Fri May 3 20:36:54 UTC 2024 I: starting to build flexbar/trixie/amd64 on jenkins on '2024-05-03 20:36' Fri May 3 20:36:54 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_36/10008/console.log Fri May 3 20:36:54 UTC 2024 I: Downloading source for trixie/flexbar=1:3.5.0-5 --2024-05-03 20:36:54-- http://deb.debian.org/debian/pool/main/f/flexbar/flexbar_3.5.0-5.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2041 (2.0K) [text/prs.lines.tag] Saving to: ‘flexbar_3.5.0-5.dsc’ 0K . 100% 217M=0s 2024-05-03 20:36:54 (217 MB/s) - ‘flexbar_3.5.0-5.dsc’ saved [2041/2041] Fri May 3 20:36:54 UTC 2024 I: flexbar_3.5.0-5.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: flexbar Binary: flexbar Architecture: any Version: 1:3.5.0-5 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Tony Travis Homepage: https://github.com/seqan/flexbar Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/flexbar Vcs-Git: https://salsa.debian.org/med-team/flexbar.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libtbb-dev, cmake, libseqan2-dev, zlib1g-dev, libbz2-dev Package-List: flexbar deb science optional arch=any Checksums-Sha1: 0c43550b73a08effdd3a7965e916dc9c6b64f8b2 44021 flexbar_3.5.0.orig.tar.gz 045efb9ac3a789f7903dd592234959f5c8865508 11436 flexbar_3.5.0-5.debian.tar.xz Checksums-Sha256: 656168934b6cb367ee6d4adad0c40506bc107c888d129fe191c6f3f3446a4ac9 44021 flexbar_3.5.0.orig.tar.gz b718a9bf496bfead917292eee67d085beb2864b750374794f34ff28bcb6e9795 11436 flexbar_3.5.0-5.debian.tar.xz Files: 0e07bf4afebfd731c4718b401383224a 44021 flexbar_3.5.0.orig.tar.gz e818565eaed0b2c567aeb296816f803c 11436 flexbar_3.5.0-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmPmH8MRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFJXQ/+PLfezlqwuyZChCZNmHcP2rYrV578PlHF mBZE2Te7xmjLkklhdrnTUK1hNzczlGUpWZKBgBAe/XMP33UI+CzpYXUZ58ZkF9oK 8JhYem/Psh0u/Xa0uNUDzCbyrcNwqOsmagiSrCB9WubuP1Ee7GpC7k5KhbhIqTMv rD63/5Oq3uH6mqsJU2xJbn7ZY7pt0rrPxDE9KdpBAmF6dtDH0n2AxBXjIlC2wBSe +BnXN8oFeNfCFYzIZ3ZcruGX7O34MtsIKcw9iB05MbK39BlAo0zVK6Xoko4aGmqK zNOtlml40nknXtjM27Iyc9PppOL8mkSB6NAfQo1fKYqLzjlIKgMaJA9H0DwswOpX Bhuc5Gqbq5Ic+Ucj/Xq5YKKv3WnLOS0s+DScRuDaU6Z3eqABv34aIdeARI29HsbU +FdnyWMdhiq4O15LUSlYqLLwC4EofhXwUGYkcznjTWlxB6oAgr5Kr2FAeyB5UrON Qn15hTMV5IIfGIizOkTC56PF+38wpiXQv4rq3WjzVoGo7hEoMguAufj4C1P1MGiy uoCQqjrtBEKFuvoYo43nwKZCzzsGNdf7ujIhLNiklUAfmEoeYQPqjQAZOaBtWREo BHFfpIWb5pitFT0dHD5Wgc0H5t5i68RjfbpEpDqakCqQHcmgNJtXsV+LY6fFgqj8 hssF4XLod0A= =IhAG -----END PGP SIGNATURE----- Fri May 3 20:36:54 UTC 2024 I: Checking whether the package is not for us Fri May 3 20:36:54 UTC 2024 I: Starting 1st build on remote node infom02-amd64.debian.net. Fri May 3 20:36:54 UTC 2024 I: Preparing to do remote build '1' on infom02-amd64.debian.net. Fri May 3 20:39:00 UTC 2024 I: Deleting $TMPDIR on infom02-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Jun 5 14:59:56 -12 2025 I: pbuilder-time-stamp: 1749178796 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 [flexbar_3.5.0-5.dsc] I: copying [./flexbar_3.5.0.orig.tar.gz] I: copying [./flexbar_3.5.0-5.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Feb 10 10:43:15 2023 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./flexbar_3.5.0-5.dsc: no acceptable signature found dpkg-source: info: extracting flexbar in flexbar-3.5.0 dpkg-source: info: unpacking flexbar_3.5.0.orig.tar.gz dpkg-source: info: unpacking flexbar_3.5.0-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no_march_native.patch dpkg-source: info: applying 195a1ab2c2715b07df5acff58dc2a0396d9cd52d.patch dpkg-source: info: applying 1c872fa10d474f090633fc95d409aa60607a3f96.patch dpkg-source: info: applying 19722f2743c96235ff57948eda82f963cf734131.patch dpkg-source: info: applying a9b0eb87a391aeaf760f8116dca777749c8b4f96.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4062390/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=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='164d27c07b78416c8a5d57a76bb91e39' 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='4062390' 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.tLXpFd9a/pbuilderrc_TZpk --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.tLXpFd9a/b1 --logfile b1/build.log flexbar_3.5.0-5.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom02-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 5 14:11 /bin -> usr/bin I: user script /srv/workspace/pbuilder/4062390/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), libtbb-dev, cmake, libseqan2-dev, zlib1g-dev, libbz2-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19695 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 libtbb-dev; however: Package libtbb-dev is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on libseqan2-dev; however: Package libseqan2-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev 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} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libhwloc15{a} libicu72{a} libjsoncpp25{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libpipeline1{a} libproc2-0{a} libpsl5t64{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libseqan2-dev{a} libssh2-1t64{a} libsub-override-perl{a} libtbb-dev{a} libtbb12{a} libtbbbind-2-5{a} libtbbmalloc2{a} libtool{a} libuchardet0{a} libuv1t64{a} libxml2{a} m4{a} man-db{a} po-debconf{a} procps{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libhwloc-plugins libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix wget 0 packages upgraded, 62 newly installed, 0 to remove and 0 not upgraded. Need to get 38.4 MB of archives. After unpacking 151 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-4 [64.6 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-4 [880 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-3+b1 [1180 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libarchive13t64 amd64 3.7.2-2 [346 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.0-2.4 [20.2 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 26 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.7.1-3 [441 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libjsoncpp25 amd64 1.9.5-6+b2 [81.9 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 librhash0 amd64 1.4.3-3+b1 [132 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.48.0-1.1 [147 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 cmake-data all 3.29.2-2 [2167 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 cmake amd64 3.29.2-2 [10.7 MB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 49 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libbz2-dev amd64 1.0.8-5.1 [31.3 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libhwloc15 amd64 2.10.0-1+b1 [161 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libseqan2-dev all 2.4.0+dfsg-16 [1216 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libtbbmalloc2 amd64 2021.11.0-2 [48.6 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libtbbbind-2-5 amd64 2021.11.0-2 [14.1 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libtbb12 amd64 2021.11.0-2 [87.6 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libtbb-dev amd64 2021.11.0-2 [193 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1 [918 kB] Fetched 38.4 MB in 1s (59.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0: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 ... 19695 files and directories currently installed.) Preparing to unpack .../00-libproc2-0_2%3a4.0.4-4_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-4) ... Selecting previously unselected package procps. Preparing to unpack .../01-procps_2%3a4.0.4-4_amd64.deb ... Unpacking procps (2:4.0.4-4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../02-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../04-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../07-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../08-groff-base_1.23.0-3+b1_amd64.deb ... Unpacking groff-base (1.23.0-3+b1) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/flexbar-3.5.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../flexbar_3.5.0-5_source.changes dpkg-buildpackage: info: source package flexbar dpkg-buildpackage: info: source version 1:3.5.0-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/flexbar-3.5.0' dh_auto_clean rm -f test/result_*fast[aq] test/result_*.log make[1]: Leaving directory '/build/reproducible-path/flexbar-3.5.0' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu .. CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The C compiler identification is GNU 13.2.0 -- The CXX compiler identification is GNU 13.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Deprecation Warning at src/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Performing Test COMPILER_SUPPORTS_CXX14 -- Performing Test COMPILER_SUPPORTS_CXX14 - Success -- Flexbar 64 bit architecture -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3") -- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version "1.0.8") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found -- Configuring done (0.9s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu dh_auto_build cd obj-x86_64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/flexbar-3.5.0 -B/build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu' make -f src/CMakeFiles/flexbar.dir/build.make src/CMakeFiles/flexbar.dir/depend make[3]: Entering directory '/build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/flexbar-3.5.0 /build/reproducible-path/flexbar-3.5.0/src /build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu /build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu/src /build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu/src/CMakeFiles/flexbar.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu' make -f src/CMakeFiles/flexbar.dir/build.make src/CMakeFiles/flexbar.dir/build make[3]: Entering directory '/build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu' [ 50%] Building CXX object src/CMakeFiles/flexbar.dir/Flexbar.cpp.o cd /build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -I/build/reproducible-path/flexbar-3.5.0/include -g -O2 -ffile-prefix-map=/build/reproducible-path/flexbar-3.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -MD -MT src/CMakeFiles/flexbar.dir/Flexbar.cpp.o -MF CMakeFiles/flexbar.dir/Flexbar.cpp.o.d -o CMakeFiles/flexbar.dir/Flexbar.cpp.o -c /build/reproducible-path/flexbar-3.5.0/src/Flexbar.cpp In file included from /usr/include/c++/13/string:51, from /build/reproducible-path/flexbar-3.5.0/src/Flexbar.h:10, from /build/reproducible-path/flexbar-3.5.0/src/Flexbar.cpp:24: In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const seqan::SimpleType; _Up = seqan::SimpleType; bool _IsMove = false]', inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const seqan::SimpleType*; _OI = seqan::SimpleType*]' at /usr/include/c++/13/bits/stl_algobase.h:506:30, inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const seqan::SimpleType*; _OI = seqan::SimpleType*]' at /usr/include/c++/13/bits/stl_algobase.h:533:42, inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = const seqan::SimpleType*; _OI = seqan::SimpleType*]' at /usr/include/c++/13/bits/stl_algobase.h:540:31, inlined from '_OI std::copy(_II, _II, _OI) [with _II = const seqan::SimpleType*; _OI = seqan::SimpleType*]' at /usr/include/c++/13/bits/stl_algobase.h:633:7, inlined from 'void seqan::_arrayCopyForwardDefault(TSource1, TSource2, TTarget) [with TTarget = SimpleType*; TSource1 = const SimpleType*; TSource2 = const SimpleType*]' at /usr/include/seqan/basic/array_construct_destruct.h:635:14, inlined from 'void seqan::arrayCopyForward(TSource1, TSource2, TTarget) [with TTarget = SimpleType*; TSource1 = const SimpleType*; TSource2 = const SimpleType*]' at /usr/include/seqan/basic/array_construct_destruct.h:644:29, inlined from 'void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = const SimpleType; TValueTarget = SimpleType]' at /usr/include/seqan/basic/array_construct_destruct.h:1003:21, inlined from 'void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = const SimpleType; TValueTarget = SimpleType]' at /usr/include/seqan/basic/array_construct_destruct.h:1031:31, inlined from 'static void seqan::AppendString_::append_(TTarget&, TSource&) [with TTarget = seqan::String, seqan::Alloc<> >; TSource = const seqan::SimpleType; TExpand = seqan::Tag]' at /usr/include/seqan/sequence/string_base.h:1238:31, inlined from 'void seqan::append(String&, const TSource&, Tag) [with TTargetValue = SimpleType; TTargetSpec = Alloc<>; TSource = SimpleType; TExpand = TagGenerous_]' at /usr/include/seqan/sequence/string_base.h:1287:42, inlined from 'void seqan::append(TTarget&&, const TSource&) [with TTarget = String, Alloc<> >&; TSource = SimpleType]' at /usr/include/seqan/sequence/sequence_interface.h:903:11, inlined from 'void SeqAlignAlgo::alignGlobal(TAlignResults&, flexbar::Alignments&, flexbar::ComputeCycle&, unsigned int, flexbar::TrimEnd) [with TSeqStr = seqan::String, seqan::Alloc<> >]' at /build/reproducible-path/flexbar-3.5.0/src/SeqAlignAlgo.h:132:85: /usr/include/c++/13/bits/stl_algobase.h:437:30: warning: 'void* __builtin_memcpy(void*, const void*, long unsigned int)' reading between 2 and 9223372036854775807 bytes from a region of size 1 [-Wstringop-overread] 437 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/flexbar-3.5.0/src/PairedAlign.h:8, from /build/reproducible-path/flexbar-3.5.0/src/Flexbar.h:34: /build/reproducible-path/flexbar-3.5.0/src/SeqAlignAlgo.h: In member function 'void SeqAlignAlgo::alignGlobal(TAlignResults&, flexbar::Alignments&, flexbar::ComputeCycle&, unsigned int, flexbar::TrimEnd) [with TSeqStr = seqan::String, seqan::Alloc<> >]': /build/reproducible-path/flexbar-3.5.0/src/SeqAlignAlgo.h:132:124: note: source object '' of size 1 132 | else if(m_umiTags && *it2 == 'N') append(a.umiTag, (TChar) *it1); | ^~~~~~~~~~~~ In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const char; _Up = char; bool _IsMove = false]', inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const char*; _OI = char*]' at /usr/include/c++/13/bits/stl_algobase.h:506:30, inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const char*; _OI = char*]' at /usr/include/c++/13/bits/stl_algobase.h:533:42, inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = const char*; _OI = char*]' at /usr/include/c++/13/bits/stl_algobase.h:540:31, inlined from '_OI std::copy(_II, _II, _OI) [with _II = const char*; _OI = char*]' at /usr/include/c++/13/bits/stl_algobase.h:633:7, inlined from 'void seqan::_arrayCopyForwardDefault(TSource1, TSource2, TTarget) [with TTarget = char*; TSource1 = const char*; TSource2 = const char*]' at /usr/include/seqan/basic/array_construct_destruct.h:635:14, inlined from 'void seqan::arrayCopyForward(TSource1, TSource2, TTarget) [with TTarget = char*; TSource1 = const char*; TSource2 = const char*]' at /usr/include/seqan/basic/array_construct_destruct.h:644:29, inlined from 'void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = const char; TValueTarget = char]' at /usr/include/seqan/basic/array_construct_destruct.h:1003:21, inlined from 'void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = const char; TValueTarget = char]' at /usr/include/seqan/basic/array_construct_destruct.h:1031:31, inlined from 'static void seqan::AssignString_::assign_(TTarget&, TSource&) [with TTarget = seqan::String >; TSource = const char [1]; TExpand = seqan::Tag]' at /usr/include/seqan/sequence/string_base.h:1011:31, inlined from 'void seqan::assign(String&, const TSource&, Tag) [with TTargetValue = char; TTargetSpec = Alloc<>; TSource = char [1]; TExpand = TagGenerous_]' at /usr/include/seqan/sequence/string_base.h:1056:42, inlined from 'void seqan::assign(String&, const TSource&) [with TTargetValue = char; TTargetSpec = Alloc<>; TSource = char [1]]' at /usr/include/seqan/sequence/string_base.h:992:11, inlined from 'seqan::String >& seqan::String >::operator=(const TSource&) [with TSource = char [1]; Dummy = void; = void; TValue = char; TSpec = void]' at /usr/include/seqan/sequence/string_alloc.h:182:15, inlined from 'int SeqAlign::alignSeqRead(flexbar::TSeqRead*, bool, flexbar::Alignments&, flexbar::ComputeCycle&, unsigned int&, const flexbar::AlignmentMode&, flexbar::TrimEnd, const TSeqStr&) [with TSeqStr = seqan::String, seqan::Alloc<> >; TString = seqan::String >; TAlgorithm = SeqAlignAlgo, seqan::Alloc<> > >]' at /build/reproducible-path/flexbar-3.5.0/src/SeqAlign.h:182:42: /usr/include/c++/13/bits/stl_algobase.h:437:30: warning: 'void* __builtin_memcpy(void*, const void*, long unsigned int)' reading between 2 and 9223372036854775807 bytes from a region of size 1 [-Wstringop-overread] 437 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [100%] Linking CXX executable ../flexbar cd /build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/flexbar.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/flexbar-3.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/flexbar.dir/Flexbar.cpp.o -o ../flexbar -lpthread /usr/lib/x86_64-linux-gnu/libtbb.so.12.11 -lz -lbz2 make[3]: Leaving directory '/build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu' [100%] Built target flexbar make[2]: Leaving directory '/build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/flexbar-3.5.0' cd test ; \ export PATH="/build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu:$PATH" ; \ echo $PATH ; \ export HOME=/tmp ; \ which flexbar ; \ ./flexbar_test.sh /build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games /build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu/flexbar Testing fasta: Test 1 OK Test 2 OK Test 3 OK Test 4 OK Test 5 OK Testing fastq: Test 1 OK Test 2 OK Test 3 OK Test 4 OK Test 5 OK Testing decompression: Test gzip OK Test bzip2 OK rm -f test/result_*fast[aq] test/result_*.log make[1]: Leaving directory '/build/reproducible-path/flexbar-3.5.0' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/flexbar/ dh_install dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'flexbar' in '../flexbar_3.5.0-5_amd64.deb'. dpkg-deb: building package 'flexbar-dbgsym' in '../flexbar-dbgsym_3.5.0-5_amd64.deb'. dpkg-genbuildinfo --build=binary -O../flexbar_3.5.0-5_amd64.buildinfo dpkg-genchanges --build=binary -O../flexbar_3.5.0-5_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/4062390 and its subdirectories I: Current time: Thu Jun 5 15:01:59 -12 2025 I: pbuilder-time-stamp: 1749178919 Fri May 3 20:39:01 UTC 2024 I: 1st build successful. Starting 2nd build on remote node infom01-amd64.debian.net. Fri May 3 20:39:01 UTC 2024 I: Preparing to do remote build '2' on infom01-amd64.debian.net. Fri May 3 20:40:49 UTC 2024 I: Deleting $TMPDIR on infom01-amd64.debian.net. Fri May 3 20:40:50 UTC 2024 I: flexbar_3.5.0-5_amd64.changes: Format: 1.8 Date: Fri, 10 Feb 2023 11:37:36 +0100 Source: flexbar Binary: flexbar flexbar-dbgsym Architecture: amd64 Version: 1:3.5.0-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: flexbar - flexible barcode and adapter removal for sequencing platforms Closes: 1008220 1011656 Changes: flexbar (1:3.5.0-5) unstable; urgency=medium . [ Andreas Tille ] * Set upstream metadata fields: Archive. * Port to onetbb (thanks to Liam Keegan - see https://github.com/seqan/flexbar/pull/41/) Closes: #1008220, #1011656 * Fix watch file . [ Étienne Mollier ] * onetbb.patch: port Paired* classes. . [ Andreas Tille ] * Standards-Version: 4.6.2 (routine-update) Checksums-Sha1: dc76bf586fe20809853e2fd6097b4d440b4056b3 4140060 flexbar-dbgsym_3.5.0-5_amd64.deb 1b930477dd9d2f51b72160a2e55e5639819610f3 6325 flexbar_3.5.0-5_amd64.buildinfo 33a5e2849fcea50dedd27ad165ed4e5b11bba378 366684 flexbar_3.5.0-5_amd64.deb Checksums-Sha256: 664d155aef0df3d97b3bfe672534e60e158c8c3c482159f752731f72e8819fd8 4140060 flexbar-dbgsym_3.5.0-5_amd64.deb 3321d71983165eb353279cacc6aac20ec9c91377a987addedea2e2dfb99d903c 6325 flexbar_3.5.0-5_amd64.buildinfo 68277fe215febfeb260fb3a68d8134b3f59207d772e9b16f44815b11a92937fe 366684 flexbar_3.5.0-5_amd64.deb Files: 1b8a1f22197990985a5b722f5539277e 4140060 debug optional flexbar-dbgsym_3.5.0-5_amd64.deb 0bad24527b565f2b8d143a373c5e9aa8 6325 science optional flexbar_3.5.0-5_amd64.buildinfo e478aa0a33a37d034eb6407ffba7d4f0 366684 science optional flexbar_3.5.0-5_amd64.deb Fri May 3 20:40:51 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_36-10008.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.tLXpFd9a/flexbar_3.5.0-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.tLXpFd9a/flexbar_3.5.0-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.tLXpFd9a/flexbar_3.5.0-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.tLXpFd9a/b1/flexbar_3.5.0-5_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.tLXpFd9a/b2/flexbar_3.5.0-5_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.447s) 0.447s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.065s) 0.065s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 837ms CPU time consumed: 837ms Fri May 3 20:40:52 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Fri May 3 20:40:52 UTC 2024 I: flexbar from trixie built successfully and reproducibly on amd64. Fri May 3 20:40:53 UTC 2024 I: Submitting .buildinfo files to external archives: Fri May 3 20:40:53 UTC 2024 I: Submitting 8.0K b1/flexbar_3.5.0-5_amd64.buildinfo.asc Fri May 3 20:40:55 UTC 2024 I: Submitting 8.0K b2/flexbar_3.5.0-5_amd64.buildinfo.asc Fri May 3 20:40:57 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri May 3 20:40:57 UTC 2024 I: Done submitting .buildinfo files. Fri May 3 20:40:57 UTC 2024 I: Removing signed flexbar_3.5.0-5_amd64.buildinfo.asc files: removed './b1/flexbar_3.5.0-5_amd64.buildinfo.asc' removed './b2/flexbar_3.5.0-5_amd64.buildinfo.asc'