-1 [22.2 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b4 [292 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 libpng16-16t64 arm64 1.6.44-1 [272 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 x11-common all 1:7.7+23.1 [216 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 xfonts-utils arm64 1:7.7+7 [89.3 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 78 http://deb.debian.org/debian trixie/main arm64 fontconfig-config arm64 2.15.0-1.1 [317 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libblas3 arm64 3.12.0-3 [91.7 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 libfontconfig1 arm64 2.15.0-1.1 [385 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 libpixman-1-0 arm64 0.42.2-1+b1 [477 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 libxau6 arm64 1:1.0.9-1+b1 [18.1 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 libxdmcp6 arm64 1:1.1.2-3+b1 [24.3 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 libxcb1 arm64 1.17.0-2 [143 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 libx11-data all 2:1.8.7-1 [328 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 libx11-6 arm64 2:1.8.7-1+b1 [775 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 libxcb-render0 arm64 1.17.0-2 [115 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 libxcb-shm0 arm64 1.17.0-2 [105 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 libxrender1 arm64 1:0.9.10-1.1+b1 [27.0 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 libcairo2 arm64 1.18.2-2 [483 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-3 [174 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.63.0-1 [71.2 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libnghttp3-9 arm64 1.4.0-1 [59.5 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libngtcp2-16 arm64 1.6.0-1 [112 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libngtcp2-crypto-gnutls8 arm64 1.6.0-1 [18.5 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.0-7 [208 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.10.1-1 [329 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.21-1 [42.2 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 libfribidi0 arm64 1.0.15-1 [71.8 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14.2.0-3 [362 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libglib2.0-0t64 arm64 2.82.1-1 [1410 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libgraphite2-3 arm64 1.3.14-2 [69.2 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libharfbuzz0b arm64 9.0.0-1 [441 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libhtscodecs2 arm64 1.6.1-1 [74.6 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libhts3t64 arm64 1.20+ds-1 [416 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 libimagequant0 arm64 2.18.0-1+b1 [34.6 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 libjbig0 arm64 2.1-6.1+b1 [30.4 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo arm64 1:2.1.5-3 [172 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.0-3 [1757 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 liblbfgsb0 arm64 3.0+dfsg.4-1+b1 [25.0 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 liblcms2-2 arm64 2.14-2+b1 [144 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 liblerc4 arm64 4.0.0+ds-4+b1 [142 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 libopenjp2-7 arm64 2.5.0-2+b3 [177 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 libraqm0 arm64 0.10.1-1+b1 [13.7 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [111 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 libwebp7 arm64 1.4.0-0.1 [267 kB] Get: 122 http://deb.debian.org/debian trixie/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 123 http://deb.debian.org/debian trixie/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [110 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 libwebpmux3 arm64 1.4.0-0.1 [122 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 python3-all arm64 3.12.6-1 [1040 B] Get: 126 http://deb.debian.org/debian trixie/main arm64 python3-numpy arm64 1:1.26.4+ds-11 [3351 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 python3-pil arm64 10.4.0-1 [480 kB] Get: 129 http://deb.debian.org/debian trixie/main arm64 python3-cairo arm64 1.26.1-2 [113 kB] Get: 130 http://deb.debian.org/debian trixie/main arm64 python3-freetype all 2.5.1-1 [89.3 kB] Get: 131 http://deb.debian.org/debian trixie/main arm64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 132 http://deb.debian.org/debian trixie/main arm64 python3-reportlab all 4.2.2-1 [1150 kB] Get: 133 http://deb.debian.org/debian trixie/main arm64 xml-core all 0.19 [20.1 kB] Get: 134 http://deb.debian.org/debian trixie/main arm64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 135 http://deb.debian.org/debian trixie/main arm64 python3-biopython arm64 1.83+dfsg1-5 [1597 kB] Get: 136 http://deb.debian.org/debian trixie/main arm64 python3-certifi all 2024.8.30-1 [159 kB] Get: 137 http://deb.debian.org/debian trixie/main arm64 python3-charset-normalizer arm64 3.3.2-4 [110 kB] Get: 138 http://deb.debian.org/debian trixie/main arm64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 139 http://deb.debian.org/debian trixie/main arm64 python3-idna all 3.8-2 [41.6 kB] Get: 140 http://deb.debian.org/debian trixie/main arm64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 141 http://deb.debian.org/debian trixie/main arm64 python3-joblib all 1.3.2-2 [218 kB] Get: 142 http://deb.debian.org/debian trixie/main arm64 python3-packaging all 24.1-1 [45.8 kB] Get: 143 http://deb.debian.org/debian trixie/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 144 http://deb.debian.org/debian trixie/main arm64 python3-pysam arm64 0.22.1+ds-2+b1 [3244 kB] Get: 145 http://deb.debian.org/debian trixie/main arm64 python3-pytest all 8.3.3-1 [249 kB] Get: 146 http://deb.debian.org/debian trixie/main arm64 python3-urllib3 all 2.0.7-2 [111 kB] Get: 147 http://deb.debian.org/debian trixie/main arm64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 148 http://deb.debian.org/debian trixie/main arm64 python3-scipy arm64 1.13.1-5 [15.4 MB] Fetched 81.6 MB in 2s (53.4 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 ... 19895 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 ... 20215 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_arm64.deb ... Unpacking python3-minimal (3.12.6-1) ... 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_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../05-libcom-err2_1.47.1-1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.1-1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../07-libkeyutils1_1.6.3-3_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (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:arm64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3_arm64.deb ... 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) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... 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 ... 21287 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.6-1_arm64.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../002-libproc2-0_2%3a4.0.4-5_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-5) ... Selecting previously unselected package procps. Preparing to unpack .../003-procps_2%3a4.0.4-5_arm64.deb ... Unpacking procps (2:4.0.4-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../005-openssl_3.3.2-1_arm64.deb ... Unpacking openssl (3.3.2-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../006-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../007-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../008-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../009-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../010-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../011-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../012-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../013-bsdextrautils_2.40.2-8_arm64.deb ... Unpacking bsdextrautils (2.40.2-8) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../014-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../015-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../016-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../017-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../018-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../019-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 .../020-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../021-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../022-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../023-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../024-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 .../025-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... 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Setting up libelf1t64:arm64 (0.191-2) ... Setting up libkrb5support0:arm64 (1.21.3-3) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-8) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Oct 1 14:34:35 UTC 2024. Universal Time is now: Tue Oct 1 14:34:35 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:arm64 (1:1.1.8-1) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:arm64 (2.82.1-1) ... No schema files found: doing nothing. 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 libjpeg62-turbo:arm64 (1:2.1.5-3) ... Setting up libx11-data (2:1.8.7-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:arm64 (1.0.15-1) ... Setting up libimagequant0:arm64 (2.18.0-1+b1) ... Setting up libproc2-0:arm64 (2:4.0.4-5) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:arm64 (1.6.44-1) ... Setting up autopoint (0.22.5-2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libk5crypto3:arm64 (1.21.3-3) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-8) ... Setting up libgfortran5:arm64 (14.2.0-3) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:arm64 (1.4.0-1) ... Setting up libwebp7:arm64 (1.4.0-0.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libtiff6:arm64 (4.5.1+git230720-5) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up procps (2:4.0.4-5) ... Setting up libopenjp2-7:arm64 (2.5.0-2+b3) ... Setting up libx11-6:arm64 (2:1.8.7-1+b1) ... Setting up netbase (6.4) ... Setting up libngtcp2-16:arm64 (1.6.0-1) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:arm64 (1.21.3-3) ... Setting up libssh2-1t64:arm64 (1.11.0-7) ... Setting up openssl (3.3.2-1) ... Setting up libwebpmux3:arm64 (1.4.0-0.1) ... Setting up readline-common (8.2-5) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.1) ... Setting up libngtcp2-crypto-gnutls8:arm64 (1.6.0-1) ... 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 libxrender1:arm64 (1:0.9.10-1.1+b1) ... Setting up libtool (2.4.7-7) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libwebpdemux2:arm64 (1.4.0-0.1) ... Setting up libxext6:arm64 (2:1.3.4-1+b1) ... Setting up libldap-2.5-0:arm64 (2.5.18+dfsg-3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-3) ... 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 xml-core (0.19) ... Setting up libharfbuzz0b:arm64 (9.0.0-1) ... Setting up libfontconfig1:arm64 (2.15.0-1.1) ... Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1+b1) ... Setting up libtirpc3t64:arm64 (1.3.4+ds-1.3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:arm64 (8.10.1-1) ... Setting up xfonts-utils (1:7.7+7) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:arm64 (1.18.2-2) ... Setting up libraqm0:arm64 (0.10.1-1+b1) ... Setting up libnsl2:arm64 (1.3.0-3+b2) ... Setting up libhts3t64:arm64 (1.20+ds-1) ... 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 fonts-urw-base35 (20200910-8) ... Setting up libpython3-stdlib:arm64 (3.12.6-1) ... Setting up python3 (3.12.6-1) ... Setting up python3-zipp (3.20.2-1) ... Setting up python3-freetype (2.5.1-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-pil:arm64 (10.4.0-1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (24.1-1) ... Setting up python3-certifi (2024.8.30-1) ... Setting up python3-idna (3.8-2) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-urllib3 (2.0.7-2) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-pysam (0.22.1+ds-2+b1) ... Setting up python3-cairo (1.26.1-2) ... Setting up python3-jaraco.functools (4.0.2-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-charset-normalizer (3.3.2-4) ... Setting up python3-pytest (8.3.3-1) ... 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 python3-rlpycairo (0.3.0-3) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up python3-setuptools (74.1.2-2) ... Setting up python3-joblib (1.3.2-2) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up python3-numpy (1:1.26.4+ds-11) ... Setting up python3-reportlab (4.2.2-1) ... Setting up dh-python (6.20240824) ... Setting up python3-scipy (1.13.1-5) ... Processing triggers for libc-bin (2.40-2) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.83+dfsg1-5) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 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/insilicoseq-2.0.1/ && 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 > ../insilicoseq_2.0.1-1_source.changes dpkg-buildpackage: info: source package insilicoseq dpkg-buildpackage: info: source version 2.0.1-1 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 LC_ALL=C.UTF-8 dh clean --buildsystem=pybuild 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: 'tests_require' warnings.warn(msg) running clean removing '/build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/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 LC_ALL=C.UTF-8 dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.12 setup.py config /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) running config 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: 'tests_require' warnings.warn(msg) running build running build_py creating /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss copying iss/version.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss copying iss/util.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss copying iss/modeller.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss copying iss/generator.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss copying iss/download.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss copying iss/bam.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss copying iss/app.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss copying iss/abundance.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss copying iss/__main__.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss copying iss/__init__.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss creating /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test copying iss/test/test_download.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test copying iss/test/test_util.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test copying iss/test/test_modeller.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test copying iss/test/test_generator.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test copying iss/test/test_error_model.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test copying iss/test/test_bam.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test copying iss/test/test_abundance.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test copying iss/test/__init__.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test creating /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/error_models copying iss/error_models/perfect.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/error_models copying iss/error_models/kde.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/error_models copying iss/error_models/basic.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/error_models copying iss/error_models/__init__.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/error_models running egg_info creating InSilicoSeq.egg-info writing InSilicoSeq.egg-info/PKG-INFO writing dependency_links to InSilicoSeq.egg-info/dependency_links.txt writing entry points to InSilicoSeq.egg-info/entry_points.txt writing requirements to InSilicoSeq.egg-info/requires.txt writing top-level names to InSilicoSeq.egg-info/top_level.txt writing manifest file 'InSilicoSeq.egg-info/SOURCES.txt' reading manifest file 'InSilicoSeq.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'InSilicoSeq.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:218: _Warning: Package 'iss.profiles' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'iss.profiles' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'iss.profiles' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'iss.profiles' to be distributed and are already explicitly excluding 'iss.profiles' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) creating /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles copying iss/profiles/HiSeq -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles copying iss/profiles/MiSeq -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles copying iss/profiles/NovaSeq -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles copying iss/profiles/miSeq_0.npz -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles copying iss/profiles/miSeq_20.npz -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles copying iss/profiles/miSeq_24.npz -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles copying iss/profiles/miSeq_28.npz -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles copying iss/profiles/miSeq_32.npz -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles copying iss/profiles/miSeq_36.npz -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles copying iss/profiles/nextSeq.npz -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/insilicoseq-2.0.1' find /build/reproducible-path/insilicoseq-2.0.1 -name read_only.fasta| xargs chmod 0444 PYTHONPATH=/build/reproducible-path/insilicoseq-2.0.1 pytest-3 -v iss ============================= test session starts ============================== platform linux -- Python 3.12.6, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3 cachedir: .pytest_cache rootdir: /build/reproducible-path/insilicoseq-2.0.1 configfile: pyproject.toml plugins: typeguard-4.3.0 collecting ... collected 46 items iss/test/test_abundance.py::test_parsing PASSED [ 2%] iss/test/test_abundance.py::test_parsing_readcounts PASSED [ 4%] iss/test/test_abundance.py::test_parsing_empty PASSED [ 6%] iss/test/test_abundance.py::test_parsing_no_exists PASSED [ 8%] iss/test/test_abundance.py::test_parsing_bad_abundance PASSED [ 10%] iss/test/test_abundance.py::test_cov_calc PASSED [ 13%] iss/test/test_abundance.py::test_distributions PASSED [ 15%] iss/test/test_abundance.py::test_abunance_draft PASSED [ 17%] iss/test/test_abundance.py::test_coverage_scaling PASSED [ 19%] iss/test/test_bam.py::test_read_fail PASSED [ 21%] iss/test/test_bam.py::test_to_model PASSED [ 23%] iss/test/test_download.py::test_ncbi SKIPPED (Test requires Internet.) [ 26%] iss/test/test_error_model.py::test_perfect_phred PASSED [ 28%] iss/test/test_error_model.py::test_basic_phred PASSED [ 30%] iss/test/test_error_model.py::test_kde_phred PASSED [ 32%] iss/test/test_error_model.py::test_introduce_errors PASSED [ 34%] iss/test/test_error_model.py::test_mut_sequence PASSED [ 36%] iss/test/test_error_model.py::test_introduce_indels PASSED [ 39%] iss/test/test_error_model.py::test_adjust_seq_length_extend PASSED [ 41%] iss/test/test_error_model.py::test_introduce_indels_rev PASSED [ 43%] iss/test/test_error_model.py::test_bad_err_mod PASSED [ 45%] iss/test/test_generator.py::test_cleanup_fail PASSED [ 47%] iss/test/test_generator.py::test_simulate_and_save PASSED [ 50%] iss/test/test_generator.py::test_simulate_and_save_short PASSED [ 52%] iss/test/test_generator.py::test_small_input PASSED [ 54%] iss/test/test_generator.py::test_basic PASSED [ 56%] iss/test/test_generator.py::test_kde PASSED [ 58%] iss/test/test_generator.py::test_kde_short PASSED [ 60%] iss/test/test_generator.py::test_amp PASSED [ 63%] iss/test/test_modeller.py::test_kde_qualities PASSED [ 65%] iss/test/test_modeller.py::test_substitutions PASSED [ 67%] iss/test/test_modeller.py::test_indels PASSED [ 69%] iss/test/test_util.py::test_phred_conversions PASSED [ 71%] iss/test/test_util.py::test_rev_comp PASSED [ 73%] iss/test/test_util.py::test_count_records PASSED [ 76%] iss/test/test_util.py::test_count_records_empty PASSED [ 78%] iss/test/test_util.py::test_split_list PASSED [ 80%] iss/test/test_util.py::test_convert_n_reads PASSED [ 82%] iss/test/test_util.py::test_convert_n_reads_bad_not_a_number PASSED [ 84%] iss/test/test_util.py::test_convert_n_reads_bad_suffix PASSED [ 86%] iss/test/test_util.py::test_genome_file_exists PASSED [ 89%] iss/test/test_util.py::test_reservoir PASSED [ 91%] iss/test/test_util.py::test_reservoir_invalid_input PASSED [ 93%] iss/test/test_util.py::test_concatenate PASSED [ 95%] iss/test/test_util.py::test_concatenate_read_only PASSED [ 97%] iss/test/test_util.py::test_compress PASSED [100%] ======================== 45 passed, 1 skipped in 6.85s ========================= make[1]: Leaving directory '/build/reproducible-path/insilicoseq-2.0.1' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/insilicoseq/ -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require' 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 egg_info writing InSilicoSeq.egg-info/PKG-INFO writing dependency_links to InSilicoSeq.egg-info/dependency_links.txt writing entry points to InSilicoSeq.egg-info/entry_points.txt writing requirements to InSilicoSeq.egg-info/requires.txt writing top-level names to InSilicoSeq.egg-info/top_level.txt reading manifest file 'InSilicoSeq.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'InSilicoSeq.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:218: _Warning: Package 'iss.profiles' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'iss.profiles' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'iss.profiles' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'iss.profiles' to be distributed and are already explicitly excluding 'iss.profiles' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) running install_lib creating /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr creating /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib creating /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12 creating /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages creating /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss creating /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/profiles copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles/nextSeq.npz -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/profiles copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles/miSeq_36.npz -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/profiles copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles/miSeq_32.npz -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/profiles copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles/miSeq_28.npz -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/profiles copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles/miSeq_24.npz -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/profiles copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles/miSeq_20.npz -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/profiles copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles/miSeq_0.npz -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/profiles copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles/NovaSeq -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/profiles copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles/MiSeq -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/profiles copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles/HiSeq -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/profiles creating /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/error_models copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/error_models/__init__.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/error_models copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/error_models/basic.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/error_models copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/error_models/kde.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/error_models copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/error_models/perfect.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/error_models creating /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test/__init__.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test/test_abundance.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test/test_bam.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test/test_error_model.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test/test_generator.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test/test_modeller.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test/test_util.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test/test_download.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/__init__.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/__main__.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/abundance.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/app.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/bam.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/download.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/generator.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/modeller.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/util.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/version.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/error_models/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/error_models/basic.py to basic.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/error_models/kde.py to kde.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/error_models/perfect.py to perfect.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test/test_abundance.py to test_abundance.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test/test_bam.py to test_bam.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test/test_error_model.py to test_error_model.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test/test_generator.py to test_generator.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test/test_modeller.py to test_modeller.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test/test_util.py to test_util.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test/test_download.py to test_download.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/__main__.py to __main__.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/abundance.py to abundance.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/app.py to app.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/bam.py to bam.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/download.py to download.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/generator.py to generator.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/modeller.py to modeller.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/util.py to util.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/version.py to version.cpython-312.pyc running install_egg_info Copying InSilicoSeq.egg-info to /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/InSilicoSeq-2.0.1.egg-info Skipping SOURCES.txt running install_scripts Installing iss script to /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/bin dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/insilicoseq-2.0.1' dh_installexamples find debian -name __pycache__ -type d | xargs rm -rf make[1]: Leaving directory '/build/reproducible-path/insilicoseq-2.0.1' dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/insilicoseq-2.0.1' dh_fixperms find debian/ -name read_only.fasta| xargs chmod 0444 make[1]: Leaving directory '/build/reproducible-path/insilicoseq-2.0.1' dh_missing -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: Recommends field of package insilicoseq: substitution variable ${python3:Recommends} used, but is not defined dpkg-gencontrol: warning: Suggests field of package insilicoseq: substitution variable ${python3:Suggests} used, but is not defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'insilicoseq' in '../insilicoseq_2.0.1-1_all.deb'. dpkg-genbuildinfo --build=binary -O../insilicoseq_2.0.1-1_arm64.buildinfo dpkg-genchanges --build=binary -O../insilicoseq_2.0.1-1_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: including full 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/3155505 and its subdirectories I: Current time: Tue Oct 1 02:36:46 -12 2024 I: pbuilder-time-stamp: 1727793406 Tue Oct 1 14:36:48 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink01-arm64.debian.net. Tue Oct 1 14:36:48 UTC 2024 I: Preparing to do remote build '2' on codethink01-arm64.debian.net. Tue Oct 1 14:36:48 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink01-arm64.debian.net is marked as down. Tue Oct 1 14:36:48 UTC 2024 - checking via ssh if codethink01-arm64.debian.net is up. removed '/tmp/read-only-fs-test-eqpCum' ==================================================================================== Mon Nov 3 20:59:49 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink01-arm64, called using "2 insilicoseq trixie /srv/reproducible-results/rbuild-debian/r-b-build.Lh7t7LAy 2.0.1-1" as arguments. Mon Nov 3 20:59:49 UTC 2025 - actually running "reproducible_build.sh" (md5sum 79f74068471242981be9b3b00196cbfb) as "/tmp/jenkins-script-fS99rRBT" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Mon Nov 3 20:59:49 UTC 2025 I: Downloading source for trixie/insilicoseq=2.0.1-1 Reading package lists... NOTICE: 'insilicoseq' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/insilicoseq.git Please use: git clone https://salsa.debian.org/med-team/insilicoseq.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 4599 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main insilicoseq 2.0.1-1 (dsc) [2411 B] Get:2 http://deb.debian.org/debian trixie/main insilicoseq 2.0.1-1 (tar) [4591 kB] Get:3 http://deb.debian.org/debian trixie/main insilicoseq 2.0.1-1 (diff) [5304 B] Fetched 4599 kB in 0s (69.0 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'insilicoseq' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/insilicoseq.git Please use: git clone https://salsa.debian.org/med-team/insilicoseq.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 4599 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main insilicoseq 2.0.1-1 (dsc) [2411 B] Get:2 http://deb.debian.org/debian trixie/main insilicoseq 2.0.1-1 (tar) [4591 kB] Get:3 http://deb.debian.org/debian trixie/main insilicoseq 2.0.1-1 (diff) [5304 B] Fetched 4599 kB in 0s (69.0 MB/s) Download complete and in download only mode ============================================================================= Re-Building insilicoseq in trixie on arm64 on codethink01-arm64 now. Date: Mon Nov 3 20:59:50 GMT 2025 Date UTC: Mon Nov 3 20:59:50 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.Lh7t7LAy + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.Lh7t7LAy/pbuilderrc_nrD7 + case ${ARCH} in + case $ARCH in + locale=nl_BE + language=nl + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' insilicoseq = debian-installer -o insilicoseq = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' insilicoseq = u-boot ']' + case "${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.Lh7t7LAy/pbuilderrc_nrD7 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Lh7t7LAy/b2 --logfile b2/build.log insilicoseq_2.0.1-1.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: Tue Nov 4 10:59:50 +14 2025 I: pbuilder-time-stamp: 1762203590 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 [insilicoseq_2.0.1-1.dsc] I: copying [./insilicoseq_2.0.1.orig.tar.gz] I: copying [./insilicoseq_2.0.1-1.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Apr 24 11:31:14 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 ./insilicoseq_2.0.1-1.dsc: no acceptable signature found dpkg-source: info: extracting insilicoseq in insilicoseq-2.0.1 dpkg-source: info: unpacking insilicoseq_2.0.1.orig.tar.gz dpkg-source: info: unpacking insilicoseq_2.0.1-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no-internet.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3843621/tmp/hooks/D01_modify_environment starting debug: Running on codethink01-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Nov 3 20:59 /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/3843621/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3843621/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]="aarch64-unknown-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=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=98aae2b82f6042a5924b3d895b3d93b0 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=3843621 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.Lh7t7LAy/pbuilderrc_nrD7 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Lh7t7LAy/b2 --logfile b2/build.log insilicoseq_2.0.1-1.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3843621/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, python3-setuptools, python3-all, python3-biopython, python3-joblib, python3-numpy, python3-pysam, python3-requests, python3-scipy, python3-pytest dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19895 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-joblib; however: Package python3-joblib is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-pysam; however: Package python3-pysam is not installed. pbuilder-satisfydepends-dummy depends on python3-requests; however: Package python3-requests is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest 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} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libcurl3t64-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnsl2{a} libopenjp2-7{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libraqm0{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libssh2-1t64{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxrender1{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} po-debconf{a} procps{a} python3{a} python3-all{a} python3-autocommand{a} python3-biopython{a} python3-cairo{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-decorator{a} python3-freetype{a} python3-idna{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-joblib{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-packaging{a} python3-pil{a} python3-pkg-resources{a} python3-pluggy{a} python3-pysam{a} python3-pytest{a} python3-reportlab{a} python3-requests{a} python3-rlpycairo{a} python3-scipy{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-urllib3{a} python3-zipp{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} tzdata{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-dejavu-extra krb5-locales libarchive-cpio-perl libglib2.0-data libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx ncbi-blast+ psmisc publicsuffix python-biopython-doc python3-olefile python3-psutil python3-pygments python3-simplejson shared-mime-info wget xdg-user-dirs 0 packages upgraded, 148 newly installed, 0 to remove and 0 not upgraded. Need to get 81.6 MB of archives. After unpacking 329 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 sgml-base all 1.31 [15.4 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libproc2-0 arm64 2:4.0.4-5 [61.3 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 procps arm64 2:4.0.4-5 [868 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 openssl arm64 3.3.2-1 [1348 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 ca-certificates all 20240203 [158 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.2-8 [96.6 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 49 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-2 [188 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-5 [9224 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.1 [630 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.20 [915 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 python3-typeguard all 4.3.0-1 [36.5 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 63 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.functools all 4.0.2-1 [11.7 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 python3-pkg-resources all 74.1.2-2 [213 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 python3-zipp all 3.20.2-1 [10.3 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 python3-setuptools all 74.1.2-2 [736 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 dh-python all 6.20240824 [109 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libfontenc1 arm64 1:1.1.8-1 [22.2 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b4 [292 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 libpng16-16t64 arm64 1.6.44-1 [272 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 x11-common all 1:7.7+23.1 [216 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 xfonts-utils arm64 1:7.7+7 [89.3 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 78 http://deb.debian.org/debian trixie/main arm64 fontconfig-config arm64 2.15.0-1.1 [317 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libblas3 arm64 3.12.0-3 [91.7 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 libfontconfig1 arm64 2.15.0-1.1 [385 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 libpixman-1-0 arm64 0.42.2-1+b1 [477 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 libxau6 arm64 1:1.0.9-1+b1 [18.1 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 libxdmcp6 arm64 1:1.1.2-3+b1 [24.3 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 libxcb1 arm64 1.17.0-2 [143 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 libx11-data all 2:1.8.7-1 [328 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 libx11-6 arm64 2:1.8.7-1+b1 [775 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 libxcb-render0 arm64 1.17.0-2 [115 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 libxcb-shm0 arm64 1.17.0-2 [105 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 libxrender1 arm64 1:0.9.10-1.1+b1 [27.0 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 libcairo2 arm64 1.18.2-2 [483 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-3 [174 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.63.0-1 [71.2 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libnghttp3-9 arm64 1.4.0-1 [59.5 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libngtcp2-16 arm64 1.6.0-1 [112 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libngtcp2-crypto-gnutls8 arm64 1.6.0-1 [18.5 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.0-7 [208 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.10.1-1 [329 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.21-1 [42.2 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 libfribidi0 arm64 1.0.15-1 [71.8 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14.2.0-3 [362 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libglib2.0-0t64 arm64 2.82.1-1 [1410 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libgraphite2-3 arm64 1.3.14-2 [69.2 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libharfbuzz0b arm64 9.0.0-1 [441 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libhtscodecs2 arm64 1.6.1-1 [74.6 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libhts3t64 arm64 1.20+ds-1 [416 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 libimagequant0 arm64 2.18.0-1+b1 [34.6 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 libjbig0 arm64 2.1-6.1+b1 [30.4 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo arm64 1:2.1.5-3 [172 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.0-3 [1757 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 liblbfgsb0 arm64 3.0+dfsg.4-1+b1 [25.0 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 liblcms2-2 arm64 2.14-2+b1 [144 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 liblerc4 arm64 4.0.0+ds-4+b1 [142 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 libopenjp2-7 arm64 2.5.0-2+b3 [177 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 libraqm0 arm64 0.10.1-1+b1 [13.7 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [111 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 libwebp7 arm64 1.4.0-0.1 [267 kB] Get: 122 http://deb.debian.org/debian trixie/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 123 http://deb.debian.org/debian trixie/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [110 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 libwebpmux3 arm64 1.4.0-0.1 [122 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 python3-all arm64 3.12.6-1 [1040 B] Get: 126 http://deb.debian.org/debian trixie/main arm64 python3-numpy arm64 1:1.26.4+ds-11 [3351 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 python3-pil arm64 10.4.0-1 [480 kB] Get: 129 http://deb.debian.org/debian trixie/main arm64 python3-cairo arm64 1.26.1-2 [113 kB] Get: 130 http://deb.debian.org/debian trixie/main arm64 python3-freetype all 2.5.1-1 [89.3 kB] Get: 131 http://deb.debian.org/debian trixie/main arm64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 132 http://deb.debian.org/debian trixie/main arm64 python3-reportlab all 4.2.2-1 [1150 kB] Get: 133 http://deb.debian.org/debian trixie/main arm64 xml-core all 0.19 [20.1 kB] Get: 134 http://deb.debian.org/debian trixie/main arm64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 135 http://deb.debian.org/debian trixie/main arm64 python3-biopython arm64 1.83+dfsg1-5 [1597 kB] Get: 136 http://deb.debian.org/debian trixie/main arm64 python3-certifi all 2024.8.30-1 [159 kB] Get: 137 http://deb.debian.org/debian trixie/main arm64 python3-charset-normalizer arm64 3.3.2-4 [110 kB] Get: 138 http://deb.debian.org/debian trixie/main arm64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 139 http://deb.debian.org/debian trixie/main arm64 python3-idna all 3.8-2 [41.6 kB] Get: 140 http://deb.debian.org/debian trixie/main arm64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 141 http://deb.debian.org/debian trixie/main arm64 python3-joblib all 1.3.2-2 [218 kB] Get: 142 http://deb.debian.org/debian trixie/main arm64 python3-packaging all 24.1-1 [45.8 kB] Get: 143 http://deb.debian.org/debian trixie/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 144 http://deb.debian.org/debian trixie/main arm64 python3-pysam arm64 0.22.1+ds-2+b1 [3244 kB] Get: 145 http://deb.debian.org/debian trixie/main arm64 python3-pytest all 8.3.3-1 [249 kB] Get: 146 http://deb.debian.org/debian trixie/main arm64 python3-urllib3 all 2.0.7-2 [111 kB] Get: 147 http://deb.debian.org/debian trixie/main arm64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 148 http://deb.debian.org/debian trixie/main arm64 python3-scipy arm64 1.13.1-5 [15.4 MB] Fetched 81.6 MB in 1s (147 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 ... 19895 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 ... 20215 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_arm64.deb ... Unpacking python3-minimal (3.12.6-1) ... 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_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../05-libcom-err2_1.47.1-1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.1-1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../07-libkeyutils1_1.6.3-3_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (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:arm64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3_arm64.deb ... 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) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... 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 ... 21287 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.6-1_arm64.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../002-libproc2-0_2%3a4.0.4-5_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-5) ... Selecting previously unselected package procps. Preparing to unpack .../003-procps_2%3a4.0.4-5_arm64.deb ... Unpacking procps (2:4.0.4-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../005-openssl_3.3.2-1_arm64.deb ... Unpacking openssl (3.3.2-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../006-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../007-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../008-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../009-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../010-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../011-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../012-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../013-bsdextrautils_2.40.2-8_arm64.deb ... Unpacking bsdextrautils (2.40.2-8) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../014-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../015-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../016-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../017-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../018-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../019-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... 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Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../026-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../027-libelf1t64_0.191-2_arm64.deb ... Unpacking libelf1t64:arm64 (0.191-2) ... Selecting previously unselected package dwz. Preparing to unpack .../028-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../029-libicu72_72.1-5_arm64.deb ... Unpacking libicu72:arm64 (72.1-5) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../030-libxml2_2.12.7+dfsg+really2.9.14-0.1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.1) ... Selecting previously unselected package gettext. Preparing to unpack .../031-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../032-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 .../033-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../034-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package python3-autocommand. Preparing to unpack .../035-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 .../036-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 .../037-python3-typing-extensions_4.12.2-2_all.deb ... Unpacking python3-typing-extensions (4.12.2-2) ... Selecting previously unselected package python3-typeguard. Preparing to unpack .../038-python3-typeguard_4.3.0-1_all.deb ... Unpacking python3-typeguard (4.3.0-1) ... Selecting previously unselected package python3-inflect. Preparing to unpack .../039-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 .../040-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 .../041-python3-jaraco.functools_4.0.2-1_all.deb ... Unpacking python3-jaraco.functools (4.0.2-1) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../042-python3-pkg-resources_74.1.2-2_all.deb ... Unpacking python3-pkg-resources (74.1.2-2) ... Selecting previously unselected package python3-zipp. Preparing to unpack .../043-python3-zipp_3.20.2-1_all.deb ... Unpacking python3-zipp (3.20.2-1) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../044-python3-setuptools_74.1.2-2_all.deb ... Unpacking python3-setuptools (74.1.2-2) ... Selecting previously unselected package dh-python. Preparing to unpack .../045-dh-python_6.20240824_all.deb ... Unpacking dh-python (6.20240824) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../046-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../047-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package libfontenc1:arm64. Preparing to unpack .../048-libfontenc1_1%3a1.1.8-1_arm64.deb ... Unpacking libfontenc1:arm64 (1:1.1.8-1) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../049-libbrotli1_1.1.0-2+b4_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b4) ... Selecting previously unselected package libpng16-16t64:arm64. Preparing to unpack .../050-libpng16-16t64_1.6.44-1_arm64.deb ... Unpacking libpng16-16t64:arm64 (1.6.44-1) ... Selecting previously unselected package libfreetype6:arm64. Preparing to unpack .../051-libfreetype6_2.13.3+dfsg-1_arm64.deb ... Unpacking libfreetype6:arm64 (2.13.3+dfsg-1) ... Selecting previously unselected package x11-common. Preparing to unpack .../052-x11-common_1%3a7.7+23.1_all.deb ... Unpacking x11-common (1:7.7+23.1) ... Selecting previously unselected package xfonts-encodings. Preparing to unpack .../053-xfonts-encodings_1%3a1.0.4-2.2_all.deb ... Unpacking xfonts-encodings (1:1.0.4-2.2) ... Selecting previously unselected package xfonts-utils. Preparing to unpack .../054-xfonts-utils_1%3a7.7+7_arm64.deb ... Unpacking xfonts-utils (1:7.7+7) ... Selecting previously unselected package fonts-urw-base35. Preparing to unpack .../055-fonts-urw-base35_20200910-8_all.deb ... Unpacking fonts-urw-base35 (20200910-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../056-fontconfig-config_2.15.0-1.1_arm64.deb ... Unpacking fontconfig-config (2.15.0-1.1) ... Selecting previously unselected package libblas3:arm64. Preparing to unpack .../057-libblas3_3.12.0-3_arm64.deb ... Unpacking libblas3:arm64 (3.12.0-3) ... Selecting previously unselected package libfontconfig1:arm64. Preparing to unpack .../058-libfontconfig1_2.15.0-1.1_arm64.deb ... Unpacking libfontconfig1:arm64 (2.15.0-1.1) ... Selecting previously unselected package libpixman-1-0:arm64. Preparing to unpack .../059-libpixman-1-0_0.42.2-1+b1_arm64.deb ... Unpacking libpixman-1-0:arm64 (0.42.2-1+b1) ... Selecting previously unselected package libxau6:arm64. 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Setting up libxcb1:arm64 (1.17.0-2) ... Setting up libicu72:arm64 (72.1-5) ... Setting up liblerc4:arm64 (4.0.0+ds-4+b1) ... Setting up bsdextrautils (2.40.2-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libxcb-render0:arm64 (1.17.0-2) ... 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 libbrotli1:arm64 (1.1.0-2+b4) ... Setting up libmagic1t64:arm64 (1:5.45-3) ... Setting up x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libpsl5t64:arm64 (0.21.2-1.1) ... Setting up libnghttp2-14:arm64 (1.63.0-1) ... Setting up libdeflate0:arm64 (1.21-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libxcb-shm0:arm64 (1.17.0-2) ... Setting up libcom-err2:arm64 (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libjbig0:arm64 (2.1-6.1+b1) ... Setting up libelf1t64:arm64 (0.191-2) ... Setting up libkrb5support0:arm64 (1.21.3-3) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-8) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Nov 3 21:00:24 UTC 2025. Universal Time is now: Mon Nov 3 21:00:24 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:arm64 (1:1.1.8-1) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:arm64 (2.82.1-1) ... No schema files found: doing nothing. 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 libjpeg62-turbo:arm64 (1:2.1.5-3) ... Setting up libx11-data (2:1.8.7-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:arm64 (1.0.15-1) ... Setting up libimagequant0:arm64 (2.18.0-1+b1) ... Setting up libproc2-0:arm64 (2:4.0.4-5) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:arm64 (1.6.44-1) ... Setting up autopoint (0.22.5-2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libk5crypto3:arm64 (1.21.3-3) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-8) ... Setting up libgfortran5:arm64 (14.2.0-3) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:arm64 (1.4.0-1) ... Setting up libwebp7:arm64 (1.4.0-0.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libtiff6:arm64 (4.5.1+git230720-5) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up procps (2:4.0.4-5) ... Setting up libopenjp2-7:arm64 (2.5.0-2+b3) ... Setting up libx11-6:arm64 (2:1.8.7-1+b1) ... Setting up netbase (6.4) ... Setting up libngtcp2-16:arm64 (1.6.0-1) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:arm64 (1.21.3-3) ... Setting up libssh2-1t64:arm64 (1.11.0-7) ... Setting up openssl (3.3.2-1) ... Setting up libwebpmux3:arm64 (1.4.0-0.1) ... Setting up readline-common (8.2-5) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.1) ... Setting up libngtcp2-crypto-gnutls8:arm64 (1.6.0-1) ... 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 libxrender1:arm64 (1:0.9.10-1.1+b1) ... Setting up libtool (2.4.7-7) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libwebpdemux2:arm64 (1.4.0-0.1) ... Setting up libxext6:arm64 (2:1.3.4-1+b1) ... Setting up libldap-2.5-0:arm64 (2.5.18+dfsg-3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-3) ... 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 xml-core (0.19) ... Setting up libharfbuzz0b:arm64 (9.0.0-1) ... Setting up libfontconfig1:arm64 (2.15.0-1.1) ... Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1+b1) ... Setting up libtirpc3t64:arm64 (1.3.4+ds-1.3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:arm64 (8.10.1-1) ... Setting up xfonts-utils (1:7.7+7) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:arm64 (1.18.2-2) ... Setting up libraqm0:arm64 (0.10.1-1+b1) ... Setting up libnsl2:arm64 (1.3.0-3+b2) ... Setting up libhts3t64:arm64 (1.20+ds-1) ... 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 fonts-urw-base35 (20200910-8) ... Setting up libpython3-stdlib:arm64 (3.12.6-1) ... Setting up python3 (3.12.6-1) ... Setting up python3-zipp (3.20.2-1) ... Setting up python3-freetype (2.5.1-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-pil:arm64 (10.4.0-1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (24.1-1) ... Setting up python3-certifi (2024.8.30-1) ... Setting up python3-idna (3.8-2) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-urllib3 (2.0.7-2) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-pysam (0.22.1+ds-2+b1) ... Setting up python3-cairo (1.26.1-2) ... Setting up python3-jaraco.functools (4.0.2-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-charset-normalizer (3.3.2-4) ... Setting up python3-pytest (8.3.3-1) ... 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 python3-rlpycairo (0.3.0-3) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up python3-setuptools (74.1.2-2) ... Setting up python3-joblib (1.3.2-2) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up python3-numpy (1:1.26.4+ds-11) ... Setting up python3-reportlab (4.2.2-1) ... Setting up dh-python (6.20240824) ... Setting up python3-scipy (1.13.1-5) ... Processing triggers for libc-bin (2.40-2) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.83+dfsg1-5) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 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: user script /srv/workspace/pbuilder/3843621/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/3843621/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/insilicoseq-2.0.1/ && 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 > ../insilicoseq_2.0.1-1_source.changes dpkg-buildpackage: info: source package insilicoseq dpkg-buildpackage: info: source version 2.0.1-1 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 LC_ALL=C.UTF-8 dh clean --buildsystem=pybuild 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: 'tests_require' warnings.warn(msg) running clean removing '/build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/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 LC_ALL=C.UTF-8 dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.12 setup.py config /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) running config 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: 'tests_require' warnings.warn(msg) running build running build_py creating /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss copying iss/version.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss copying iss/util.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss copying iss/modeller.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss copying iss/generator.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss copying iss/download.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss copying iss/bam.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss copying iss/app.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss copying iss/abundance.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss copying iss/__main__.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss copying iss/__init__.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss creating /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test copying iss/test/test_download.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test copying iss/test/test_util.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test copying iss/test/test_modeller.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test copying iss/test/test_generator.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test copying iss/test/test_error_model.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test copying iss/test/test_bam.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test copying iss/test/test_abundance.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test copying iss/test/__init__.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test creating /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/error_models copying iss/error_models/perfect.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/error_models copying iss/error_models/kde.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/error_models copying iss/error_models/basic.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/error_models copying iss/error_models/__init__.py -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/error_models running egg_info creating InSilicoSeq.egg-info writing InSilicoSeq.egg-info/PKG-INFO writing dependency_links to InSilicoSeq.egg-info/dependency_links.txt writing entry points to InSilicoSeq.egg-info/entry_points.txt writing requirements to InSilicoSeq.egg-info/requires.txt writing top-level names to InSilicoSeq.egg-info/top_level.txt writing manifest file 'InSilicoSeq.egg-info/SOURCES.txt' reading manifest file 'InSilicoSeq.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'InSilicoSeq.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:218: _Warning: Package 'iss.profiles' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'iss.profiles' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'iss.profiles' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'iss.profiles' to be distributed and are already explicitly excluding 'iss.profiles' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) creating /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles copying iss/profiles/HiSeq -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles copying iss/profiles/MiSeq -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles copying iss/profiles/NovaSeq -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles copying iss/profiles/miSeq_0.npz -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles copying iss/profiles/miSeq_20.npz -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles copying iss/profiles/miSeq_24.npz -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles copying iss/profiles/miSeq_28.npz -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles copying iss/profiles/miSeq_32.npz -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles copying iss/profiles/miSeq_36.npz -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles copying iss/profiles/nextSeq.npz -> /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/insilicoseq-2.0.1' find /build/reproducible-path/insilicoseq-2.0.1 -name read_only.fasta| xargs chmod 0444 PYTHONPATH=/build/reproducible-path/insilicoseq-2.0.1 pytest-3 -v iss ============================= test session starts ============================== platform linux -- Python 3.12.6, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3 cachedir: .pytest_cache rootdir: /build/reproducible-path/insilicoseq-2.0.1 configfile: pyproject.toml plugins: typeguard-4.3.0 collecting ... collected 46 items iss/test/test_abundance.py::test_parsing PASSED [ 2%] iss/test/test_abundance.py::test_parsing_readcounts PASSED [ 4%] iss/test/test_abundance.py::test_parsing_empty PASSED [ 6%] iss/test/test_abundance.py::test_parsing_no_exists PASSED [ 8%] iss/test/test_abundance.py::test_parsing_bad_abundance PASSED [ 10%] iss/test/test_abundance.py::test_cov_calc PASSED [ 13%] iss/test/test_abundance.py::test_distributions PASSED [ 15%] iss/test/test_abundance.py::test_abunance_draft PASSED [ 17%] iss/test/test_abundance.py::test_coverage_scaling PASSED [ 19%] iss/test/test_bam.py::test_read_fail PASSED [ 21%] iss/test/test_bam.py::test_to_model PASSED [ 23%] iss/test/test_download.py::test_ncbi SKIPPED (Test requires Internet.) [ 26%] iss/test/test_error_model.py::test_perfect_phred PASSED [ 28%] iss/test/test_error_model.py::test_basic_phred PASSED [ 30%] iss/test/test_error_model.py::test_kde_phred PASSED [ 32%] iss/test/test_error_model.py::test_introduce_errors PASSED [ 34%] iss/test/test_error_model.py::test_mut_sequence PASSED [ 36%] iss/test/test_error_model.py::test_introduce_indels PASSED [ 39%] iss/test/test_error_model.py::test_adjust_seq_length_extend PASSED [ 41%] iss/test/test_error_model.py::test_introduce_indels_rev PASSED [ 43%] iss/test/test_error_model.py::test_bad_err_mod PASSED [ 45%] iss/test/test_generator.py::test_cleanup_fail PASSED [ 47%] iss/test/test_generator.py::test_simulate_and_save PASSED [ 50%] iss/test/test_generator.py::test_simulate_and_save_short PASSED [ 52%] iss/test/test_generator.py::test_small_input PASSED [ 54%] iss/test/test_generator.py::test_basic PASSED [ 56%] iss/test/test_generator.py::test_kde PASSED [ 58%] iss/test/test_generator.py::test_kde_short PASSED [ 60%] iss/test/test_generator.py::test_amp PASSED [ 63%] iss/test/test_modeller.py::test_kde_qualities PASSED [ 65%] iss/test/test_modeller.py::test_substitutions PASSED [ 67%] iss/test/test_modeller.py::test_indels PASSED [ 69%] iss/test/test_util.py::test_phred_conversions PASSED [ 71%] iss/test/test_util.py::test_rev_comp PASSED [ 73%] iss/test/test_util.py::test_count_records PASSED [ 76%] iss/test/test_util.py::test_count_records_empty PASSED [ 78%] iss/test/test_util.py::test_split_list PASSED [ 80%] iss/test/test_util.py::test_convert_n_reads PASSED [ 82%] iss/test/test_util.py::test_convert_n_reads_bad_not_a_number PASSED [ 84%] iss/test/test_util.py::test_convert_n_reads_bad_suffix PASSED [ 86%] iss/test/test_util.py::test_genome_file_exists PASSED [ 89%] iss/test/test_util.py::test_reservoir PASSED [ 91%] iss/test/test_util.py::test_reservoir_invalid_input PASSED [ 93%] iss/test/test_util.py::test_concatenate PASSED [ 95%] iss/test/test_util.py::test_concatenate_read_only PASSED [ 97%] iss/test/test_util.py::test_compress PASSED [100%] ======================== 45 passed, 1 skipped in 4.41s ========================= make[1]: Leaving directory '/build/reproducible-path/insilicoseq-2.0.1' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/insilicoseq/ -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require' 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 egg_info writing InSilicoSeq.egg-info/PKG-INFO writing dependency_links to InSilicoSeq.egg-info/dependency_links.txt writing entry points to InSilicoSeq.egg-info/entry_points.txt writing requirements to InSilicoSeq.egg-info/requires.txt writing top-level names to InSilicoSeq.egg-info/top_level.txt reading manifest file 'InSilicoSeq.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'InSilicoSeq.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:218: _Warning: Package 'iss.profiles' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'iss.profiles' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'iss.profiles' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'iss.profiles' to be distributed and are already explicitly excluding 'iss.profiles' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) running install_lib creating /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr creating /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib creating /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12 creating /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages creating /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss creating /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/profiles copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles/nextSeq.npz -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/profiles copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles/miSeq_36.npz -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/profiles copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles/miSeq_32.npz -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/profiles copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles/miSeq_28.npz -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/profiles copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles/miSeq_24.npz -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/profiles copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles/miSeq_20.npz -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/profiles copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles/miSeq_0.npz -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/profiles copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles/NovaSeq -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/profiles copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles/MiSeq -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/profiles copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/profiles/HiSeq -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/profiles creating /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/error_models copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/error_models/__init__.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/error_models copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/error_models/basic.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/error_models copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/error_models/kde.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/error_models copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/error_models/perfect.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/error_models creating /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test/__init__.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test/test_abundance.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test/test_bam.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test/test_error_model.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test/test_generator.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test/test_modeller.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test/test_util.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/test/test_download.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/__init__.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/__main__.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/abundance.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/app.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/bam.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/download.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/generator.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/modeller.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/util.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss copying /build/reproducible-path/insilicoseq-2.0.1/.pybuild/cpython3_3.12_insilicoseq/build/iss/version.py -> /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/error_models/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/error_models/basic.py to basic.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/error_models/kde.py to kde.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/error_models/perfect.py to perfect.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test/test_abundance.py to test_abundance.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test/test_bam.py to test_bam.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test/test_error_model.py to test_error_model.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test/test_generator.py to test_generator.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test/test_modeller.py to test_modeller.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test/test_util.py to test_util.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/test/test_download.py to test_download.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/__main__.py to __main__.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/abundance.py to abundance.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/app.py to app.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/bam.py to bam.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/download.py to download.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/generator.py to generator.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/modeller.py to modeller.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/util.py to util.cpython-312.pyc byte-compiling /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/iss/version.py to version.cpython-312.pyc running install_egg_info Copying InSilicoSeq.egg-info to /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/lib/python3.12/dist-packages/InSilicoSeq-2.0.1.egg-info Skipping SOURCES.txt running install_scripts Installing iss script to /build/reproducible-path/insilicoseq-2.0.1/debian/insilicoseq/usr/bin dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/insilicoseq-2.0.1' dh_installexamples find debian -name __pycache__ -type d | xargs rm -rf make[1]: Leaving directory '/build/reproducible-path/insilicoseq-2.0.1' dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/insilicoseq-2.0.1' dh_fixperms find debian/ -name read_only.fasta| xargs chmod 0444 make[1]: Leaving directory '/build/reproducible-path/insilicoseq-2.0.1' dh_missing -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: Recommends field of package insilicoseq: substitution variable ${python3:Recommends} used, but is not defined dpkg-gencontrol: warning: Suggests field of package insilicoseq: substitution variable ${python3:Suggests} used, but is not defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'insilicoseq' in '../insilicoseq_2.0.1-1_all.deb'. dpkg-genbuildinfo --build=binary -O../insilicoseq_2.0.1-1_arm64.buildinfo dpkg-genchanges --build=binary -O../insilicoseq_2.0.1-1_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: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3843621/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3843621/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/3843621 and its subdirectories I: Current time: Tue Nov 4 11:02:10 +14 2025 I: pbuilder-time-stamp: 1762203730 + false + set +x Mon Nov 3 21:02:10 UTC 2025 I: Signing ./b2/insilicoseq_2.0.1-1_arm64.buildinfo as insilicoseq_2.0.1-1_arm64.buildinfo.asc Mon Nov 3 21:02:10 UTC 2025 I: Signed ./b2/insilicoseq_2.0.1-1_arm64.buildinfo as ./b2/insilicoseq_2.0.1-1_arm64.buildinfo.asc Mon Nov 3 21:02:10 UTC 2025 - build #2 for insilicoseq/trixie/arm64 on codethink01-arm64 done. Starting cleanup. All cleanup done. Mon Nov 3 21:02:10 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-fS99rRBT, removing. /srv/reproducible-results/rbuild-debian/r-b-build.Lh7t7LAy: total 108 drwxr-xr-x 2 jenkins jenkins 4096 Oct 1 14:36 b1 drwxr-xr-x 2 jenkins jenkins 4096 Oct 1 14:39 b2 -rw-r--r-- 1 jenkins jenkins 2411 Apr 24 11:40 insilicoseq_2.0.1-1.dsc -rw------- 1 jenkins jenkins 93534 Oct 1 14:36 rbuildlog.lsaSoAB /srv/reproducible-results/rbuild-debian/r-b-build.Lh7t7LAy/b1: total 8772 -rw-r--r-- 1 jenkins jenkins 89689 Oct 1 14:36 build.log -rw-r--r-- 1 jenkins jenkins 5304 Oct 1 14:36 insilicoseq_2.0.1-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2411 Oct 1 14:36 insilicoseq_2.0.1-1.dsc -rw-r--r-- 1 jenkins jenkins 4234292 Oct 1 14:36 insilicoseq_2.0.1-1_all.deb -rw-r--r-- 1 jenkins jenkins 8432 Oct 1 14:36 insilicoseq_2.0.1-1_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 9314 Oct 1 14:36 insilicoseq_2.0.1-1_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1129 Oct 1 14:36 insilicoseq_2.0.1-1_arm64.changes -rw-r--r-- 1 jenkins jenkins 1556 Oct 1 14:36 insilicoseq_2.0.1-1_source.changes -rw-r--r-- 1 jenkins jenkins 4591338 Oct 1 14:36 insilicoseq_2.0.1.orig.tar.gz /srv/reproducible-results/rbuild-debian/r-b-build.Lh7t7LAy/b2: total 8756 -rw-r--r-- 1 jenkins jenkins 91631 Oct 1 14:39 build.log -rw-r--r-- 1 jenkins jenkins 5304 Oct 1 14:39 insilicoseq_2.0.1-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2411 Oct 1 14:39 insilicoseq_2.0.1-1.dsc -rw-r--r-- 1 jenkins jenkins 4234292 Oct 1 14:39 insilicoseq_2.0.1-1_all.deb -rw-r--r-- 1 jenkins jenkins 8432 Oct 1 14:39 insilicoseq_2.0.1-1_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 9314 Oct 1 14:39 insilicoseq_2.0.1-1_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1129 Oct 1 14:39 insilicoseq_2.0.1-1_arm64.changes -rw-r--r-- 1 jenkins jenkins 1556 Oct 1 14:39 insilicoseq_2.0.1-1_source.changes -rw-r--r-- 1 jenkins jenkins 4591338 Oct 1 14:39 insilicoseq_2.0.1.orig.tar.gz Tue Oct 1 14:39:12 UTC 2024 I: Deleting $TMPDIR on codethink01-arm64.debian.net. Tue Oct 1 14:39:13 UTC 2024 I: insilicoseq_2.0.1-1_arm64.changes: Format: 1.8 Date: Wed, 24 Apr 2024 13:27:35 +0200 Source: insilicoseq Binary: insilicoseq Architecture: all Version: 2.0.1-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: insilicoseq - sequencing simulator producing realistic Illumina reads Changes: insilicoseq (2.0.1-1) unstable; urgency=medium . * New upstream version 2.0.1 * d/control: declare compliance to standards version 4.7.0. Checksums-Sha1: 55a75e6699632121c676ffca71e4f205e065c81a 4234292 insilicoseq_2.0.1-1_all.deb feea4b34c777b46554b3a809e78e1ff4ee26b274 8432 insilicoseq_2.0.1-1_arm64.buildinfo Checksums-Sha256: 0296ac24c20ce5318c4ccbab305b50b3757c1c62c95703565d15e19afcd6c3a1 4234292 insilicoseq_2.0.1-1_all.deb 2ed68972152afef52ec2dfacaa747f44df4880fa834fb22d3e66f7964ba2e744 8432 insilicoseq_2.0.1-1_arm64.buildinfo Files: 0088e3a6fd15a19bde3f2d38cdf0ba27 4234292 science optional insilicoseq_2.0.1-1_all.deb 5a98e8cb0076575b70e28b21ab673d1a 8432 science optional insilicoseq_2.0.1-1_arm64.buildinfo removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/insilicoseq_2.0.1-1.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/insilicoseq_2.0.1-1.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/insilicoseq_2.0.1-1.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/insilicoseq_2.0.1-1.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/trixie/arm64/insilicoseq_2.0.1-1_arm64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/insilicoseq_2.0.1-1.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2024-10-01 14:36:47.557117359 +0000 +++ b2/build.log 2024-10-01 14:39:11.898965979 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Oct 1 02:33:44 -12 2024 -I: pbuilder-time-stamp: 1727793224 +I: Current time: Tue Nov 4 10:59:50 +14 2025 +I: pbuilder-time-stamp: 1762203590 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -28,52 +28,84 @@ dpkg-source: info: applying no-internet.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3155505/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3843621/tmp/hooks/D01_modify_environment starting +debug: Running on codethink01-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Nov 3 20:59 /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/3843621/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3843621/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' + 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]="aarch64-unknown-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=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='a5c93f1b15954144959bbfb8ec035dba' - 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='3155505' - PS1='# ' - PS2='> ' + INVOCATION_ID=98aae2b82f6042a5924b3d895b3d93b0 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3843621 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.Lh7t7LAy/pbuilderrc_u6mF --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.Lh7t7LAy/b1 --logfile b1/build.log insilicoseq_2.0.1-1.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' + 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.Lh7t7LAy/pbuilderrc_nrD7 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Lh7t7LAy/b2 --logfile b2/build.log insilicoseq_2.0.1-1.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3155505/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3843621/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -277,7 +309,7 @@ Get: 146 http://deb.debian.org/debian trixie/main arm64 python3-urllib3 all 2.0.7-2 [111 kB] Get: 147 http://deb.debian.org/debian trixie/main arm64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 148 http://deb.debian.org/debian trixie/main arm64 python3-scipy arm64 1.13.1-5 [15.4 MB] -Fetched 81.6 MB in 2s (53.4 MB/s) +Fetched 81.6 MB in 1s (147 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 ... 19895 files and directories currently installed.) @@ -775,8 +807,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Oct 1 14:34:35 UTC 2024. -Universal Time is now: Tue Oct 1 14:34:35 UTC 2024. +Local time is now: Mon Nov 3 21:00:24 UTC 2025. +Universal Time is now: Mon Nov 3 21:00:24 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:arm64 (1:1.1.8-1) ... @@ -911,7 +943,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/insilicoseq-2.0.1/ && 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 > ../insilicoseq_2.0.1-1_source.changes +I: user script /srv/workspace/pbuilder/3843621/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3843621/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/insilicoseq-2.0.1/ && 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 > ../insilicoseq_2.0.1-1_source.changes dpkg-buildpackage: info: source package insilicoseq dpkg-buildpackage: info: source version 2.0.1-1 dpkg-buildpackage: info: source distribution unstable @@ -1093,7 +1129,7 @@ iss/test/test_util.py::test_concatenate_read_only PASSED [ 97%] iss/test/test_util.py::test_compress PASSED [100%] -======================== 45 passed, 1 skipped in 6.85s ========================= +======================== 45 passed, 1 skipped in 4.41s ========================= make[1]: Leaving directory '/build/reproducible-path/insilicoseq-2.0.1' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild @@ -1272,12 +1308,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3843621/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3843621/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/3155505 and its subdirectories -I: Current time: Tue Oct 1 02:36:46 -12 2024 -I: pbuilder-time-stamp: 1727793406 +I: removing directory /srv/workspace/pbuilder/3843621 and its subdirectories +I: Current time: Tue Nov 4 11:02:10 +14 2025 +I: pbuilder-time-stamp: 1762203730 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/insilicoseq_2.0.1-1.diff: 66.2% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/insilicoseq_2.0.1-1.diff.gz b2/build.log: 83.5% -- replaced with stdout Compressing the 1st log... b1/build.log: 83.9% -- replaced with stdout Tue Oct 1 14:39:14 UTC 2024 I: diffoscope 278 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_insilicoseq_trixie_arm64_1727793554 + touch /var/log/reproducible-builds/diffoscope_stamp_insilicoseq_trixie_arm64_1727793554 + RESULT=0 + systemd-run '--description=diffoscope on insilicoseq/2.0.1-1 in trixie/arm64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-arm64_6-59338 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.Lh7t7LAy --run-session -c jenkins-reproducible-trixie-diffoscope-2e5cb6b0-ee35-405f-b96b-51c193d7ac83 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.Lh7t7LAy/dbd-tmp-m8CwVhd ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.Lh7t7LAy/insilicoseq_2.0.1-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.Lh7t7LAy/insilicoseq_2.0.1-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.Lh7t7LAy/insilicoseq_2.0.1-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.Lh7t7LAy/b1/insilicoseq_2.0.1-1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.Lh7t7LAy/b2/insilicoseq_2.0.1-1_arm64.changes' + false + set +x Running as unit: rb-diffoscope-arm64_6-59338.service Warning: program compiled against libxml 212 using older 209 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.Lh7t7LAy/insilicoseq_2.0.1-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.Lh7t7LAy/insilicoseq_2.0.1-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.Lh7t7LAy/insilicoseq_2.0.1-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.Lh7t7LAy/b1/insilicoseq_2.0.1-1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.Lh7t7LAy/b2/insilicoseq_2.0.1-1_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: 0.510s) 0.510s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.060s) 0.060s 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: 857ms CPU time consumed: 850ms _ _ _ _ (_)_ __ ___(_) (_) ___ ___ ___ ___ __ _ | | '_ \/ __| | | |/ __/ _ \/ __|/ _ \/ _` | | | | | \__ \ | | | (_| (_) \__ \ __/ (_| | |_|_| |_|___/_|_|_|\___\___/|___/\___|\__, | |_| Tue Oct 1 14:39:15 UTC 2024 I: diffoscope 278 found no differences in the changes files, and a .buildinfo file also exists. Tue Oct 1 14:39:15 UTC 2024 I: insilicoseq from trixie built successfully and reproducibly on arm64. INSERT 0 1 INSERT 0 1 DELETE 1 [2024-10-01 14:39:16] INFO: Starting at 2024-10-01 14:39:16.197991 [2024-10-01 14:39:16] INFO: Generating the pages of 1 package(s) [2024-10-01 14:39:16] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/arm64/insilicoseq didn't produce a buildlog, even though it has been built. [2024-10-01 14:39:16] INFO: Finished at 2024-10-01 14:39:16.620530, took: 0:00:00.422546 Tue Oct 1 14:39:16 UTC 2024 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/arm64/insilicoseq.html Tue Oct 1 14:39:16 UTC 2024 I: Submitting .buildinfo files to external archives: Tue Oct 1 14:39:16 UTC 2024 I: Submitting 12K b1/insilicoseq_2.0.1-1_arm64.buildinfo.asc https://buildinfo.debian.net/feea4b34c777b46554b3a809e78e1ff4ee26b274/insilicoseq_2.0.1-1_all Tue Oct 1 14:39:17 UTC 2024 I: Submitting 12K b2/insilicoseq_2.0.1-1_arm64.buildinfo.asc https://buildinfo.debian.net/f3a1717b67996ee58b5c8faf8600ce670363240d/insilicoseq_2.0.1-1_all Tue Oct 1 14:39:18 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Oct 1 14:39:18 UTC 2024 I: Done submitting .buildinfo files. Tue Oct 1 14:39:18 UTC 2024 I: Removing signed insilicoseq_2.0.1-1_arm64.buildinfo.asc files: removed './b1/insilicoseq_2.0.1-1_arm64.buildinfo.asc' removed './b2/insilicoseq_2.0.1-1_arm64.buildinfo.asc' 1727793558 arm64 trixie insilicoseq Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/insilicoseq_2.0.1-1.rbuild.log: 82.0% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/insilicoseq_2.0.1-1.rbuild.log.gz [2024-10-01 14:39:19] INFO: Starting at 2024-10-01 14:39:19.051134 [2024-10-01 14:39:19] INFO: Generating the pages of 1 package(s) [2024-10-01 14:39:19] INFO: Finished at 2024-10-01 14:39:19.464163, took: 0:00:00.413037 All cleanup done. Tue Oct 1 14:39:19 UTC 2024 - total duration: 0h 5m 44s. Tue Oct 1 14:39:19 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-Ofzvhxqu, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 5min 48.004s CPU time consumed: 8.898s