Running as unit: rb-build-amd64_4-55578.service ==================================================================================== Thu Jun 5 12:45:50 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_4) on jenkins, called using "ionos15-amd64 ionos1-amd64" as arguments. Thu Jun 5 12:45:50 UTC 2025 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-63ldPwyi" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Jun 5 12:45:50 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Thu Jun 5 12:45:50 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-Np492I' Thu Jun 5 12:45:51 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Thu Jun 5 12:45:51 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-nzBIlf' ok, let's check if tiddit is building anywhere yet… ok, tiddit is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of tiddit in trixie on amd64 on jenkins now. 1st build will be done on ionos15-amd64.debian.net. 2nd build will be done on ionos1-amd64.debian.net. ============================================================================= Thu Jun 5 12:46:15 UTC 2025 I: starting to build tiddit/trixie/amd64 on jenkins on '2025-06-05 12:45' Thu Jun 5 12:46:15 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_4/55578/console.log 1749127575 amd64 trixie tiddit Thu Jun 5 12:46:15 UTC 2025 I: Downloading source for trixie/tiddit=3.6.1+dfsg-2 --2025-06-05 12:46:15-- http://deb.debian.org/debian/pool/main/t/tiddit/tiddit_3.6.1%2bdfsg-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2227 (2.2K) [text/prs.lines.tag] Saving to: ‘tiddit_3.6.1+dfsg-2.dsc’ 0K .. 100% 264M=0s 2025-06-05 12:46:15 (264 MB/s) - ‘tiddit_3.6.1+dfsg-2.dsc’ saved [2227/2227] --2025-06-05 12:46:15-- http://deb.debian.org/debian/pool/main/t/tiddit/tiddit_3.6.1%2bdfsg-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2227 (2.2K) [text/prs.lines.tag] Saving to: ‘tiddit_3.6.1+dfsg-2.dsc’ 0K .. 100% 264M=0s 2025-06-05 12:46:15 (264 MB/s) - ‘tiddit_3.6.1+dfsg-2.dsc’ saved [2227/2227] Thu Jun 5 12:46:15 UTC 2025 I: tiddit_3.6.1+dfsg-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: tiddit Binary: tiddit Architecture: any Version: 3.6.1+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/SciLifeLab/TIDDIT Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/tiddit Vcs-Git: https://salsa.debian.org/med-team/tiddit.git Testsuite: autopkgtest Testsuite-Triggers: samtools Build-Depends: debhelper-compat (= 13), dh-sequence-python3, cython3, python3-all-dev, python3-setuptools, python3-numpy, python3-pysam Package-List: tiddit deb science optional arch=any Checksums-Sha1: 27a0f672af1ff377655c55d7fa053bcc617c3a57 19516 tiddit_3.6.1+dfsg.orig.tar.xz a75bd07a522ff491f29dfc82a5b11e97cd9cfc5f 1731888 tiddit_3.6.1+dfsg-2.debian.tar.xz Checksums-Sha256: 7dd3dcb7fc861f87daf38b0e3c1b430764555ebba89177da2f84553607454a69 19516 tiddit_3.6.1+dfsg.orig.tar.xz d1129d64a78641625956277a2ae2cb1f61837bfb7ea825a2562ef35c2bc2d1fa 1731888 tiddit_3.6.1+dfsg-2.debian.tar.xz Files: 6f59a022dc62485c94b35623bc1f65c4 19516 tiddit_3.6.1+dfsg.orig.tar.xz 2f39026d3c7dbee9322040ce49ddf285 1731888 tiddit_3.6.1+dfsg-2.debian.tar.xz Dgit: d599bad4170d7b53ce283f44082351bc43d14dbb debian archive/debian/3.6.1+dfsg-2 https://git.dgit.debian.org/tiddit -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmenoH0UHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdrlHw//Q4CrmgAr1KmnJ3OaJ0BaCJ+uRDVz unam5Z+B99LBSU7hklKWtLykcfWgDFK3pe2/84GFtQWXcgohsbwukykSNa2S0gvG RtR9o2wnGQXVXj895IbuNTPEURSilJrMutG0V8axiVdDY903zBaghq93QixmR4sa gIr2zGkQxgaJ0/NluInlNkXFZ0K0nk2i9WYzbeggP8I1q0Eg4PnXmizmgHR1TkKT T0pnxYprzeKc+5BoUw4jnSvRpeCfGXRysm9uiv3t1EaTxKLOn5Zzxf0Ba0KBlKus 551wSRTn7Yvo6uYHKlntlVVv4NqlXbLaJdFtipMnfkZ85zJHZxEr84QVtZM3zWRF e22E8tRX9IE0H2U7IlBeWVaJ8ohCGe2N4fmJvaYFu+sMfJUfMZD3ui5yVNplgHih zoeeMueaWHCKFhPFoDCFACZI1wTvaA2Ofe9hvvgqnBOaIiAYGsdaMXTyIJYOVMIv dc5Ks9tpmOSSTIeAadMGn7NAvt2MpSx0/J9dUIPaqFP0D9tq38qMM/d4dJIsrITp Yi1uGns7t+RmUWeafKutURlnpLR2WJ6ROibVGBovMXYqmi2t77cO5bT/EUAptZJN Ysn9Aq/N6rBzL74O+8zNH75ACuFr12JWTebcojiuaHwAZ7bZsDGzsXAFYIJZCDHL ENS41SJGDGJ0ecI= =ce8u -----END PGP SIGNATURE----- Thu Jun 5 12:46:15 UTC 2025 I: Checking whether the package is not for us Thu Jun 5 12:46:16 UTC 2025 I: Starting 1st build on remote node ionos15-amd64.debian.net. Thu Jun 5 12:46:16 UTC 2025 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Thu Jun 5 12:46:16 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Thu Jun 5 12:46:16 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-PB8VJS' ==================================================================================== Wed Jul 8 19:09:16 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos15-amd64, called using "1 tiddit trixie /srv/reproducible-results/rbuild-debian/r-b-build.VvnRmSVy 3.6.1+dfsg-2" as arguments. Wed Jul 8 19:09:16 UTC 2026 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-ZY4dNOjh" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Jul 8 19:09:16 UTC 2026 I: Downloading source for trixie/tiddit=3.6.1+dfsg-2 Reading package lists... NOTICE: 'tiddit' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/tiddit.git Please use: git clone https://salsa.debian.org/med-team/tiddit.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1754 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main tiddit 3.6.1+dfsg-2 (dsc) [2227 B] Get:2 http://deb.debian.org/debian trixie/main tiddit 3.6.1+dfsg-2 (tar) [19.5 kB] Get:3 http://deb.debian.org/debian trixie/main tiddit 3.6.1+dfsg-2 (diff) [1732 kB] Fetched 1754 kB in 0s (27.6 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'tiddit' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/tiddit.git Please use: git clone https://salsa.debian.org/med-team/tiddit.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1754 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main tiddit 3.6.1+dfsg-2 (dsc) [2227 B] Get:2 http://deb.debian.org/debian trixie/main tiddit 3.6.1+dfsg-2 (tar) [19.5 kB] Get:3 http://deb.debian.org/debian trixie/main tiddit 3.6.1+dfsg-2 (diff) [1732 kB] Fetched 1754 kB in 0s (27.6 MB/s) Download complete and in download only mode ============================================================================= Building tiddit in trixie on amd64 on ionos15-amd64 now. Date: Wed Jul 8 19:09:17 UTC 2026 Date UTC: Wed Jul 8 19:09:17 UTC 2026 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Wed Jul 8 07:09:17 -12 2026 I: pbuilder-time-stamp: 1783537757 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 [tiddit_3.6.1+dfsg-2.dsc] I: copying [./tiddit_3.6.1+dfsg.orig.tar.xz] I: copying [./tiddit_3.6.1+dfsg-2.debian.tar.xz] I: Extracting source error: the following required arguments were not provided: --keyring Usage: sqv --keyring --cleartext --output For more information, try '--help'. dpkg-source: warning: cannot verify inline signature for ./tiddit_3.6.1+dfsg-2.dsc: no acceptable signature found dpkg-source: info: extracting tiddit in tiddit-3.6.1+dfsg dpkg-source: info: unpacking tiddit_3.6.1+dfsg.orig.tar.xz dpkg-source: info: unpacking tiddit_3.6.1+dfsg-2.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/109851/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='bb5a7fdde3e5427ca397e4ca3e5008e5' 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='109851' 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.VvnRmSVy/pbuilderrc_JinT --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.VvnRmSVy/b1 --logfile b1/build.log tiddit_3.6.1+dfsg-2.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.12.22+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.22-1~bpo12+1 (2025-04-25) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/109851/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, cython3, python3-all-dev, python3-setuptools, python3-numpy, python3-pysam dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19850 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 cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools 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. 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} cython3{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgnutls30t64{a} libgssapi-krb5-2{a} libhts3t64{a} libhtscodecs2{a} libidn2-0{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libldap2{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libp11-kit0{a} libpipeline1{a} libpsl5t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libtasn1-6{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-all{a} python3-all-dev{a} python3-autocommand{a} python3-dev{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-numpy-dev{a} python3-pkg-resources{a} python3-pysam{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 100 newly installed, 0 to remove and 0 not upgraded. Need to get 48.1 MB of archives. After unpacking 214 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.3-2 [861 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.7.1-1 [108 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.3-2 [2212 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.3-1 [27.2 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2025b-3 [260 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.8-2 [24.1 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.3-2 [1953 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.3-2 [751 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.3-1 [10.2 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.3-1 [28.2 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1 [139 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:2.2.4+ds-1 [5096 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-8 [1187 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-8 [294 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-4 [862 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 cython3 amd64 3.0.11+dfsg-2+b1 [2504 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-4 [539 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 42 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-1 [698 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.2 [919 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20250414 [116 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-1+b1 [24.3 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.8-2 [109 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 60 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.9+dfsg-2 [194 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1.1 [76.0 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.13.0-5 [375 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libexpat1-dev amd64 2.7.1-1 [161 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libpython3.13 amd64 3.13.3-2 [2156 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libpython3.13-dev amd64 3.13.3-2 [5015 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libpython3-dev amd64 3.13.3-1 [10.4 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libpython3-all-dev amd64 3.13.3-1 [1068 B] Get: 85 http://deb.debian.org/debian trixie/main amd64 python3-all amd64 3.13.3-1 [1048 B] Get: 86 http://deb.debian.org/debian trixie/main amd64 python3.13-dev amd64 3.13.3-2 [508 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 python3-dev amd64 3.13.3-1 [26.1 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 python3-all-dev amd64 3.13.3-1 [1068 B] Get: 89 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.7.0-1 [67.4 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.13.2-1 [90.5 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.2-1 [37.3 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 100 http://deb.debian.org/debian trixie/main amd64 python3-pysam amd64 0.23.0+ds-1+b1 [3665 kB] Fetched 48.1 MB in 4s (11.1 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19850 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.3-2_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.3-2) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.7.1-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-1) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.3-2_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.3-2) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.3-2_amd64.deb ... Unpacking python3.13 (3.13.3-2) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Preparing to unpack .../44-libk5crypto3_1.21.3-5_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-5) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../45-libkeyutils1_1.6.3-6_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-6) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../46-libkrb5-3_1.21.3-5_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-5) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../47-libgssapi-krb5-2_1.21.3-5_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-5) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../48-libsasl2-modules-db_2.1.28+dfsg1-9_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../49-libsasl2-2_2.1.28+dfsg1-9_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libldap2:amd64. Preparing to unpack .../50-libldap2_2.6.9+dfsg-2_amd64.deb ... Unpacking libldap2:amd64 (2.6.9+dfsg-2) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../51-libnghttp2-14_1.64.0-1.1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.64.0-1.1) ... Selecting previously unselected package libnghttp3-9:amd64. Preparing to unpack .../52-libnghttp3-9_1.8.0-1_amd64.deb ... Unpacking libnghttp3-9:amd64 (1.8.0-1) ... Selecting previously unselected package libngtcp2-16:amd64. Preparing to unpack .../53-libngtcp2-16_1.11.0-1_amd64.deb ... Unpacking libngtcp2-16:amd64 (1.11.0-1) ... Selecting previously unselected package libngtcp2-crypto-gnutls8:amd64. Preparing to unpack .../54-libngtcp2-crypto-gnutls8_1.11.0-1_amd64.deb ... Unpacking libngtcp2-crypto-gnutls8:amd64 (1.11.0-1) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../55-libpsl5t64_0.21.2-1.1+b1_amd64.deb ... 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Setting up libnghttp2-14:amd64 (1.64.0-1.1) ... Setting up libdeflate0:amd64 (1.23-2) ... Setting up gettext-base (0.23.1-2) ... Setting up m4 (1.4.19-8) ... Setting up libcom-err2:amd64 (1.47.2-1+b1) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libkrb5support0:amd64 (1.21.3-5) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Setting up tzdata (2025b-3) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Jul 8 19:09:46 UTC 2026. Universal Time is now: Wed Jul 8 19:09:46 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... Setting up libblas3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libexpat1-dev:amd64 (2.7.1-1) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1) ... 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Setting up libpython3.13:amd64 (3.13.3-2) ... Setting up libgnutls30t64:amd64 (3.8.9-2) ... Setting up python3.13 (3.13.3-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up python3 (3.13.3-1) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libpython3.13-dev:amd64 (3.13.3-2) ... Setting up cython3 (3.0.11+dfsg-2+b1) ... Setting up python3-typing-extensions (4.13.2-1) ... Setting up python3-numpy (1:2.2.4+ds-1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.11.0-1) ... Setting up dh-python (6.20250414) ... Setting up python3-more-itertools (10.7.0-1) ... Setting up libpython3-dev:amd64 (3.13.3-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up python3.13-dev (3.13.3-2) ... Setting up python3-typeguard (4.4.2-1) ... Setting up libcurl3t64-gnutls:amd64 (8.13.0-5) ... Setting up python3-all (3.13.3-1) ... Setting up debhelper (13.24.2) ... Setting up python3-inflect (7.3.1-2) ... Setting up libpython3-all-dev:amd64 (3.13.3-1) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.13.3-1) ... Setting up libhts3t64:amd64 (1.21+ds-1) ... Setting up python3-pkg-resources (78.1.1-0.1) ... Setting up python3-all-dev (3.13.3-1) ... Setting up python3-pysam (0.23.0+ds-1+b1) ... Setting up python3-setuptools (78.1.1-0.1) ... Processing triggers for libc-bin (2.41-8) ... 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/tiddit-3.6.1+dfsg/ && 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 > ../tiddit_3.6.1+dfsg-2_source.changes dpkg-buildpackage: info: source package tiddit dpkg-buildpackage: info: source version 3.6.1+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py clean /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tiddit-3.6.1+dfsg/tiddit/tiddit_cluster.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tiddit-3.6.1+dfsg/tiddit/tiddit_contig_analysis.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tiddit-3.6.1+dfsg/tiddit/tiddit_coverage.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tiddit-3.6.1+dfsg/tiddit/tiddit_coverage_analysis.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tiddit-3.6.1+dfsg/tiddit/tiddit_signal.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tiddit-3.6.1+dfsg/tiddit/tiddit_variant.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling tiddit/tiddit_signal.pyx because it changed. Compiling tiddit/tiddit_coverage.pyx because it changed. Compiling tiddit/tiddit_cluster.pyx because it changed. Compiling tiddit/tiddit_coverage_analysis.pyx because it changed. Compiling tiddit/tiddit_variant.pyx because it changed. Compiling tiddit/tiddit_contig_analysis.pyx because it changed. [1/6] Cythonizing tiddit/tiddit_cluster.pyx [2/6] Cythonizing tiddit/tiddit_contig_analysis.pyx [3/6] Cythonizing tiddit/tiddit_coverage.pyx [4/6] Cythonizing tiddit/tiddit_coverage_analysis.pyx [5/6] Cythonizing tiddit/tiddit_signal.pyx [6/6] Cythonizing tiddit/tiddit_variant.pyx running clean removing '/build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.13' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/tiddit-3.6.1+dfsg' dh_clean rm -f tiddit/*.c make[1]: Leaving directory '/build/reproducible-path/tiddit-3.6.1+dfsg' debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py config /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tiddit-3.6.1+dfsg/tiddit/tiddit_cluster.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tiddit-3.6.1+dfsg/tiddit/tiddit_contig_analysis.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tiddit-3.6.1+dfsg/tiddit/tiddit_coverage.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tiddit-3.6.1+dfsg/tiddit/tiddit_coverage_analysis.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tiddit-3.6.1+dfsg/tiddit/tiddit_signal.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tiddit-3.6.1+dfsg/tiddit/tiddit_variant.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling tiddit/tiddit_signal.pyx because it changed. Compiling tiddit/tiddit_coverage.pyx because it changed. Compiling tiddit/tiddit_cluster.pyx because it changed. Compiling tiddit/tiddit_coverage_analysis.pyx because it changed. Compiling tiddit/tiddit_variant.pyx because it changed. Compiling tiddit/tiddit_contig_analysis.pyx because it changed. [1/6] Cythonizing tiddit/tiddit_cluster.pyx [2/6] Cythonizing tiddit/tiddit_contig_analysis.pyx [3/6] Cythonizing tiddit/tiddit_coverage.pyx [4/6] Cythonizing tiddit/tiddit_coverage_analysis.pyx [5/6] Cythonizing tiddit/tiddit_signal.pyx [6/6] Cythonizing tiddit/tiddit_variant.pyx running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build running build running build_py creating /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit copying tiddit/tiddit_vcf_header.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit copying tiddit/__main__.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit copying tiddit/DBSCAN.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit copying tiddit/__init__.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit copying tiddit/tiddit_stats.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit running build_ext building 'tiddit.tiddit_signal' extension creating build/temp.linux-x86_64-cpython-313/tiddit x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tiddit-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c tiddit/tiddit_signal.c -o build/temp.linux-x86_64-cpython-313/tiddit/tiddit_signal.o x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tiddit-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/tiddit/tiddit_signal.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_signal.cpython-313-x86_64-linux-gnu.so building 'tiddit.tiddit_coverage' extension x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tiddit-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c tiddit/tiddit_coverage.c -o build/temp.linux-x86_64-cpython-313/tiddit/tiddit_coverage.o In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from tiddit/tiddit_coverage.c:1240: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tiddit-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/tiddit/tiddit_coverage.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_coverage.cpython-313-x86_64-linux-gnu.so building 'tiddit.tiddit_cluster' extension x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tiddit-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c tiddit/tiddit_cluster.c -o build/temp.linux-x86_64-cpython-313/tiddit/tiddit_cluster.o x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tiddit-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/tiddit/tiddit_cluster.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_cluster.cpython-313-x86_64-linux-gnu.so building 'tiddit.tiddit_coverage_analysis' extension x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tiddit-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c tiddit/tiddit_coverage_analysis.c -o build/temp.linux-x86_64-cpython-313/tiddit/tiddit_coverage_analysis.o In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from tiddit/tiddit_coverage_analysis.c:1240: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tiddit-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/tiddit/tiddit_coverage_analysis.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_coverage_analysis.cpython-313-x86_64-linux-gnu.so building 'tiddit.tiddit_variant' extension x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tiddit-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c tiddit/tiddit_variant.c -o build/temp.linux-x86_64-cpython-313/tiddit/tiddit_variant.o x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tiddit-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/tiddit/tiddit_variant.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_variant.cpython-313-x86_64-linux-gnu.so building 'tiddit.tiddit_contig_analysis' extension x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tiddit-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c tiddit/tiddit_contig_analysis.c -o build/temp.linux-x86_64-cpython-313/tiddit/tiddit_contig_analysis.o x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tiddit-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/tiddit/tiddit_contig_analysis.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_contig_analysis.cpython-313-x86_64-linux-gnu.so dh_auto_test -O--buildsystem=pybuild I: pybuild base:311: cd /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build; python3.13 -m unittest discover -v ---------------------------------------------------------------------- Ran 0 tests in 0.000s NO TESTS RAN create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/tiddit/ -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running build_ext running install_lib creating /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages creating /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_vcf_header.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/__main__.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit creating /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit/__pycache__ copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit/__pycache__ copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_contig_analysis.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_cluster.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_signal.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/DBSCAN.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_coverage_analysis.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/__init__.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_coverage.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_variant.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_stats.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit byte-compiling /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit/tiddit_vcf_header.py to tiddit_vcf_header.cpython-313.pyc byte-compiling /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit/__main__.py to __main__.cpython-313.pyc byte-compiling /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit/DBSCAN.py to DBSCAN.cpython-313.pyc byte-compiling /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit/tiddit_stats.py to tiddit_stats.cpython-313.pyc running install_egg_info running egg_info creating tiddit.egg-info writing tiddit.egg-info/PKG-INFO writing dependency_links to tiddit.egg-info/dependency_links.txt writing entry points to tiddit.egg-info/entry_points.txt writing requirements to tiddit.egg-info/requires.txt writing top-level names to tiddit.egg-info/top_level.txt writing manifest file 'tiddit.egg-info/SOURCES.txt' reading manifest file 'tiddit.egg-info/SOURCES.txt' adding license file 'COPYING' adding license file 'AUTHORS' writing manifest file 'tiddit.egg-info/SOURCES.txt' Copying tiddit.egg-info to /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit-3.6.1.egg-info Skipping SOURCES.txt running install_scripts Installing tiddit script to /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/bin dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/tiddit-3.6.1+dfsg' dh_installman --language=C make[1]: Leaving directory '/build/reproducible-path/tiddit-3.6.1+dfsg' debian/rules override_dh_python3 make[1]: Entering directory '/build/reproducible-path/tiddit-3.6.1+dfsg' dh_numpy3 Possible precedence issue with control flow operator (return) at /usr/bin/dh_numpy3 line 57. dh_python3 --shebang=/usr/bin/python3 I: dh_python3 tools:114: replacing shebang in debian/tiddit/usr/bin/tiddit make[1]: Leaving directory '/build/reproducible-path/tiddit-3.6.1+dfsg' dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'tiddit' in '../tiddit_3.6.1+dfsg-2_amd64.deb'. dpkg-deb: building package 'tiddit-dbgsym' in '../tiddit-dbgsym_3.6.1+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../tiddit_3.6.1+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../tiddit_3.6.1+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/109851 and its subdirectories I: Current time: Wed Jul 8 07:11:47 -12 2026 I: pbuilder-time-stamp: 1783537907 Wed Jul 8 19:11:47 UTC 2026 I: Signing ./b1/tiddit_3.6.1+dfsg-2_amd64.buildinfo as tiddit_3.6.1+dfsg-2_amd64.buildinfo.asc Wed Jul 8 19:11:47 UTC 2026 I: Signed ./b1/tiddit_3.6.1+dfsg-2_amd64.buildinfo as ./b1/tiddit_3.6.1+dfsg-2_amd64.buildinfo.asc Wed Jul 8 19:11:47 UTC 2026 - build #1 for tiddit/trixie/amd64 on ionos15-amd64 done. Starting cleanup. All cleanup done. Wed Jul 8 19:11:47 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-ZY4dNOjh, removing. /srv/reproducible-results/rbuild-debian/r-b-build.VvnRmSVy: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Jun 5 12:48 b1 drwxr-xr-x 2 jenkins jenkins 4096 Jun 5 12:46 b2 -rw------- 1 jenkins jenkins 3344 Jun 5 12:46 rbuildlog.KsmKjEO -rw-r--r-- 1 jenkins jenkins 2227 Feb 8 18:33 tiddit_3.6.1+dfsg-2.dsc /srv/reproducible-results/rbuild-debian/r-b-build.VvnRmSVy/b1: total 4064 -rw-r--r-- 1 jenkins jenkins 65211 Jun 5 12:48 build.log -rw-r--r-- 1 jenkins jenkins 1981036 Jun 5 12:48 tiddit-dbgsym_3.6.1+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 1731888 Jun 5 12:48 tiddit_3.6.1+dfsg-2.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2227 Jun 5 12:48 tiddit_3.6.1+dfsg-2.dsc -rw-r--r-- 1 jenkins jenkins 7192 Jun 5 12:48 tiddit_3.6.1+dfsg-2_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 8074 Jun 5 12:48 tiddit_3.6.1+dfsg-2_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1486 Jun 5 12:48 tiddit_3.6.1+dfsg-2_amd64.changes -rw-r--r-- 1 jenkins jenkins 331968 Jun 5 12:48 tiddit_3.6.1+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 1373 Jun 5 12:48 tiddit_3.6.1+dfsg-2_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.VvnRmSVy/b2: total 0 Thu Jun 5 12:48:48 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Jul 8 07:09:17 -12 2026 I: pbuilder-time-stamp: 1783537757 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 [tiddit_3.6.1+dfsg-2.dsc] I: copying [./tiddit_3.6.1+dfsg.orig.tar.xz] I: copying [./tiddit_3.6.1+dfsg-2.debian.tar.xz] I: Extracting source error: the following required arguments were not provided: --keyring Usage: sqv --keyring --cleartext --output For more information, try '--help'. dpkg-source: warning: cannot verify inline signature for ./tiddit_3.6.1+dfsg-2.dsc: no acceptable signature found dpkg-source: info: extracting tiddit in tiddit-3.6.1+dfsg dpkg-source: info: unpacking tiddit_3.6.1+dfsg.orig.tar.xz dpkg-source: info: unpacking tiddit_3.6.1+dfsg-2.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/109851/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='bb5a7fdde3e5427ca397e4ca3e5008e5' 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='109851' 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.VvnRmSVy/pbuilderrc_JinT --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.VvnRmSVy/b1 --logfile b1/build.log tiddit_3.6.1+dfsg-2.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.12.22+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.22-1~bpo12+1 (2025-04-25) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/109851/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, cython3, python3-all-dev, python3-setuptools, python3-numpy, python3-pysam dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19850 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 cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools 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. 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} cython3{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgnutls30t64{a} libgssapi-krb5-2{a} libhts3t64{a} libhtscodecs2{a} libidn2-0{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libldap2{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libp11-kit0{a} libpipeline1{a} libpsl5t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libtasn1-6{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-all{a} python3-all-dev{a} python3-autocommand{a} python3-dev{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-numpy-dev{a} python3-pkg-resources{a} python3-pysam{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 100 newly installed, 0 to remove and 0 not upgraded. Need to get 48.1 MB of archives. After unpacking 214 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.3-2 [861 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.7.1-1 [108 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.3-2 [2212 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.3-1 [27.2 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2025b-3 [260 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.8-2 [24.1 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.3-2 [1953 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.3-2 [751 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.3-1 [10.2 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.3-1 [28.2 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1 [139 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:2.2.4+ds-1 [5096 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-8 [1187 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-8 [294 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-4 [862 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 cython3 amd64 3.0.11+dfsg-2+b1 [2504 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-4 [539 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 42 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-1 [698 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.2 [919 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20250414 [116 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-1+b1 [24.3 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.8-2 [109 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 60 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.9+dfsg-2 [194 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1.1 [76.0 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.13.0-5 [375 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libexpat1-dev amd64 2.7.1-1 [161 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libpython3.13 amd64 3.13.3-2 [2156 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libpython3.13-dev amd64 3.13.3-2 [5015 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libpython3-dev amd64 3.13.3-1 [10.4 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libpython3-all-dev amd64 3.13.3-1 [1068 B] Get: 85 http://deb.debian.org/debian trixie/main amd64 python3-all amd64 3.13.3-1 [1048 B] Get: 86 http://deb.debian.org/debian trixie/main amd64 python3.13-dev amd64 3.13.3-2 [508 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 python3-dev amd64 3.13.3-1 [26.1 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 python3-all-dev amd64 3.13.3-1 [1068 B] Get: 89 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.7.0-1 [67.4 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.13.2-1 [90.5 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.2-1 [37.3 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 100 http://deb.debian.org/debian trixie/main amd64 python3-pysam amd64 0.23.0+ds-1+b1 [3665 kB] Fetched 48.1 MB in 4s (11.1 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19850 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.3-2_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.3-2) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.7.1-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.3-2_amd64.deb ... Unpacking python3.13-minimal (3.13.3-2) ... Setting up libpython3.13-minimal:amd64 (3.13.3-2) ... Setting up libexpat1:amd64 (2.7.1-1) ... Setting up python3.13-minimal (3.13.3-2) ... 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 ... 20184 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.3-1_amd64.deb ... Unpacking python3-minimal (3.13.3-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_13.0.0_all.deb ... Unpacking media-types (13.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.5_all.deb ... Unpacking netbase (6.5) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025b-3_all.deb ... Unpacking tzdata (2025b-3) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../4-libffi8_3.4.8-2_amd64.deb ... Unpacking libffi8:amd64 (3.4.8-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../6-libreadline8t64_8.2-6_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.3-2_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.3-2) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.3-2_amd64.deb ... Unpacking python3.13 (3.13.3-2) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Setting up autopoint (0.23.1-2) ... Setting up libk5crypto3:amd64 (1.21.3-5) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Setting up libgfortran5:amd64 (14.2.0-19) ... Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:amd64 (1.8.0-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:amd64 (3.4.8-2) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libtasn1-6:amd64 (4.20.0-2) ... Setting up netbase (6.5) ... Setting up libngtcp2-16:amd64 (1.11.0-1) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-1) ... Setting up libldap2:amd64 (2.6.9+dfsg-2) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up liblapack3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.23.1-2) ... Setting up libtool (2.5.4-4) ... Setting up libidn2-0:amd64 (2.3.8-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up libjs-sphinxdoc (8.1.3-5) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-8) ... Setting up libpython3.13-stdlib:amd64 (3.13.3-2) ... Setting up libpython3-stdlib:amd64 (3.13.3-1) ... Setting up libpython3.13:amd64 (3.13.3-2) ... Setting up libgnutls30t64:amd64 (3.8.9-2) ... Setting up python3.13 (3.13.3-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up python3 (3.13.3-1) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libpython3.13-dev:amd64 (3.13.3-2) ... Setting up cython3 (3.0.11+dfsg-2+b1) ... Setting up python3-typing-extensions (4.13.2-1) ... Setting up python3-numpy (1:2.2.4+ds-1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.11.0-1) ... Setting up dh-python (6.20250414) ... Setting up python3-more-itertools (10.7.0-1) ... Setting up libpython3-dev:amd64 (3.13.3-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up python3.13-dev (3.13.3-2) ... Setting up python3-typeguard (4.4.2-1) ... Setting up libcurl3t64-gnutls:amd64 (8.13.0-5) ... Setting up python3-all (3.13.3-1) ... Setting up debhelper (13.24.2) ... Setting up python3-inflect (7.3.1-2) ... Setting up libpython3-all-dev:amd64 (3.13.3-1) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.13.3-1) ... Setting up libhts3t64:amd64 (1.21+ds-1) ... Setting up python3-pkg-resources (78.1.1-0.1) ... Setting up python3-all-dev (3.13.3-1) ... Setting up python3-pysam (0.23.0+ds-1+b1) ... Setting up python3-setuptools (78.1.1-0.1) ... Processing triggers for libc-bin (2.41-8) ... 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/tiddit-3.6.1+dfsg/ && 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 > ../tiddit_3.6.1+dfsg-2_source.changes dpkg-buildpackage: info: source package tiddit dpkg-buildpackage: info: source version 3.6.1+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py clean /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tiddit-3.6.1+dfsg/tiddit/tiddit_cluster.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tiddit-3.6.1+dfsg/tiddit/tiddit_contig_analysis.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tiddit-3.6.1+dfsg/tiddit/tiddit_coverage.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tiddit-3.6.1+dfsg/tiddit/tiddit_coverage_analysis.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tiddit-3.6.1+dfsg/tiddit/tiddit_signal.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tiddit-3.6.1+dfsg/tiddit/tiddit_variant.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling tiddit/tiddit_signal.pyx because it changed. Compiling tiddit/tiddit_coverage.pyx because it changed. Compiling tiddit/tiddit_cluster.pyx because it changed. Compiling tiddit/tiddit_coverage_analysis.pyx because it changed. Compiling tiddit/tiddit_variant.pyx because it changed. Compiling tiddit/tiddit_contig_analysis.pyx because it changed. [1/6] Cythonizing tiddit/tiddit_cluster.pyx [2/6] Cythonizing tiddit/tiddit_contig_analysis.pyx [3/6] Cythonizing tiddit/tiddit_coverage.pyx [4/6] Cythonizing tiddit/tiddit_coverage_analysis.pyx [5/6] Cythonizing tiddit/tiddit_signal.pyx [6/6] Cythonizing tiddit/tiddit_variant.pyx running clean removing '/build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.13' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/tiddit-3.6.1+dfsg' dh_clean rm -f tiddit/*.c make[1]: Leaving directory '/build/reproducible-path/tiddit-3.6.1+dfsg' debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py config /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tiddit-3.6.1+dfsg/tiddit/tiddit_cluster.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tiddit-3.6.1+dfsg/tiddit/tiddit_contig_analysis.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tiddit-3.6.1+dfsg/tiddit/tiddit_coverage.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tiddit-3.6.1+dfsg/tiddit/tiddit_coverage_analysis.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tiddit-3.6.1+dfsg/tiddit/tiddit_signal.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tiddit-3.6.1+dfsg/tiddit/tiddit_variant.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling tiddit/tiddit_signal.pyx because it changed. Compiling tiddit/tiddit_coverage.pyx because it changed. Compiling tiddit/tiddit_cluster.pyx because it changed. Compiling tiddit/tiddit_coverage_analysis.pyx because it changed. Compiling tiddit/tiddit_variant.pyx because it changed. Compiling tiddit/tiddit_contig_analysis.pyx because it changed. [1/6] Cythonizing tiddit/tiddit_cluster.pyx [2/6] Cythonizing tiddit/tiddit_contig_analysis.pyx [3/6] Cythonizing tiddit/tiddit_coverage.pyx [4/6] Cythonizing tiddit/tiddit_coverage_analysis.pyx [5/6] Cythonizing tiddit/tiddit_signal.pyx [6/6] Cythonizing tiddit/tiddit_variant.pyx running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build running build running build_py creating /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit copying tiddit/tiddit_vcf_header.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit copying tiddit/__main__.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit copying tiddit/DBSCAN.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit copying tiddit/__init__.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit copying tiddit/tiddit_stats.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit running build_ext building 'tiddit.tiddit_signal' extension creating build/temp.linux-x86_64-cpython-313/tiddit x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tiddit-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c tiddit/tiddit_signal.c -o build/temp.linux-x86_64-cpython-313/tiddit/tiddit_signal.o x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tiddit-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/tiddit/tiddit_signal.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_signal.cpython-313-x86_64-linux-gnu.so building 'tiddit.tiddit_coverage' extension x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tiddit-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c tiddit/tiddit_coverage.c -o build/temp.linux-x86_64-cpython-313/tiddit/tiddit_coverage.o In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from tiddit/tiddit_coverage.c:1240: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tiddit-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/tiddit/tiddit_coverage.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_coverage.cpython-313-x86_64-linux-gnu.so building 'tiddit.tiddit_cluster' extension x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tiddit-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c tiddit/tiddit_cluster.c -o build/temp.linux-x86_64-cpython-313/tiddit/tiddit_cluster.o x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tiddit-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/tiddit/tiddit_cluster.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_cluster.cpython-313-x86_64-linux-gnu.so building 'tiddit.tiddit_coverage_analysis' extension x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tiddit-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c tiddit/tiddit_coverage_analysis.c -o build/temp.linux-x86_64-cpython-313/tiddit/tiddit_coverage_analysis.o In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from tiddit/tiddit_coverage_analysis.c:1240: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tiddit-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/tiddit/tiddit_coverage_analysis.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_coverage_analysis.cpython-313-x86_64-linux-gnu.so building 'tiddit.tiddit_variant' extension x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tiddit-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c tiddit/tiddit_variant.c -o build/temp.linux-x86_64-cpython-313/tiddit/tiddit_variant.o x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tiddit-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/tiddit/tiddit_variant.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_variant.cpython-313-x86_64-linux-gnu.so building 'tiddit.tiddit_contig_analysis' extension x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tiddit-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c tiddit/tiddit_contig_analysis.c -o build/temp.linux-x86_64-cpython-313/tiddit/tiddit_contig_analysis.o x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tiddit-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/tiddit/tiddit_contig_analysis.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_contig_analysis.cpython-313-x86_64-linux-gnu.so dh_auto_test -O--buildsystem=pybuild I: pybuild base:311: cd /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build; python3.13 -m unittest discover -v ---------------------------------------------------------------------- Ran 0 tests in 0.000s NO TESTS RAN create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/tiddit/ -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running build_ext running install_lib creating /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages creating /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_vcf_header.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/__main__.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit creating /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit/__pycache__ copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit/__pycache__ copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_contig_analysis.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_cluster.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_signal.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/DBSCAN.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_coverage_analysis.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/__init__.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_coverage.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_variant.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_stats.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit byte-compiling /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit/tiddit_vcf_header.py to tiddit_vcf_header.cpython-313.pyc byte-compiling /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit/__main__.py to __main__.cpython-313.pyc byte-compiling /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit/DBSCAN.py to DBSCAN.cpython-313.pyc byte-compiling /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit/tiddit_stats.py to tiddit_stats.cpython-313.pyc running install_egg_info running egg_info creating tiddit.egg-info writing tiddit.egg-info/PKG-INFO writing dependency_links to tiddit.egg-info/dependency_links.txt writing entry points to tiddit.egg-info/entry_points.txt writing requirements to tiddit.egg-info/requires.txt writing top-level names to tiddit.egg-info/top_level.txt writing manifest file 'tiddit.egg-info/SOURCES.txt' reading manifest file 'tiddit.egg-info/SOURCES.txt' adding license file 'COPYING' adding license file 'AUTHORS' writing manifest file 'tiddit.egg-info/SOURCES.txt' Copying tiddit.egg-info to /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit-3.6.1.egg-info Skipping SOURCES.txt running install_scripts Installing tiddit script to /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/bin dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/tiddit-3.6.1+dfsg' dh_installman --language=C make[1]: Leaving directory '/build/reproducible-path/tiddit-3.6.1+dfsg' debian/rules override_dh_python3 make[1]: Entering directory '/build/reproducible-path/tiddit-3.6.1+dfsg' dh_numpy3 Possible precedence issue with control flow operator (return) at /usr/bin/dh_numpy3 line 57. dh_python3 --shebang=/usr/bin/python3 I: dh_python3 tools:114: replacing shebang in debian/tiddit/usr/bin/tiddit make[1]: Leaving directory '/build/reproducible-path/tiddit-3.6.1+dfsg' dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'tiddit' in '../tiddit_3.6.1+dfsg-2_amd64.deb'. dpkg-deb: building package 'tiddit-dbgsym' in '../tiddit-dbgsym_3.6.1+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../tiddit_3.6.1+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../tiddit_3.6.1+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/109851 and its subdirectories I: Current time: Wed Jul 8 07:11:47 -12 2026 I: pbuilder-time-stamp: 1783537907 Thu Jun 5 12:48:48 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Thu Jun 5 12:48:48 UTC 2025 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Thu Jun 5 12:48:48 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Thu Jun 5 12:48:48 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-gzUa4K' ==================================================================================== Thu Jun 5 12:48:49 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos1-amd64, called using "2 tiddit trixie /srv/reproducible-results/rbuild-debian/r-b-build.VvnRmSVy 3.6.1+dfsg-2" as arguments. Thu Jun 5 12:48:49 UTC 2025 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-vvxZFcHa" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Jun 5 12:48:49 UTC 2025 I: Downloading source for trixie/tiddit=3.6.1+dfsg-2 Reading package lists... NOTICE: 'tiddit' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/tiddit.git Please use: git clone https://salsa.debian.org/med-team/tiddit.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1754 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main tiddit 3.6.1+dfsg-2 (dsc) [2227 B] Get:2 http://deb.debian.org/debian trixie/main tiddit 3.6.1+dfsg-2 (tar) [19.5 kB] Get:3 http://deb.debian.org/debian trixie/main tiddit 3.6.1+dfsg-2 (diff) [1732 kB] Fetched 1754 kB in 0s (21.9 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'tiddit' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/tiddit.git Please use: git clone https://salsa.debian.org/med-team/tiddit.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1754 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main tiddit 3.6.1+dfsg-2 (dsc) [2227 B] Get:2 http://deb.debian.org/debian trixie/main tiddit 3.6.1+dfsg-2 (tar) [19.5 kB] Get:3 http://deb.debian.org/debian trixie/main tiddit 3.6.1+dfsg-2 (diff) [1732 kB] Fetched 1754 kB in 0s (21.9 MB/s) Download complete and in download only mode ============================================================================= Re-Building tiddit in trixie on amd64 on ionos1-amd64 now. Date: Thu Jun 5 12:48:49 UTC 2025 Date UTC: Thu Jun 5 12:48:49 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.VvnRmSVy + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.VvnRmSVy/pbuilderrc_F4Jj + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' tiddit = debian-installer -o tiddit = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' tiddit = u-boot ']' + case "${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.VvnRmSVy/pbuilderrc_F4Jj --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.VvnRmSVy/b2 --logfile b2/build.log tiddit_3.6.1+dfsg-2.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Fri Jun 6 02:48:49 +14 2025 I: pbuilder-time-stamp: 1749127729 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 [tiddit_3.6.1+dfsg-2.dsc] I: copying [./tiddit_3.6.1+dfsg.orig.tar.xz] I: copying [./tiddit_3.6.1+dfsg-2.debian.tar.xz] I: Extracting source error: the following required arguments were not provided: --keyring Usage: sqv --keyring --cleartext --output For more information, try '--help'. dpkg-source: warning: cannot verify inline signature for ./tiddit_3.6.1+dfsg-2.dsc: no acceptable signature found dpkg-source: info: extracting tiddit in tiddit-3.6.1+dfsg dpkg-source: info: unpacking tiddit_3.6.1+dfsg.orig.tar.xz dpkg-source: info: unpacking tiddit_3.6.1+dfsg-2.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3606384/tmp/hooks/D01_modify_environment starting debug: Running on ionos1-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jun 5 12:49 /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/3606384/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3606384/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]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=28b941fea21e48bba769209609448ea3 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=3606384 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.VvnRmSVy/pbuilderrc_F4Jj --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.VvnRmSVy/b2 --logfile b2/build.log tiddit_3.6.1+dfsg-2.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-37-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.140-1 (2025-05-22) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3606384/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, cython3, python3-all-dev, python3-setuptools, python3-numpy, python3-pysam dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19850 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 cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools 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. 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} cython3{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgnutls30t64{a} libgssapi-krb5-2{a} libhts3t64{a} libhtscodecs2{a} libidn2-0{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libldap2{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libp11-kit0{a} libpipeline1{a} libpsl5t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libtasn1-6{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-all{a} python3-all-dev{a} python3-autocommand{a} python3-dev{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-numpy-dev{a} python3-pkg-resources{a} python3-pysam{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 100 newly installed, 0 to remove and 0 not upgraded. Need to get 48.1 MB of archives. After unpacking 214 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.3-2 [861 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.7.1-1 [108 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.3-2 [2212 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.3-1 [27.2 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2025b-3 [260 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.8-2 [24.1 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.3-2 [1953 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.3-2 [751 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.3-1 [10.2 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.3-1 [28.2 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1 [139 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:2.2.4+ds-1 [5096 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-8 [1187 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-8 [294 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-4 [862 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 cython3 amd64 3.0.11+dfsg-2+b1 [2504 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-4 [539 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 42 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-1 [698 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.2 [919 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20250414 [116 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-1+b1 [24.3 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.8-2 [109 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 60 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.9+dfsg-2 [194 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1.1 [76.0 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.13.0-5 [375 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libexpat1-dev amd64 2.7.1-1 [161 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libpython3.13 amd64 3.13.3-2 [2156 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libpython3.13-dev amd64 3.13.3-2 [5015 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libpython3-dev amd64 3.13.3-1 [10.4 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libpython3-all-dev amd64 3.13.3-1 [1068 B] Get: 85 http://deb.debian.org/debian trixie/main amd64 python3-all amd64 3.13.3-1 [1048 B] Get: 86 http://deb.debian.org/debian trixie/main amd64 python3.13-dev amd64 3.13.3-2 [508 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 python3-dev amd64 3.13.3-1 [26.1 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 python3-all-dev amd64 3.13.3-1 [1068 B] Get: 89 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.7.0-1 [67.4 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.13.2-1 [90.5 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.2-1 [37.3 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 100 http://deb.debian.org/debian trixie/main amd64 python3-pysam amd64 0.23.0+ds-1+b1 [3665 kB] Fetched 48.1 MB in 5s (10.1 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19850 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.3-2_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.3-2) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.7.1-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.3-2_amd64.deb ... Unpacking python3.13-minimal (3.13.3-2) ... Setting up libpython3.13-minimal:amd64 (3.13.3-2) ... Setting up libexpat1:amd64 (2.7.1-1) ... Setting up python3.13-minimal (3.13.3-2) ... 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 ... 20184 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.3-1_amd64.deb ... Unpacking python3-minimal (3.13.3-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_13.0.0_all.deb ... Unpacking media-types (13.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.5_all.deb ... Unpacking netbase (6.5) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025b-3_all.deb ... Unpacking tzdata (2025b-3) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../4-libffi8_3.4.8-2_amd64.deb ... Unpacking libffi8:amd64 (3.4.8-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../6-libreadline8t64_8.2-6_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.3-2_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.3-2) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.3-2_amd64.deb ... Unpacking python3.13 (3.13.3-2) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.13.3-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.13.3-1) ... Setting up python3-minimal (3.13.3-1) ... 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 ... 21196 files and directories currently installed.) Preparing to unpack .../00-python3_3.13.3-1_amd64.deb ... Unpacking python3 (3.13.3-1) ... Selecting previously unselected package python3-numpy-dev:amd64. Preparing to unpack .../01-python3-numpy-dev_1%3a2.2.4+ds-1_amd64.deb ... Unpacking python3-numpy-dev:amd64 (1:2.2.4+ds-1) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../02-libblas3_3.12.1-2_amd64.deb ... Unpacking libblas3:amd64 (3.12.1-2) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../03-libgfortran5_14.2.0-19_amd64.deb ... Unpacking libgfortran5:amd64 (14.2.0-19) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../04-liblapack3_3.12.1-2_amd64.deb ... Unpacking liblapack3:amd64 (3.12.1-2) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../05-python3-numpy_1%3a2.2.4+ds-1_amd64.deb ... Unpacking python3-numpy (1:2.2.4+ds-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. 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Setting up libnghttp2-14:amd64 (1.64.0-1.1) ... Setting up libdeflate0:amd64 (1.23-2) ... Setting up gettext-base (0.23.1-2) ... Setting up m4 (1.4.19-8) ... Setting up libcom-err2:amd64 (1.47.2-1+b1) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libkrb5support0:amd64 (1.21.3-5) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Setting up tzdata (2025b-3) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Jun 5 12:49:50 UTC 2025. Universal Time is now: Thu Jun 5 12:49:50 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... Setting up libblas3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libexpat1-dev:amd64 (2.7.1-1) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/3606384/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/3606384/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/tiddit-3.6.1+dfsg/ && 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 > ../tiddit_3.6.1+dfsg-2_source.changes dpkg-buildpackage: info: source package tiddit dpkg-buildpackage: info: source version 3.6.1+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py clean /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tiddit-3.6.1+dfsg/tiddit/tiddit_cluster.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tiddit-3.6.1+dfsg/tiddit/tiddit_contig_analysis.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tiddit-3.6.1+dfsg/tiddit/tiddit_coverage.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tiddit-3.6.1+dfsg/tiddit/tiddit_coverage_analysis.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tiddit-3.6.1+dfsg/tiddit/tiddit_signal.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tiddit-3.6.1+dfsg/tiddit/tiddit_variant.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling tiddit/tiddit_signal.pyx because it changed. Compiling tiddit/tiddit_coverage.pyx because it changed. Compiling tiddit/tiddit_cluster.pyx because it changed. Compiling tiddit/tiddit_coverage_analysis.pyx because it changed. Compiling tiddit/tiddit_variant.pyx because it changed. Compiling tiddit/tiddit_contig_analysis.pyx because it changed. [1/6] Cythonizing tiddit/tiddit_cluster.pyx [2/6] Cythonizing tiddit/tiddit_contig_analysis.pyx [3/6] Cythonizing tiddit/tiddit_coverage.pyx [4/6] Cythonizing tiddit/tiddit_coverage_analysis.pyx [5/6] Cythonizing tiddit/tiddit_signal.pyx [6/6] Cythonizing tiddit/tiddit_variant.pyx running clean removing '/build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.13' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/tiddit-3.6.1+dfsg' dh_clean rm -f tiddit/*.c make[1]: Leaving directory '/build/reproducible-path/tiddit-3.6.1+dfsg' debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py config /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tiddit-3.6.1+dfsg/tiddit/tiddit_cluster.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tiddit-3.6.1+dfsg/tiddit/tiddit_contig_analysis.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tiddit-3.6.1+dfsg/tiddit/tiddit_coverage.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tiddit-3.6.1+dfsg/tiddit/tiddit_coverage_analysis.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tiddit-3.6.1+dfsg/tiddit/tiddit_signal.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tiddit-3.6.1+dfsg/tiddit/tiddit_variant.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling tiddit/tiddit_signal.pyx because it changed. Compiling tiddit/tiddit_coverage.pyx because it changed. Compiling tiddit/tiddit_cluster.pyx because it changed. Compiling tiddit/tiddit_coverage_analysis.pyx because it changed. Compiling tiddit/tiddit_variant.pyx because it changed. Compiling tiddit/tiddit_contig_analysis.pyx because it changed. [1/6] Cythonizing tiddit/tiddit_cluster.pyx [2/6] Cythonizing tiddit/tiddit_contig_analysis.pyx [3/6] Cythonizing tiddit/tiddit_coverage.pyx [4/6] Cythonizing tiddit/tiddit_coverage_analysis.pyx [5/6] Cythonizing tiddit/tiddit_signal.pyx [6/6] Cythonizing tiddit/tiddit_variant.pyx running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build running build running build_py creating /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit copying tiddit/tiddit_vcf_header.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit copying tiddit/DBSCAN.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit copying tiddit/__init__.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit copying tiddit/tiddit_stats.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit copying tiddit/__main__.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit running build_ext building 'tiddit.tiddit_signal' extension creating build/temp.linux-x86_64-cpython-313/tiddit x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tiddit-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c tiddit/tiddit_signal.c -o build/temp.linux-x86_64-cpython-313/tiddit/tiddit_signal.o x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tiddit-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/tiddit/tiddit_signal.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_signal.cpython-313-x86_64-linux-gnu.so building 'tiddit.tiddit_coverage' extension x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tiddit-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c tiddit/tiddit_coverage.c -o build/temp.linux-x86_64-cpython-313/tiddit/tiddit_coverage.o In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from tiddit/tiddit_coverage.c:1240: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tiddit-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/tiddit/tiddit_coverage.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_coverage.cpython-313-x86_64-linux-gnu.so building 'tiddit.tiddit_cluster' extension x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tiddit-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c tiddit/tiddit_cluster.c -o build/temp.linux-x86_64-cpython-313/tiddit/tiddit_cluster.o x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tiddit-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/tiddit/tiddit_cluster.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_cluster.cpython-313-x86_64-linux-gnu.so building 'tiddit.tiddit_coverage_analysis' extension x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tiddit-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c tiddit/tiddit_coverage_analysis.c -o build/temp.linux-x86_64-cpython-313/tiddit/tiddit_coverage_analysis.o In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from tiddit/tiddit_coverage_analysis.c:1240: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tiddit-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/tiddit/tiddit_coverage_analysis.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_coverage_analysis.cpython-313-x86_64-linux-gnu.so building 'tiddit.tiddit_variant' extension x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tiddit-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c tiddit/tiddit_variant.c -o build/temp.linux-x86_64-cpython-313/tiddit/tiddit_variant.o x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tiddit-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/tiddit/tiddit_variant.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_variant.cpython-313-x86_64-linux-gnu.so building 'tiddit.tiddit_contig_analysis' extension x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tiddit-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c tiddit/tiddit_contig_analysis.c -o build/temp.linux-x86_64-cpython-313/tiddit/tiddit_contig_analysis.o x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tiddit-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/tiddit/tiddit_contig_analysis.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_contig_analysis.cpython-313-x86_64-linux-gnu.so dh_auto_test -O--buildsystem=pybuild I: pybuild base:311: cd /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build; python3.13 -m unittest discover -v ---------------------------------------------------------------------- Ran 0 tests in 0.000s NO TESTS RAN create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/tiddit/ -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running build_ext running install_lib creating /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages creating /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_coverage.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_signal.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit creating /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit/__pycache__ copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit/__pycache__ copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_cluster.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_vcf_header.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_contig_analysis.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_coverage_analysis.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/DBSCAN.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/__init__.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_stats.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_variant.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/__main__.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit byte-compiling /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit/tiddit_vcf_header.py to tiddit_vcf_header.cpython-313.pyc byte-compiling /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit/DBSCAN.py to DBSCAN.cpython-313.pyc byte-compiling /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit/tiddit_stats.py to tiddit_stats.cpython-313.pyc byte-compiling /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit/__main__.py to __main__.cpython-313.pyc running install_egg_info running egg_info creating tiddit.egg-info writing tiddit.egg-info/PKG-INFO writing dependency_links to tiddit.egg-info/dependency_links.txt writing entry points to tiddit.egg-info/entry_points.txt writing requirements to tiddit.egg-info/requires.txt writing top-level names to tiddit.egg-info/top_level.txt writing manifest file 'tiddit.egg-info/SOURCES.txt' reading manifest file 'tiddit.egg-info/SOURCES.txt' adding license file 'COPYING' adding license file 'AUTHORS' writing manifest file 'tiddit.egg-info/SOURCES.txt' Copying tiddit.egg-info to /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit-3.6.1.egg-info Skipping SOURCES.txt running install_scripts Installing tiddit script to /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/bin dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/tiddit-3.6.1+dfsg' dh_installman --language=C make[1]: Leaving directory '/build/reproducible-path/tiddit-3.6.1+dfsg' debian/rules override_dh_python3 make[1]: Entering directory '/build/reproducible-path/tiddit-3.6.1+dfsg' dh_numpy3 Possible precedence issue with control flow operator (return) at /usr/bin/dh_numpy3 line 57. dh_python3 --shebang=/usr/bin/python3 I: dh_python3 tools:114: replacing shebang in debian/tiddit/usr/bin/tiddit make[1]: Leaving directory '/build/reproducible-path/tiddit-3.6.1+dfsg' dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'tiddit' in '../tiddit_3.6.1+dfsg-2_amd64.deb'. dpkg-deb: building package 'tiddit-dbgsym' in '../tiddit-dbgsym_3.6.1+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../tiddit_3.6.1+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../tiddit_3.6.1+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3606384/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3606384/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/3606384 and its subdirectories I: Current time: Fri Jun 6 02:51:31 +14 2025 I: pbuilder-time-stamp: 1749127891 + false + set +x Thu Jun 5 12:51:31 UTC 2025 I: Signing ./b2/tiddit_3.6.1+dfsg-2_amd64.buildinfo as tiddit_3.6.1+dfsg-2_amd64.buildinfo.asc Thu Jun 5 12:51:32 UTC 2025 I: Signed ./b2/tiddit_3.6.1+dfsg-2_amd64.buildinfo as ./b2/tiddit_3.6.1+dfsg-2_amd64.buildinfo.asc Thu Jun 5 12:51:32 UTC 2025 - build #2 for tiddit/trixie/amd64 on ionos1-amd64 done. Starting cleanup. All cleanup done. Thu Jun 5 12:51:32 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-vvxZFcHa, removing. /srv/reproducible-results/rbuild-debian/r-b-build.VvnRmSVy: total 84 drwxr-xr-x 2 jenkins jenkins 4096 Jun 5 12:48 b1 drwxr-xr-x 2 jenkins jenkins 4096 Jun 5 12:51 b2 -rw------- 1 jenkins jenkins 68842 Jun 5 12:48 rbuildlog.KsmKjEO -rw-r--r-- 1 jenkins jenkins 2227 Feb 8 18:33 tiddit_3.6.1+dfsg-2.dsc /srv/reproducible-results/rbuild-debian/r-b-build.VvnRmSVy/b1: total 4064 -rw-r--r-- 1 jenkins jenkins 65211 Jun 5 12:48 build.log -rw-r--r-- 1 jenkins jenkins 1981036 Jun 5 12:48 tiddit-dbgsym_3.6.1+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 1731888 Jun 5 12:48 tiddit_3.6.1+dfsg-2.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2227 Jun 5 12:48 tiddit_3.6.1+dfsg-2.dsc -rw-r--r-- 1 jenkins jenkins 7192 Jun 5 12:48 tiddit_3.6.1+dfsg-2_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 8074 Jun 5 12:48 tiddit_3.6.1+dfsg-2_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1486 Jun 5 12:48 tiddit_3.6.1+dfsg-2_amd64.changes -rw-r--r-- 1 jenkins jenkins 331968 Jun 5 12:48 tiddit_3.6.1+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 1373 Jun 5 12:48 tiddit_3.6.1+dfsg-2_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.VvnRmSVy/b2: total 4052 -rw-r--r-- 1 jenkins jenkins 67131 Jun 5 12:51 build.log -rw-r--r-- 1 jenkins jenkins 1981036 Jun 5 12:51 tiddit-dbgsym_3.6.1+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 1731888 Jun 5 12:51 tiddit_3.6.1+dfsg-2.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2227 Jun 5 12:51 tiddit_3.6.1+dfsg-2.dsc -rw-r--r-- 1 jenkins jenkins 7181 Jun 5 12:51 tiddit_3.6.1+dfsg-2_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 8063 Jun 5 12:51 tiddit_3.6.1+dfsg-2_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1486 Jun 5 12:51 tiddit_3.6.1+dfsg-2_amd64.changes -rw-r--r-- 1 jenkins jenkins 331968 Jun 5 12:51 tiddit_3.6.1+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 1373 Jun 5 12:51 tiddit_3.6.1+dfsg-2_source.changes Thu Jun 5 12:51:32 UTC 2025 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Thu Jun 5 12:51:32 UTC 2025 I: tiddit_3.6.1+dfsg-2_amd64.changes: Format: 1.8 Date: Sat, 08 Feb 2025 18:51:43 +0100 Source: tiddit Binary: tiddit tiddit-dbgsym Architecture: amd64 Version: 3.6.1+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: tiddit - structural variant calling Closes: 1095285 Changes: tiddit (3.6.1+dfsg-2) unstable; urgency=medium . * Team upload. * d/rules: invoke dh_numpy3 to include ABI dependencies. (Closes: #1095285) * d/control: declare compliance to standards version 4.7.0. Checksums-Sha1: b5a2a3a71704b57192830577ad7d05ff772fa5ef 1981036 tiddit-dbgsym_3.6.1+dfsg-2_amd64.deb 1b0c1af72eb70925e13a55e1258ffef06e777748 7192 tiddit_3.6.1+dfsg-2_amd64.buildinfo ca6068f454e4082e30a0df69f3a9ba2ada41e278 331968 tiddit_3.6.1+dfsg-2_amd64.deb Checksums-Sha256: e41b020ccfd997a34b02f6cbec357c6e3530328df01cfc81e972a16320c5a858 1981036 tiddit-dbgsym_3.6.1+dfsg-2_amd64.deb f44d149245595b97dec76815483a18e455379c9a4c9f93f0202042594e1d48e9 7192 tiddit_3.6.1+dfsg-2_amd64.buildinfo 0345829059ab247abe4cc3b691402be5b488d9a8c03aa133226e822dd8c94ea1 331968 tiddit_3.6.1+dfsg-2_amd64.deb Files: 8e8ee4478a9c9ff859868b544dd014b8 1981036 debug optional tiddit-dbgsym_3.6.1+dfsg-2_amd64.deb 83a0cf39dbb4fe485b9b12e55452556a 7192 science optional tiddit_3.6.1+dfsg-2_amd64.buildinfo 16444aa8a3e28ea88c84b1700e41ec04 331968 science optional tiddit_3.6.1+dfsg-2_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/tiddit_3.6.1+dfsg-2.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/tiddit_3.6.1+dfsg-2.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/tiddit_3.6.1+dfsg-2.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/tiddit_3.6.1+dfsg-2.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/trixie/amd64/tiddit_3.6.1+dfsg-2_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/tiddit_3.6.1+dfsg-2.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-06-05 12:48:47.946638988 +0000 +++ b2/build.log 2025-06-05 12:51:32.415714941 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Jul 8 07:09:17 -12 2026 -I: pbuilder-time-stamp: 1783537757 +I: Current time: Fri Jun 6 02:48:49 +14 2025 +I: pbuilder-time-stamp: 1749127729 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: unpacking tiddit_3.6.1+dfsg-2.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/109851/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3606384/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 5 12:49 /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/3606384/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3606384/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='bb5a7fdde3e5427ca397e4ca3e5008e5' - 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='109851' - PS1='# ' - PS2='> ' + INVOCATION_ID=28b941fea21e48bba769209609448ea3 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3606384 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.VvnRmSVy/pbuilderrc_JinT --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.VvnRmSVy/b1 --logfile b1/build.log tiddit_3.6.1+dfsg-2.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.VvnRmSVy/pbuilderrc_F4Jj --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.VvnRmSVy/b2 --logfile b2/build.log tiddit_3.6.1+dfsg-2.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.12.22+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.22-1~bpo12+1 (2025-04-25) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-37-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.140-1 (2025-05-22) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/109851/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3606384/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -221,7 +253,7 @@ Get: 98 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 100 http://deb.debian.org/debian trixie/main amd64 python3-pysam amd64 0.23.0+ds-1+b1 [3665 kB] -Fetched 48.1 MB in 4s (11.1 MB/s) +Fetched 48.1 MB in 5s (10.1 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19850 files and directories currently installed.) @@ -556,8 +588,8 @@ Setting up tzdata (2025b-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Wed Jul 8 19:09:46 UTC 2026. -Universal Time is now: Wed Jul 8 19:09:46 UTC 2026. +Local time is now: Thu Jun 5 12:49:50 UTC 2025. +Universal Time is now: Thu Jun 5 12:49:50 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... @@ -650,7 +682,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/tiddit-3.6.1+dfsg/ && 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 > ../tiddit_3.6.1+dfsg-2_source.changes +I: user script /srv/workspace/pbuilder/3606384/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3606384/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/tiddit-3.6.1+dfsg/ && 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 > ../tiddit_3.6.1+dfsg-2_source.changes dpkg-buildpackage: info: source package tiddit dpkg-buildpackage: info: source version 3.6.1+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -732,10 +768,10 @@ running build_py creating /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit copying tiddit/tiddit_vcf_header.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit -copying tiddit/__main__.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit copying tiddit/DBSCAN.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit copying tiddit/__init__.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit copying tiddit/tiddit_stats.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit +copying tiddit/__main__.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit running build_ext building 'tiddit.tiddit_signal' extension creating build/temp.linux-x86_64-cpython-313/tiddit @@ -802,24 +838,24 @@ running install_lib creating /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages creating /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit -copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_vcf_header.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit -copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/__main__.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit +copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_coverage.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit +copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_signal.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit creating /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit/__pycache__ copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit/__pycache__ -copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_contig_analysis.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_cluster.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit -copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_signal.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit -copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/DBSCAN.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit +copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_vcf_header.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit +copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_contig_analysis.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_coverage_analysis.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit +copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/DBSCAN.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/__init__.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit -copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_coverage.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit -copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_variant.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_stats.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit +copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/tiddit_variant.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit +copying /build/reproducible-path/tiddit-3.6.1+dfsg/.pybuild/cpython3_3.13_tiddit/build/tiddit/__main__.py -> /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit byte-compiling /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit/tiddit_vcf_header.py to tiddit_vcf_header.cpython-313.pyc -byte-compiling /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit/__main__.py to __main__.cpython-313.pyc byte-compiling /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit/DBSCAN.py to DBSCAN.cpython-313.pyc byte-compiling /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit/tiddit_stats.py to tiddit_stats.cpython-313.pyc +byte-compiling /build/reproducible-path/tiddit-3.6.1+dfsg/debian/tiddit/usr/lib/python3.13/dist-packages/tiddit/__main__.py to __main__.cpython-313.pyc running install_egg_info running egg_info creating tiddit.egg-info @@ -874,12 +910,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3606384/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3606384/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/109851 and its subdirectories -I: Current time: Wed Jul 8 07:11:47 -12 2026 -I: pbuilder-time-stamp: 1783537907 +I: removing directory /srv/workspace/pbuilder/3606384 and its subdirectories +I: Current time: Fri Jun 6 02:51:31 +14 2025 +I: pbuilder-time-stamp: 1749127891 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/tiddit_3.6.1+dfsg-2.diff: 77.1% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/tiddit_3.6.1+dfsg-2.diff.gz b2/build.log: 83.2% -- replaced with stdout Compressing the 1st log... b1/build.log: 83.7% -- replaced with stdout Thu Jun 5 12:51:33 UTC 2025 I: diffoscope 297 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_tiddit_trixie_amd64_1749127893 + touch /var/log/reproducible-builds/diffoscope_stamp_tiddit_trixie_amd64_1749127893 + RESULT=0 + systemd-run '--description=diffoscope on tiddit/3.6.1+dfsg-2 in trixie/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_4-55578 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.VvnRmSVy --run-session -c jenkins-reproducible-trixie-diffoscope-a9f2aae4-c3cb-4de2-941e-d9023abdb474 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.VvnRmSVy/dbd-tmp-IeGCdFI ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.VvnRmSVy/tiddit_3.6.1+dfsg-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.VvnRmSVy/tiddit_3.6.1+dfsg-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.VvnRmSVy/tiddit_3.6.1+dfsg-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.VvnRmSVy/b1/tiddit_3.6.1+dfsg-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.VvnRmSVy/b2/tiddit_3.6.1+dfsg-2_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_4-55578.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.VvnRmSVy/tiddit_3.6.1+dfsg-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.VvnRmSVy/tiddit_3.6.1+dfsg-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.VvnRmSVy/tiddit_3.6.1+dfsg-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.VvnRmSVy/b1/tiddit_3.6.1+dfsg-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.VvnRmSVy/b2/tiddit_3.6.1+dfsg-2_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 160ms CPU time consumed: 162ms _ _ _ _ _ _ | |_(_) __| | __| (_) |_ | __| |/ _` |/ _` | | __| | |_| | (_| | (_| | | |_ \__|_|\__,_|\__,_|_|\__| Thu Jun 5 12:51:33 UTC 2025 I: diffoscope 297 found no differences in the changes files, and a .buildinfo file also exists. Thu Jun 5 12:51:33 UTC 2025 I: tiddit from trixie built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-06-05 12:51:34] INFO: Starting at 2025-06-05 12:51:34.245755 [2025-06-05 12:51:34] INFO: Generating the pages of 1 package(s) [2025-06-05 12:51:34] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/amd64/tiddit didn't produce a buildlog, even though it has been built. [2025-06-05 12:51:34] INFO: Finished at 2025-06-05 12:51:34.428387, took: 0:00:00.182635 Thu Jun 5 12:51:34 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/amd64/tiddit.html Thu Jun 5 12:51:34 UTC 2025 I: Removing signed tiddit_3.6.1+dfsg-2_amd64.buildinfo.asc files: removed './b1/tiddit_3.6.1+dfsg-2_amd64.buildinfo.asc' removed './b2/tiddit_3.6.1+dfsg-2_amd64.buildinfo.asc' 1749127894 amd64 trixie tiddit Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/tiddit_3.6.1+dfsg-2.rbuild.log: 81.0% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/tiddit_3.6.1+dfsg-2.rbuild.log.gz [2025-06-05 12:51:34] INFO: Starting at 2025-06-05 12:51:34.685437 [2025-06-05 12:51:34] INFO: Generating the pages of 1 package(s) [2025-06-05 12:51:34] INFO: Finished at 2025-06-05 12:51:34.865132, took: 0:00:00.179697 All cleanup done. Thu Jun 5 12:51:34 UTC 2025 - total duration: 0h 5m 43s. Thu Jun 5 12:51:34 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-63ldPwyi, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 5min 44.010s CPU time consumed: 4.457s