Running as unit: rb-build-arm64_8-53077.service ==================================================================================== Tue Mar 11 00:01:53 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_8) on jenkins, called using "codethink04-arm64 codethink03-arm64" as arguments. Tue Mar 11 00:01:53 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-i49Kxmxk" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue Mar 11 00:01:53 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Tue Mar 11 00:01:53 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-RXIRWB' Tue Mar 11 00:01:54 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Tue Mar 11 00:01:54 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-1yPp5q' ok, let's check if dnaclust is building anywhere yet… ok, dnaclust is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of dnaclust in trixie on arm64 on jenkins now. 1st build will be done on codethink04-arm64.debian.net. 2nd build will be done on codethink03-arm64.debian.net. ============================================================================= Tue Mar 11 00:02:12 UTC 2025 I: starting to build dnaclust/trixie/arm64 on jenkins on '2025-03-11 00:01' Tue Mar 11 00:02:12 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_8/53077/console.log 1741651332 arm64 trixie dnaclust Tue Mar 11 00:02:12 UTC 2025 I: Downloading source for trixie/dnaclust=3-7 --2025-03-11 00:02:12-- http://deb.debian.org/debian/pool/main/d/dnaclust/dnaclust_3-7.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1977 (1.9K) [text/prs.lines.tag] Saving to: ‘dnaclust_3-7.dsc’ 0K . 100% 322M=0s 2025-03-11 00:02:12 (322 MB/s) - ‘dnaclust_3-7.dsc’ saved [1977/1977] --2025-03-11 00:02:12-- http://deb.debian.org/debian/pool/main/d/dnaclust/dnaclust_3-7.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1977 (1.9K) [text/prs.lines.tag] Saving to: ‘dnaclust_3-7.dsc’ 0K . 100% 322M=0s 2025-03-11 00:02:12 (322 MB/s) - ‘dnaclust_3-7.dsc’ saved [1977/1977] Tue Mar 11 00:02:12 UTC 2025 I: dnaclust_3-7.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: dnaclust Binary: dnaclust Architecture: any Version: 3-7 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://dnaclust.sourceforge.net/ Standards-Version: 4.4.0 Vcs-Browser: https://salsa.debian.org/med-team/dnaclust Vcs-Git: https://salsa.debian.org/med-team/dnaclust.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 12), libboost-dev, libboost-program-options-dev, rename Package-List: dnaclust deb science optional arch=any Checksums-Sha1: 6d61297157dd954b35122b15d43cc78b5d1a749e 23485 dnaclust_3.orig.tar.gz 883ed45d787563dce965d96f20ac0b110d82de59 36972 dnaclust_3-7.debian.tar.xz Checksums-Sha256: f7fccc3b0507229a03f227af7e104bf218e9976c453c3a8ef9c4a3c2db83fc74 23485 dnaclust_3.orig.tar.gz e18171ee25c15cad70174292b01fdef7763f239c1026e728a848c2653e641c6f 36972 dnaclust_3-7.debian.tar.xz Files: 68e8c69bc10c75b94aea684222f847a9 23485 dnaclust_3.orig.tar.gz 65d934be94276ff7bd5c3fb8a038691e 36972 dnaclust_3-7.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJCBAEBCAAsFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl1NO0MOHHRpbGxlYUBy a2kuZGUACgkQV4oElNHGRtFgkQ//W1dstemveb65X8UResC6Qe/+ek1ud+EShwvH HHbGX6fRaGLD7rNEwUBPYIk3nL6KimUODYn1GyY5yqXirmfkF+b6x7laKFCCQd8m 1KLpNSYWELA8OzZCzwsmpx0JXKqiZtHqDVZl1qh1w6+VlwcLl4MpNZ6nEs1TMZLf ujIxQoZAD9P5vFiiTWcwqY0DQmN+N9McEoastfjTu1If72VAJT74lHUKdImHyIR2 Pimv+v+iy+SUm4t+1p0CUmb+ryoLp0y3e3ZHdRqzOcpcVGaX3jcnRYFi/2o+Cxzv A/PsvAaFWUekFJD0txSHsNuEkE8GsgXSMlF4aLlsPq3lkeWXFTS/haRgpP81Roh6 a3TdOcK55g9qQAb0FidyXyDKiqyfekqxiTNfSzMaFeBi25czy5e3iE+6c5i99qlW p1KUFvNXinnYYkF9zKeyjr1Npjojb9n7r1GdqgpdrLRZvJG56yfKLx/XWsvyofUI GcQJq3D8am9PpWy7It+qFWFWfQLjeoj7ZXag+wIsHw7pwrrF1xB683FE/iD4m+DM 13n0XLSOFI+QN3pi7cfnrnSW+xmNTPtjNGaoyG7fZ0phdm7GVYm2JtU3MgRUf/Nr UrIH/Tk5cXtpq3W48RZasxlWhgpVUh575a25P4qWs7XEARLWSr9XyGC7WbN6mrMe MZODn/g= =gTvt -----END PGP SIGNATURE----- Tue Mar 11 00:02:12 UTC 2025 I: Checking whether the package is not for us Tue Mar 11 00:02:12 UTC 2025 I: Starting 1st build on remote node codethink04-arm64.debian.net. Tue Mar 11 00:02:12 UTC 2025 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Tue Mar 11 00:02:12 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Tue Mar 11 00:02:12 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-WJKl6I' ==================================================================================== Tue Mar 11 00:02:14 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink04-arm64, called using "1 dnaclust trixie /srv/reproducible-results/rbuild-debian/r-b-build.evYOjC59 3-7" as arguments. Tue Mar 11 00:02:14 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-UZabJWv0" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue Mar 11 00:02:14 UTC 2025 I: Downloading source for trixie/dnaclust=3-7 Reading package lists... NOTICE: 'dnaclust' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/dnaclust.git Please use: git clone https://salsa.debian.org/med-team/dnaclust.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 62.4 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main dnaclust 3-7 (dsc) [1977 B] Get:2 http://deb.debian.org/debian trixie/main dnaclust 3-7 (tar) [23.5 kB] Get:3 http://deb.debian.org/debian trixie/main dnaclust 3-7 (diff) [37.0 kB] Fetched 62.4 kB in 0s (1187 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'dnaclust' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/dnaclust.git Please use: git clone https://salsa.debian.org/med-team/dnaclust.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 62.4 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main dnaclust 3-7 (dsc) [1977 B] Get:2 http://deb.debian.org/debian trixie/main dnaclust 3-7 (tar) [23.5 kB] Get:3 http://deb.debian.org/debian trixie/main dnaclust 3-7 (diff) [37.0 kB] Fetched 62.4 kB in 0s (1187 kB/s) Download complete and in download only mode ============================================================================= Building dnaclust in trixie on arm64 on codethink04-arm64 now. Date: Tue Mar 11 00:02:14 GMT 2025 Date UTC: Tue Mar 11 00:02:14 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Mon Mar 10 12:02:14 -12 2025 I: pbuilder-time-stamp: 1741651334 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 [dnaclust_3-7.dsc] I: copying [./dnaclust_3.orig.tar.gz] I: copying [./dnaclust_3-7.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./dnaclust_3-7.dsc: unsupported subcommand dpkg-source: info: extracting dnaclust in dnaclust-3 dpkg-source: info: unpacking dnaclust_3.orig.tar.gz dpkg-source: info: unpacking dnaclust_3-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_shel_path.patch dpkg-source: info: applying do_not_staically_linking.patch dpkg-source: info: applying resolve_name_space_conflict_fastasort.patch dpkg-source: info: applying build_with_gcc6.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/246141/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='5fb4c56ea91f4bd585633640c2ede2f6' 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='246141' 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.evYOjC59/pbuilderrc_xNk3 --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.evYOjC59/b1 --logfile b1/build.log dnaclust_3-7.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/246141/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 12), libboost-dev, libboost-program-options-dev, rename dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19914 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 (= 12); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-program-options-dev; however: Package libboost-program-options-dev is not installed. pbuilder-satisfydepends-dummy depends on rename; however: Package rename is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libboost-dev{a} libboost-program-options-dev{a} libboost-program-options1.83-dev{a} libboost-program-options1.83.0{a} libboost1.83-dev{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} rename{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 36 newly installed, 0 to remove and 0 not upgraded. Need to get 31.4 MB of archives. After unpacking 247 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.4-5 [92.0 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-7 [285 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.17-3 [862 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-4 [539 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 22 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b2 [630 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.24.1 [920 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libboost1.83-dev arm64 1.83.0-4.1 [10.6 MB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libboost-dev arm64 1.83.0.2+b2 [3828 B] Get: 33 http://deb.debian.org/debian trixie/main arm64 libboost-program-options1.83.0 arm64 1.83.0-4.1 [331 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libboost-program-options1.83-dev arm64 1.83.0-4.1 [369 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libboost-program-options-dev arm64 1.83.0.2+b2 [3600 B] Get: 36 http://deb.debian.org/debian trixie/main arm64 rename all 2.02-1 [21.8 kB] Fetched 31.4 MB in 0s (178 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (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 ... 19914 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-1_arm64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-7_arm64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.4-5_arm64.deb ... Unpacking bsdextrautils (2.40.4-5) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-7_arm64.deb ... Unpacking m4 (1.4.19-7) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-3_all.deb ... Unpacking automake (1:1.17-3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.24.1_all.deb ... Unpacking libdebhelper-perl (13.24.1) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../21-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../23-libunistring5_1.3-1_arm64.deb ... Unpacking libunistring5:arm64 (1.3-1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../24-libicu72_72.1-6_arm64.deb ... Unpacking libicu72:arm64 (72.1-6) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.2+b2_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b2) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.23.1-1_arm64.deb ... Unpacking gettext (0.23.1-1) ... 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Reading state information... fakeroot is already the newest version (1.37-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/reproducible-path/dnaclust-3/ && 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 > ../dnaclust_3-7_source.changes dpkg-buildpackage: info: source package dnaclust dpkg-buildpackage: info: source version 3-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Saira Hussain dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_auto_clean make -j12 clean make[1]: Entering directory '/build/reproducible-path/dnaclust-3' rm -f dnaclust.o dnaclust fasta.o fastaselect.o fastaselect fastasort fastasort.o make[1]: Leaving directory '/build/reproducible-path/dnaclust-3' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j12 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/dnaclust-3' g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/dnaclust-3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -std=c++98 -O2 dnaclust.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/dnaclust-3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -std=c++98 -O2 fasta.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/dnaclust-3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -std=c++98 -O2 fastaselect.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/dnaclust-3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -std=c++98 -O2 fastasort.cpp -o fastasort.o In file included from /usr/include/boost/any/fwd.hpp:20, from /usr/include/boost/any.hpp:22, from /usr/include/boost/program_options/value_semantic.hpp:12, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from fastaselect.cpp:8: /usr/include/boost/any/fwd.hpp:34:1: note: '#pragma message: C++03 support is deprecated in Boost.Any 1.82 and will be removed in Boost.Any 1.84.' 34 | BOOST_PRAGMA_MESSAGE("C++03 support is deprecated in Boost.Any 1.82 and will be removed in Boost.Any 1.84.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/type_index.hpp:39:1: note: '#pragma message: C++03 support is deprecated in Boost.TypeIndex 1.82 and will be removed in Boost.TypeIndex 1.84.' 39 | BOOST_PRAGMA_MESSAGE("C++03 support is deprecated in Boost.TypeIndex 1.82 and will be removed in Boost.TypeIndex 1.84.") | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/any/fwd.hpp:20, from /usr/include/boost/any.hpp:22, from /usr/include/boost/program_options/value_semantic.hpp:12, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from fastasort.cpp:8: /usr/include/boost/any/fwd.hpp:34:1: note: '#pragma message: C++03 support is deprecated in Boost.Any 1.82 and will be removed in Boost.Any 1.84.' 34 | BOOST_PRAGMA_MESSAGE("C++03 support is deprecated in Boost.Any 1.82 and will be removed in Boost.Any 1.84.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/type_index.hpp:39:1: note: '#pragma message: C++03 support is deprecated in Boost.TypeIndex 1.82 and will be removed in Boost.TypeIndex 1.84.' 39 | BOOST_PRAGMA_MESSAGE("C++03 support is deprecated in Boost.TypeIndex 1.82 and will be removed in Boost.TypeIndex 1.84.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/container_hash/detail/requires_cxx11.hpp:18:1: note: '#pragma message: C++03 support was deprecated in Boost.ContainerHash 1.82 and will be removed in Boost.ContainerHash 1.84. Please open an issue in https://github.com/boostorg/container_hash if you want it retained.' 18 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.ContainerHash 1.82 and will be removed in Boost.ContainerHash 1.84. Please open an issue in https://github.com/boostorg/container_hash if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/container_hash/detail/requires_cxx11.hpp:18:1: note: '#pragma message: C++03 support was deprecated in Boost.ContainerHash 1.82 and will be removed in Boost.ContainerHash 1.84. Please open an issue in https://github.com/boostorg/container_hash if you want it retained.' 18 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.ContainerHash 1.82 and will be removed in Boost.ContainerHash 1.84. Please open an issue in https://github.com/boostorg/container_hash if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/function/detail/requires_cxx11.hpp:18:1: note: '#pragma message: C++03 support was deprecated in Boost.Function 1.82 and will be removed in Boost.Function 1.84. Please open an issue in https://github.com/boostorg/function if you want it retained.' 18 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.Function 1.82 and will be removed in Boost.Function 1.84. Please open an issue in https://github.com/boostorg/function if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/function/detail/requires_cxx11.hpp:18:1: note: '#pragma message: C++03 support was deprecated in Boost.Function 1.82 and will be removed in Boost.Function 1.84. Please open an issue in https://github.com/boostorg/function if you want it retained.' 18 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.Function 1.82 and will be removed in Boost.Function 1.84. Please open an issue in https://github.com/boostorg/function if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/bind/detail/requires_cxx11.hpp:18:1: note: '#pragma message: C++03 support was deprecated in Boost.Bind 1.82 and will be removed in Boost.Bind 1.84. Please open an issue in https://github.com/boostorg/bind if you want it retained.' 18 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.Bind 1.82 and will be removed in Boost.Bind 1.84. Please open an issue in https://github.com/boostorg/bind if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/bind/detail/requires_cxx11.hpp:18:1: note: '#pragma message: C++03 support was deprecated in Boost.Bind 1.82 and will be removed in Boost.Bind 1.84. Please open an issue in https://github.com/boostorg/bind if you want it retained.' 18 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.Bind 1.82 and will be removed in Boost.Bind 1.84. Please open an issue in https://github.com/boostorg/bind if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/lexical_cast.hpp:40:1: note: '#pragma message: C++03 support is deprecated in Boost.LexicalCast 1.82 and will be removed in Boost.LexicalCast 1.84.' 40 | BOOST_PRAGMA_MESSAGE("C++03 support is deprecated in Boost.LexicalCast 1.82 and will be removed in Boost.LexicalCast 1.84.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/lexical_cast.hpp:40:1: note: '#pragma message: C++03 support is deprecated in Boost.LexicalCast 1.82 and will be removed in Boost.LexicalCast 1.84.' 40 | BOOST_PRAGMA_MESSAGE("C++03 support is deprecated in Boost.LexicalCast 1.82 and will be removed in Boost.LexicalCast 1.84.") | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/any/fwd.hpp:20, from /usr/include/boost/any.hpp:22, from /usr/include/boost/program_options/value_semantic.hpp:12, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from dnaclust.cpp:14: /usr/include/boost/any/fwd.hpp:34:1: note: '#pragma message: C++03 support is deprecated in Boost.Any 1.82 and will be removed in Boost.Any 1.84.' 34 | BOOST_PRAGMA_MESSAGE("C++03 support is deprecated in Boost.Any 1.82 and will be removed in Boost.Any 1.84.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/type_index.hpp:39:1: note: '#pragma message: C++03 support is deprecated in Boost.TypeIndex 1.82 and will be removed in Boost.TypeIndex 1.84.' 39 | BOOST_PRAGMA_MESSAGE("C++03 support is deprecated in Boost.TypeIndex 1.82 and will be removed in Boost.TypeIndex 1.84.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/container_hash/detail/requires_cxx11.hpp:18:1: note: '#pragma message: C++03 support was deprecated in Boost.ContainerHash 1.82 and will be removed in Boost.ContainerHash 1.84. Please open an issue in https://github.com/boostorg/container_hash if you want it retained.' 18 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.ContainerHash 1.82 and will be removed in Boost.ContainerHash 1.84. Please open an issue in https://github.com/boostorg/container_hash if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/function/detail/requires_cxx11.hpp:18:1: note: '#pragma message: C++03 support was deprecated in Boost.Function 1.82 and will be removed in Boost.Function 1.84. Please open an issue in https://github.com/boostorg/function if you want it retained.' 18 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.Function 1.82 and will be removed in Boost.Function 1.84. Please open an issue in https://github.com/boostorg/function if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/bind/detail/requires_cxx11.hpp:18:1: note: '#pragma message: C++03 support was deprecated in Boost.Bind 1.82 and will be removed in Boost.Bind 1.84. Please open an issue in https://github.com/boostorg/bind if you want it retained.' 18 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.Bind 1.82 and will be removed in Boost.Bind 1.84. Please open an issue in https://github.com/boostorg/bind if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/lexical_cast.hpp:40:1: note: '#pragma message: C++03 support is deprecated in Boost.LexicalCast 1.82 and will be removed in Boost.LexicalCast 1.84.' 40 | BOOST_PRAGMA_MESSAGE("C++03 support is deprecated in Boost.LexicalCast 1.82 and will be removed in Boost.LexicalCast 1.84.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:19:1: note: '#pragma message: C++03 support was deprecated in Boost.SmartPtr 1.82 and will be removed in Boost.SmartPtr 1.84. Please open an issue in https://github.com/boostorg/smart_ptr if you want it retained.' 19 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.SmartPtr 1.82 and will be removed in Boost.SmartPtr 1.84. Please open an issue in https://github.com/boostorg/smart_ptr if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:19:1: note: '#pragma message: C++03 support was deprecated in Boost.SmartPtr 1.82 and will be removed in Boost.SmartPtr 1.84. Please open an issue in https://github.com/boostorg/smart_ptr if you want it retained.' 19 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.SmartPtr 1.82 and will be removed in Boost.SmartPtr 1.84. Please open an issue in https://github.com/boostorg/smart_ptr if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:19:1: note: '#pragma message: C++03 support was deprecated in Boost.SmartPtr 1.82 and will be removed in Boost.SmartPtr 1.84. Please open an issue in https://github.com/boostorg/smart_ptr if you want it retained.' 19 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.SmartPtr 1.82 and will be removed in Boost.SmartPtr 1.84. Please open an issue in https://github.com/boostorg/smart_ptr if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ dnaclust.cpp: In function 'void makeCluster()': dnaclust.cpp:1337:12: warning: variable 'num_threads_to_use' set but not used [-Wunused-but-set-variable] 1337 | size_t num_threads_to_use = num_threads; | ^~~~~~~~~~~~~~~~~~ dnaclust.cpp:1443:11: warning: variable 'num_threads_to_use' set but not used [-Wunused-but-set-variable] 1443 | int num_threads_to_use = num_threads; | ^~~~~~~~~~~~~~~~~~ dnaclust.cpp: In function 'int main(int, char**)': dnaclust.cpp:1945:11: warning: variable 'num_threads_to_use' set but not used [-Wunused-but-set-variable] 1945 | int num_threads_to_use = num_threads; | ^~~~~~~~~~~~~~~~~~ dnaclust.cpp:2135:14: warning: variable 'num_threads_to_use' set but not used [-Wunused-but-set-variable] 2135 | size_t num_threads_to_use = num_threads; | ^~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/dnaclust-3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -std=c++98 -O2 -Wl,-z,relro -Wl,-z,now fastasort.o fasta.o -lboost_program_options -o fastasort g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/dnaclust-3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -std=c++98 -O2 -Wl,-z,relro -Wl,-z,now fastaselect.o fasta.o -lboost_program_options -o fastaselect g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/dnaclust-3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -std=c++98 -O2 -Wl,-z,relro -Wl,-z,now dnaclust.o fasta.o -lboost_program_options -o dnaclust -lpthread make[1]: Leaving directory '/build/reproducible-path/dnaclust-3' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/dnaclust/ debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/dnaclust-3' dh_install prename 's/\.sh//' /build/reproducible-path/dnaclust-3/debian/dnaclust/usr/bin/* make[1]: Leaving directory '/build/reproducible-path/dnaclust-3' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz dh_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'dnaclust' in '../dnaclust_3-7_arm64.deb'. dpkg-deb: building package 'dnaclust-dbgsym' in '../dnaclust-dbgsym_3-7_arm64.deb'. dpkg-genbuildinfo --build=binary -O../dnaclust_3-7_arm64.buildinfo dpkg-genchanges --build=binary -O../dnaclust_3-7_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/246141 and its subdirectories I: Current time: Mon Mar 10 12:02:59 -12 2025 I: pbuilder-time-stamp: 1741651379 Tue Mar 11 00:02:59 UTC 2025 I: Signing ./b1/dnaclust_3-7_arm64.buildinfo as dnaclust_3-7_arm64.buildinfo.asc Tue Mar 11 00:02:59 UTC 2025 I: Signed ./b1/dnaclust_3-7_arm64.buildinfo as ./b1/dnaclust_3-7_arm64.buildinfo.asc Tue Mar 11 00:02:59 UTC 2025 - build #1 for dnaclust/trixie/arm64 on codethink04-arm64 done. Starting cleanup. All cleanup done. Tue Mar 11 00:02:59 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-UZabJWv0, removing. /srv/reproducible-results/rbuild-debian/r-b-build.evYOjC59: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Mar 11 00:03 b1 drwxr-xr-x 2 jenkins jenkins 4096 Mar 11 00:02 b2 -rw-r--r-- 1 jenkins jenkins 1977 Aug 9 2019 dnaclust_3-7.dsc -rw------- 1 jenkins jenkins 3069 Mar 11 00:02 rbuildlog.OYj7LcN /srv/reproducible-results/rbuild-debian/r-b-build.evYOjC59/b1: total 1360 -rw-r--r-- 1 jenkins jenkins 34219 Mar 11 00:03 build.log -rw-r--r-- 1 jenkins jenkins 1172676 Mar 11 00:03 dnaclust-dbgsym_3-7_arm64.deb -rw-r--r-- 1 jenkins jenkins 36972 Mar 11 00:03 dnaclust_3-7.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 1977 Mar 11 00:03 dnaclust_3-7.dsc -rw-r--r-- 1 jenkins jenkins 5052 Mar 11 00:03 dnaclust_3-7_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 5934 Mar 11 00:03 dnaclust_3-7_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1578 Mar 11 00:03 dnaclust_3-7_arm64.changes -rw-r--r-- 1 jenkins jenkins 107344 Mar 11 00:03 dnaclust_3-7_arm64.deb -rw-r--r-- 1 jenkins jenkins 1430 Mar 11 00:03 dnaclust_3-7_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.evYOjC59/b2: total 0 Tue Mar 11 00:03:00 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Mar 10 12:02:14 -12 2025 I: pbuilder-time-stamp: 1741651334 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 [dnaclust_3-7.dsc] I: copying [./dnaclust_3.orig.tar.gz] I: copying [./dnaclust_3-7.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./dnaclust_3-7.dsc: unsupported subcommand dpkg-source: info: extracting dnaclust in dnaclust-3 dpkg-source: info: unpacking dnaclust_3.orig.tar.gz dpkg-source: info: unpacking dnaclust_3-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_shel_path.patch dpkg-source: info: applying do_not_staically_linking.patch dpkg-source: info: applying resolve_name_space_conflict_fastasort.patch dpkg-source: info: applying build_with_gcc6.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/246141/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='5fb4c56ea91f4bd585633640c2ede2f6' 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='246141' 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.evYOjC59/pbuilderrc_xNk3 --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.evYOjC59/b1 --logfile b1/build.log dnaclust_3-7.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/246141/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 12), libboost-dev, libboost-program-options-dev, rename dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19914 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 (= 12); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-program-options-dev; however: Package libboost-program-options-dev is not installed. pbuilder-satisfydepends-dummy depends on rename; however: Package rename is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libboost-dev{a} libboost-program-options-dev{a} libboost-program-options1.83-dev{a} libboost-program-options1.83.0{a} libboost1.83-dev{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} rename{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 36 newly installed, 0 to remove and 0 not upgraded. Need to get 31.4 MB of archives. After unpacking 247 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.4-5 [92.0 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-7 [285 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.17-3 [862 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-4 [539 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 22 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b2 [630 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.24.1 [920 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libboost1.83-dev arm64 1.83.0-4.1 [10.6 MB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libboost-dev arm64 1.83.0.2+b2 [3828 B] Get: 33 http://deb.debian.org/debian trixie/main arm64 libboost-program-options1.83.0 arm64 1.83.0-4.1 [331 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libboost-program-options1.83-dev arm64 1.83.0-4.1 [369 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libboost-program-options-dev arm64 1.83.0.2+b2 [3600 B] Get: 36 http://deb.debian.org/debian trixie/main arm64 rename all 2.02-1 [21.8 kB] Fetched 31.4 MB in 0s (178 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (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 ... 19914 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-1_arm64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-7_arm64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.4-5_arm64.deb ... Unpacking bsdextrautils (2.40.4-5) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-7_arm64.deb ... Unpacking m4 (1.4.19-7) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-3_all.deb ... Unpacking automake (1:1.17-3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.24.1_all.deb ... Unpacking libdebhelper-perl (13.24.1) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../21-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../23-libunistring5_1.3-1_arm64.deb ... Unpacking libunistring5:arm64 (1.3-1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../24-libicu72_72.1-6_arm64.deb ... Unpacking libicu72:arm64 (72.1-6) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.2+b2_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b2) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.23.1-1_arm64.deb ... Unpacking gettext (0.23.1-1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.24.1_all.deb ... Unpacking debhelper (13.24.1) ... Selecting previously unselected package libboost1.83-dev:arm64. Preparing to unpack .../30-libboost1.83-dev_1.83.0-4.1_arm64.deb ... Unpacking libboost1.83-dev:arm64 (1.83.0-4.1) ... Selecting previously unselected package libboost-dev:arm64. Preparing to unpack .../31-libboost-dev_1.83.0.2+b2_arm64.deb ... Unpacking libboost-dev:arm64 (1.83.0.2+b2) ... Selecting previously unselected package libboost-program-options1.83.0:arm64. Preparing to unpack .../32-libboost-program-options1.83.0_1.83.0-4.1_arm64.deb ... Unpacking libboost-program-options1.83.0:arm64 (1.83.0-4.1) ... Selecting previously unselected package libboost-program-options1.83-dev:arm64. Preparing to unpack .../33-libboost-program-options1.83-dev_1.83.0-4.1_arm64.deb ... Unpacking libboost-program-options1.83-dev:arm64 (1.83.0-4.1) ... Selecting previously unselected package libboost-program-options-dev:arm64. Preparing to unpack .../34-libboost-program-options-dev_1.83.0.2+b2_arm64.deb ... Unpacking libboost-program-options-dev:arm64 (1.83.0.2+b2) ... Selecting previously unselected package rename. Preparing to unpack .../35-rename_2.02-1_all.deb ... Unpacking rename (2.02-1) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libboost-program-options1.83.0:arm64 (1.83.0-4.1) ... Setting up libboost1.83-dev:arm64 (1.83.0-4.1) ... Setting up libicu72:arm64 (72.1-6) ... Setting up bsdextrautils (2.40.4-5) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up libboost-program-options1.83-dev:arm64 (1.83.0-4.1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-7) ... Setting up rename (2.02-1) ... update-alternatives: using /usr/bin/file-rename to provide /usr/bin/rename (rename) in auto mode Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up libboost-program-options-dev:arm64 (1.83.0.2+b2) ... Setting up libunistring5:arm64 (1.3-1) ... Setting up autopoint (0.23.1-1) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libboost-dev:arm64 (1.83.0.2+b2) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b2) ... Setting up automake (1:1.17-3) ... 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 gettext (0.23.1-1) ... Setting up libtool (2.5.4-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.1) ... Processing triggers for libc-bin (2.40-7) ... 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 Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.37-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/reproducible-path/dnaclust-3/ && 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 > ../dnaclust_3-7_source.changes dpkg-buildpackage: info: source package dnaclust dpkg-buildpackage: info: source version 3-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Saira Hussain dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_auto_clean make -j12 clean make[1]: Entering directory '/build/reproducible-path/dnaclust-3' rm -f dnaclust.o dnaclust fasta.o fastaselect.o fastaselect fastasort fastasort.o make[1]: Leaving directory '/build/reproducible-path/dnaclust-3' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j12 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/dnaclust-3' g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/dnaclust-3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -std=c++98 -O2 dnaclust.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/dnaclust-3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -std=c++98 -O2 fasta.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/dnaclust-3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -std=c++98 -O2 fastaselect.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/dnaclust-3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -std=c++98 -O2 fastasort.cpp -o fastasort.o In file included from /usr/include/boost/any/fwd.hpp:20, from /usr/include/boost/any.hpp:22, from /usr/include/boost/program_options/value_semantic.hpp:12, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from fastaselect.cpp:8: /usr/include/boost/any/fwd.hpp:34:1: note: '#pragma message: C++03 support is deprecated in Boost.Any 1.82 and will be removed in Boost.Any 1.84.' 34 | BOOST_PRAGMA_MESSAGE("C++03 support is deprecated in Boost.Any 1.82 and will be removed in Boost.Any 1.84.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/type_index.hpp:39:1: note: '#pragma message: C++03 support is deprecated in Boost.TypeIndex 1.82 and will be removed in Boost.TypeIndex 1.84.' 39 | BOOST_PRAGMA_MESSAGE("C++03 support is deprecated in Boost.TypeIndex 1.82 and will be removed in Boost.TypeIndex 1.84.") | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/any/fwd.hpp:20, from /usr/include/boost/any.hpp:22, from /usr/include/boost/program_options/value_semantic.hpp:12, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from fastasort.cpp:8: /usr/include/boost/any/fwd.hpp:34:1: note: '#pragma message: C++03 support is deprecated in Boost.Any 1.82 and will be removed in Boost.Any 1.84.' 34 | BOOST_PRAGMA_MESSAGE("C++03 support is deprecated in Boost.Any 1.82 and will be removed in Boost.Any 1.84.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/type_index.hpp:39:1: note: '#pragma message: C++03 support is deprecated in Boost.TypeIndex 1.82 and will be removed in Boost.TypeIndex 1.84.' 39 | BOOST_PRAGMA_MESSAGE("C++03 support is deprecated in Boost.TypeIndex 1.82 and will be removed in Boost.TypeIndex 1.84.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/container_hash/detail/requires_cxx11.hpp:18:1: note: '#pragma message: C++03 support was deprecated in Boost.ContainerHash 1.82 and will be removed in Boost.ContainerHash 1.84. Please open an issue in https://github.com/boostorg/container_hash if you want it retained.' 18 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.ContainerHash 1.82 and will be removed in Boost.ContainerHash 1.84. Please open an issue in https://github.com/boostorg/container_hash if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/container_hash/detail/requires_cxx11.hpp:18:1: note: '#pragma message: C++03 support was deprecated in Boost.ContainerHash 1.82 and will be removed in Boost.ContainerHash 1.84. Please open an issue in https://github.com/boostorg/container_hash if you want it retained.' 18 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.ContainerHash 1.82 and will be removed in Boost.ContainerHash 1.84. Please open an issue in https://github.com/boostorg/container_hash if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/function/detail/requires_cxx11.hpp:18:1: note: '#pragma message: C++03 support was deprecated in Boost.Function 1.82 and will be removed in Boost.Function 1.84. Please open an issue in https://github.com/boostorg/function if you want it retained.' 18 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.Function 1.82 and will be removed in Boost.Function 1.84. Please open an issue in https://github.com/boostorg/function if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/function/detail/requires_cxx11.hpp:18:1: note: '#pragma message: C++03 support was deprecated in Boost.Function 1.82 and will be removed in Boost.Function 1.84. Please open an issue in https://github.com/boostorg/function if you want it retained.' 18 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.Function 1.82 and will be removed in Boost.Function 1.84. Please open an issue in https://github.com/boostorg/function if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/bind/detail/requires_cxx11.hpp:18:1: note: '#pragma message: C++03 support was deprecated in Boost.Bind 1.82 and will be removed in Boost.Bind 1.84. Please open an issue in https://github.com/boostorg/bind if you want it retained.' 18 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.Bind 1.82 and will be removed in Boost.Bind 1.84. Please open an issue in https://github.com/boostorg/bind if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/bind/detail/requires_cxx11.hpp:18:1: note: '#pragma message: C++03 support was deprecated in Boost.Bind 1.82 and will be removed in Boost.Bind 1.84. Please open an issue in https://github.com/boostorg/bind if you want it retained.' 18 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.Bind 1.82 and will be removed in Boost.Bind 1.84. Please open an issue in https://github.com/boostorg/bind if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/lexical_cast.hpp:40:1: note: '#pragma message: C++03 support is deprecated in Boost.LexicalCast 1.82 and will be removed in Boost.LexicalCast 1.84.' 40 | BOOST_PRAGMA_MESSAGE("C++03 support is deprecated in Boost.LexicalCast 1.82 and will be removed in Boost.LexicalCast 1.84.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/lexical_cast.hpp:40:1: note: '#pragma message: C++03 support is deprecated in Boost.LexicalCast 1.82 and will be removed in Boost.LexicalCast 1.84.' 40 | BOOST_PRAGMA_MESSAGE("C++03 support is deprecated in Boost.LexicalCast 1.82 and will be removed in Boost.LexicalCast 1.84.") | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/any/fwd.hpp:20, from /usr/include/boost/any.hpp:22, from /usr/include/boost/program_options/value_semantic.hpp:12, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from dnaclust.cpp:14: /usr/include/boost/any/fwd.hpp:34:1: note: '#pragma message: C++03 support is deprecated in Boost.Any 1.82 and will be removed in Boost.Any 1.84.' 34 | BOOST_PRAGMA_MESSAGE("C++03 support is deprecated in Boost.Any 1.82 and will be removed in Boost.Any 1.84.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/type_index.hpp:39:1: note: '#pragma message: C++03 support is deprecated in Boost.TypeIndex 1.82 and will be removed in Boost.TypeIndex 1.84.' 39 | BOOST_PRAGMA_MESSAGE("C++03 support is deprecated in Boost.TypeIndex 1.82 and will be removed in Boost.TypeIndex 1.84.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/container_hash/detail/requires_cxx11.hpp:18:1: note: '#pragma message: C++03 support was deprecated in Boost.ContainerHash 1.82 and will be removed in Boost.ContainerHash 1.84. Please open an issue in https://github.com/boostorg/container_hash if you want it retained.' 18 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.ContainerHash 1.82 and will be removed in Boost.ContainerHash 1.84. Please open an issue in https://github.com/boostorg/container_hash if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/function/detail/requires_cxx11.hpp:18:1: note: '#pragma message: C++03 support was deprecated in Boost.Function 1.82 and will be removed in Boost.Function 1.84. Please open an issue in https://github.com/boostorg/function if you want it retained.' 18 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.Function 1.82 and will be removed in Boost.Function 1.84. Please open an issue in https://github.com/boostorg/function if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/bind/detail/requires_cxx11.hpp:18:1: note: '#pragma message: C++03 support was deprecated in Boost.Bind 1.82 and will be removed in Boost.Bind 1.84. Please open an issue in https://github.com/boostorg/bind if you want it retained.' 18 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.Bind 1.82 and will be removed in Boost.Bind 1.84. Please open an issue in https://github.com/boostorg/bind if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/lexical_cast.hpp:40:1: note: '#pragma message: C++03 support is deprecated in Boost.LexicalCast 1.82 and will be removed in Boost.LexicalCast 1.84.' 40 | BOOST_PRAGMA_MESSAGE("C++03 support is deprecated in Boost.LexicalCast 1.82 and will be removed in Boost.LexicalCast 1.84.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:19:1: note: '#pragma message: C++03 support was deprecated in Boost.SmartPtr 1.82 and will be removed in Boost.SmartPtr 1.84. Please open an issue in https://github.com/boostorg/smart_ptr if you want it retained.' 19 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.SmartPtr 1.82 and will be removed in Boost.SmartPtr 1.84. Please open an issue in https://github.com/boostorg/smart_ptr if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:19:1: note: '#pragma message: C++03 support was deprecated in Boost.SmartPtr 1.82 and will be removed in Boost.SmartPtr 1.84. Please open an issue in https://github.com/boostorg/smart_ptr if you want it retained.' 19 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.SmartPtr 1.82 and will be removed in Boost.SmartPtr 1.84. Please open an issue in https://github.com/boostorg/smart_ptr if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:19:1: note: '#pragma message: C++03 support was deprecated in Boost.SmartPtr 1.82 and will be removed in Boost.SmartPtr 1.84. Please open an issue in https://github.com/boostorg/smart_ptr if you want it retained.' 19 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.SmartPtr 1.82 and will be removed in Boost.SmartPtr 1.84. Please open an issue in https://github.com/boostorg/smart_ptr if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ dnaclust.cpp: In function 'void makeCluster()': dnaclust.cpp:1337:12: warning: variable 'num_threads_to_use' set but not used [-Wunused-but-set-variable] 1337 | size_t num_threads_to_use = num_threads; | ^~~~~~~~~~~~~~~~~~ dnaclust.cpp:1443:11: warning: variable 'num_threads_to_use' set but not used [-Wunused-but-set-variable] 1443 | int num_threads_to_use = num_threads; | ^~~~~~~~~~~~~~~~~~ dnaclust.cpp: In function 'int main(int, char**)': dnaclust.cpp:1945:11: warning: variable 'num_threads_to_use' set but not used [-Wunused-but-set-variable] 1945 | int num_threads_to_use = num_threads; | ^~~~~~~~~~~~~~~~~~ dnaclust.cpp:2135:14: warning: variable 'num_threads_to_use' set but not used [-Wunused-but-set-variable] 2135 | size_t num_threads_to_use = num_threads; | ^~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/dnaclust-3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -std=c++98 -O2 -Wl,-z,relro -Wl,-z,now fastasort.o fasta.o -lboost_program_options -o fastasort g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/dnaclust-3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -std=c++98 -O2 -Wl,-z,relro -Wl,-z,now fastaselect.o fasta.o -lboost_program_options -o fastaselect g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/dnaclust-3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -std=c++98 -O2 -Wl,-z,relro -Wl,-z,now dnaclust.o fasta.o -lboost_program_options -o dnaclust -lpthread make[1]: Leaving directory '/build/reproducible-path/dnaclust-3' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/dnaclust/ debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/dnaclust-3' dh_install prename 's/\.sh//' /build/reproducible-path/dnaclust-3/debian/dnaclust/usr/bin/* make[1]: Leaving directory '/build/reproducible-path/dnaclust-3' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz dh_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'dnaclust' in '../dnaclust_3-7_arm64.deb'. dpkg-deb: building package 'dnaclust-dbgsym' in '../dnaclust-dbgsym_3-7_arm64.deb'. dpkg-genbuildinfo --build=binary -O../dnaclust_3-7_arm64.buildinfo dpkg-genchanges --build=binary -O../dnaclust_3-7_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/246141 and its subdirectories I: Current time: Mon Mar 10 12:02:59 -12 2025 I: pbuilder-time-stamp: 1741651379 Tue Mar 11 00:03:01 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Tue Mar 11 00:03:01 UTC 2025 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Tue Mar 11 00:03:01 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Tue Mar 11 00:03:01 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-QR8gVA' ==================================================================================== Mon Apr 13 06:25:59 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink03-arm64, called using "2 dnaclust trixie /srv/reproducible-results/rbuild-debian/r-b-build.evYOjC59 3-7" as arguments. Mon Apr 13 06:25:59 UTC 2026 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-QsmwtgUB" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Mon Apr 13 06:25:59 UTC 2026 I: Downloading source for trixie/dnaclust=3-7 Reading package lists... NOTICE: 'dnaclust' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/dnaclust.git Please use: git clone https://salsa.debian.org/med-team/dnaclust.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 62.4 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main dnaclust 3-7 (dsc) [1977 B] Get:2 http://deb.debian.org/debian trixie/main dnaclust 3-7 (tar) [23.5 kB] Get:3 http://deb.debian.org/debian trixie/main dnaclust 3-7 (diff) [37.0 kB] Fetched 62.4 kB in 0s (3799 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'dnaclust' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/dnaclust.git Please use: git clone https://salsa.debian.org/med-team/dnaclust.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 62.4 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main dnaclust 3-7 (dsc) [1977 B] Get:2 http://deb.debian.org/debian trixie/main dnaclust 3-7 (tar) [23.5 kB] Get:3 http://deb.debian.org/debian trixie/main dnaclust 3-7 (diff) [37.0 kB] Fetched 62.4 kB in 0s (3799 kB/s) Download complete and in download only mode ============================================================================= Re-Building dnaclust in trixie on arm64 on codethink03-arm64 now. Date: Mon Apr 13 07:26:00 BST 2026 Date UTC: Mon Apr 13 06:26:00 UTC 2026 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.evYOjC59 + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.evYOjC59/pbuilderrc_RMqL + case ${ARCH} in + case $ARCH in + locale=nl_BE + language=nl + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' dnaclust = debian-installer -o dnaclust = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' dnaclust = u-boot ']' + case "${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.evYOjC59/pbuilderrc_RMqL --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.evYOjC59/b2 --logfile b2/build.log dnaclust_3-7.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: Mon Apr 13 20:26:00 +14 2026 I: pbuilder-time-stamp: 1776061560 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 [dnaclust_3-7.dsc] I: copying [./dnaclust_3.orig.tar.gz] I: copying [./dnaclust_3-7.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./dnaclust_3-7.dsc: unsupported subcommand dpkg-source: info: extracting dnaclust in dnaclust-3 dpkg-source: info: unpacking dnaclust_3.orig.tar.gz dpkg-source: info: unpacking dnaclust_3-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_shel_path.patch dpkg-source: info: applying do_not_staically_linking.patch dpkg-source: info: applying resolve_name_space_conflict_fastasort.patch dpkg-source: info: applying build_with_gcc6.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/600495/tmp/hooks/D01_modify_environment starting debug: Running on codethink03-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Apr 13 06:26 /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/600495/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/600495/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]="aarch64-unknown-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=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=b72a26f5248b48a8a57a2e6c4a5ab658 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=600495 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.evYOjC59/pbuilderrc_RMqL --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.evYOjC59/b2 --logfile b2/build.log dnaclust_3-7.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/600495/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 12), libboost-dev, libboost-program-options-dev, rename dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19914 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 (= 12); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-program-options-dev; however: Package libboost-program-options-dev is not installed. pbuilder-satisfydepends-dummy depends on rename; however: Package rename is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libboost-dev{a} libboost-program-options-dev{a} libboost-program-options1.83-dev{a} libboost-program-options1.83.0{a} libboost1.83-dev{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} rename{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 36 newly installed, 0 to remove and 0 not upgraded. Need to get 31.4 MB of archives. After unpacking 247 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.4-5 [92.0 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-7 [285 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.17-3 [862 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-4 [539 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 22 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b2 [630 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.24.1 [920 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libboost1.83-dev arm64 1.83.0-4.1 [10.6 MB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libboost-dev arm64 1.83.0.2+b2 [3828 B] Get: 33 http://deb.debian.org/debian trixie/main arm64 libboost-program-options1.83.0 arm64 1.83.0-4.1 [331 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libboost-program-options1.83-dev arm64 1.83.0-4.1 [369 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libboost-program-options-dev arm64 1.83.0.2+b2 [3600 B] Get: 36 http://deb.debian.org/debian trixie/main arm64 rename all 2.02-1 [21.8 kB] Fetched 31.4 MB in 0s (85.4 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (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 ... 19914 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. 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Reading state information... fakeroot is already the newest version (1.37-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/600495/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/600495/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/dnaclust-3/ && 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 > ../dnaclust_3-7_source.changes dpkg-buildpackage: info: source package dnaclust dpkg-buildpackage: info: source version 3-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Saira Hussain dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_auto_clean make -j12 clean make[1]: Entering directory '/build/reproducible-path/dnaclust-3' rm -f dnaclust.o dnaclust fasta.o fastaselect.o fastaselect fastasort fastasort.o make[1]: Leaving directory '/build/reproducible-path/dnaclust-3' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j12 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/dnaclust-3' g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/dnaclust-3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -std=c++98 -O2 dnaclust.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/dnaclust-3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -std=c++98 -O2 fasta.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/dnaclust-3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -std=c++98 -O2 fastaselect.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/dnaclust-3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -std=c++98 -O2 fastasort.cpp -o fastasort.o In file included from /usr/include/boost/any/fwd.hpp:20, from /usr/include/boost/any.hpp:22, from /usr/include/boost/program_options/value_semantic.hpp:12, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from fastasort.cpp:8: /usr/include/boost/any/fwd.hpp:34:1: note: '#pragma message: C++03 support is deprecated in Boost.Any 1.82 and will be removed in Boost.Any 1.84.' 34 | BOOST_PRAGMA_MESSAGE("C++03 support is deprecated in Boost.Any 1.82 and will be removed in Boost.Any 1.84.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/type_index.hpp:39:1: note: '#pragma message: C++03 support is deprecated in Boost.TypeIndex 1.82 and will be removed in Boost.TypeIndex 1.84.' 39 | BOOST_PRAGMA_MESSAGE("C++03 support is deprecated in Boost.TypeIndex 1.82 and will be removed in Boost.TypeIndex 1.84.") | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/any/fwd.hpp:20, from /usr/include/boost/any.hpp:22, from /usr/include/boost/program_options/value_semantic.hpp:12, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from fastaselect.cpp:8: /usr/include/boost/any/fwd.hpp:34:1: note: '#pragma message: C++03 support is deprecated in Boost.Any 1.82 and will be removed in Boost.Any 1.84.' 34 | BOOST_PRAGMA_MESSAGE("C++03 support is deprecated in Boost.Any 1.82 and will be removed in Boost.Any 1.84.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/type_index.hpp:39:1: note: '#pragma message: C++03 support is deprecated in Boost.TypeIndex 1.82 and will be removed in Boost.TypeIndex 1.84.' 39 | BOOST_PRAGMA_MESSAGE("C++03 support is deprecated in Boost.TypeIndex 1.82 and will be removed in Boost.TypeIndex 1.84.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/container_hash/detail/requires_cxx11.hpp:18:1: note: '#pragma message: C++03 support was deprecated in Boost.ContainerHash 1.82 and will be removed in Boost.ContainerHash 1.84. Please open an issue in https://github.com/boostorg/container_hash if you want it retained.' 18 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.ContainerHash 1.82 and will be removed in Boost.ContainerHash 1.84. Please open an issue in https://github.com/boostorg/container_hash if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/container_hash/detail/requires_cxx11.hpp:18:1: note: '#pragma message: C++03 support was deprecated in Boost.ContainerHash 1.82 and will be removed in Boost.ContainerHash 1.84. Please open an issue in https://github.com/boostorg/container_hash if you want it retained.' 18 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.ContainerHash 1.82 and will be removed in Boost.ContainerHash 1.84. Please open an issue in https://github.com/boostorg/container_hash if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/function/detail/requires_cxx11.hpp:18:1: note: '#pragma message: C++03 support was deprecated in Boost.Function 1.82 and will be removed in Boost.Function 1.84. Please open an issue in https://github.com/boostorg/function if you want it retained.' 18 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.Function 1.82 and will be removed in Boost.Function 1.84. Please open an issue in https://github.com/boostorg/function if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/any/fwd.hpp:20, from /usr/include/boost/any.hpp:22, from /usr/include/boost/program_options/value_semantic.hpp:12, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from dnaclust.cpp:14: /usr/include/boost/any/fwd.hpp:34:1: note: '#pragma message: C++03 support is deprecated in Boost.Any 1.82 and will be removed in Boost.Any 1.84.' 34 | BOOST_PRAGMA_MESSAGE("C++03 support is deprecated in Boost.Any 1.82 and will be removed in Boost.Any 1.84.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/type_index.hpp:39:1: note: '#pragma message: C++03 support is deprecated in Boost.TypeIndex 1.82 and will be removed in Boost.TypeIndex 1.84.' 39 | BOOST_PRAGMA_MESSAGE("C++03 support is deprecated in Boost.TypeIndex 1.82 and will be removed in Boost.TypeIndex 1.84.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/function/detail/requires_cxx11.hpp:18:1: note: '#pragma message: C++03 support was deprecated in Boost.Function 1.82 and will be removed in Boost.Function 1.84. Please open an issue in https://github.com/boostorg/function if you want it retained.' 18 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.Function 1.82 and will be removed in Boost.Function 1.84. Please open an issue in https://github.com/boostorg/function if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/bind/detail/requires_cxx11.hpp:18:1: note: '#pragma message: C++03 support was deprecated in Boost.Bind 1.82 and will be removed in Boost.Bind 1.84. Please open an issue in https://github.com/boostorg/bind if you want it retained.' 18 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.Bind 1.82 and will be removed in Boost.Bind 1.84. Please open an issue in https://github.com/boostorg/bind if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/container_hash/detail/requires_cxx11.hpp:18:1: note: '#pragma message: C++03 support was deprecated in Boost.ContainerHash 1.82 and will be removed in Boost.ContainerHash 1.84. Please open an issue in https://github.com/boostorg/container_hash if you want it retained.' 18 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.ContainerHash 1.82 and will be removed in Boost.ContainerHash 1.84. Please open an issue in https://github.com/boostorg/container_hash if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/bind/detail/requires_cxx11.hpp:18:1: note: '#pragma message: C++03 support was deprecated in Boost.Bind 1.82 and will be removed in Boost.Bind 1.84. Please open an issue in https://github.com/boostorg/bind if you want it retained.' 18 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.Bind 1.82 and will be removed in Boost.Bind 1.84. Please open an issue in https://github.com/boostorg/bind if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/lexical_cast.hpp:40:1: note: '#pragma message: C++03 support is deprecated in Boost.LexicalCast 1.82 and will be removed in Boost.LexicalCast 1.84.' 40 | BOOST_PRAGMA_MESSAGE("C++03 support is deprecated in Boost.LexicalCast 1.82 and will be removed in Boost.LexicalCast 1.84.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/lexical_cast.hpp:40:1: note: '#pragma message: C++03 support is deprecated in Boost.LexicalCast 1.82 and will be removed in Boost.LexicalCast 1.84.' 40 | BOOST_PRAGMA_MESSAGE("C++03 support is deprecated in Boost.LexicalCast 1.82 and will be removed in Boost.LexicalCast 1.84.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/function/detail/requires_cxx11.hpp:18:1: note: '#pragma message: C++03 support was deprecated in Boost.Function 1.82 and will be removed in Boost.Function 1.84. Please open an issue in https://github.com/boostorg/function if you want it retained.' 18 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.Function 1.82 and will be removed in Boost.Function 1.84. Please open an issue in https://github.com/boostorg/function if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/bind/detail/requires_cxx11.hpp:18:1: note: '#pragma message: C++03 support was deprecated in Boost.Bind 1.82 and will be removed in Boost.Bind 1.84. Please open an issue in https://github.com/boostorg/bind if you want it retained.' 18 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.Bind 1.82 and will be removed in Boost.Bind 1.84. Please open an issue in https://github.com/boostorg/bind if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/lexical_cast.hpp:40:1: note: '#pragma message: C++03 support is deprecated in Boost.LexicalCast 1.82 and will be removed in Boost.LexicalCast 1.84.' 40 | BOOST_PRAGMA_MESSAGE("C++03 support is deprecated in Boost.LexicalCast 1.82 and will be removed in Boost.LexicalCast 1.84.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:19:1: note: '#pragma message: C++03 support was deprecated in Boost.SmartPtr 1.82 and will be removed in Boost.SmartPtr 1.84. Please open an issue in https://github.com/boostorg/smart_ptr if you want it retained.' 19 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.SmartPtr 1.82 and will be removed in Boost.SmartPtr 1.84. Please open an issue in https://github.com/boostorg/smart_ptr if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:19:1: note: '#pragma message: C++03 support was deprecated in Boost.SmartPtr 1.82 and will be removed in Boost.SmartPtr 1.84. Please open an issue in https://github.com/boostorg/smart_ptr if you want it retained.' 19 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.SmartPtr 1.82 and will be removed in Boost.SmartPtr 1.84. Please open an issue in https://github.com/boostorg/smart_ptr if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:19:1: note: '#pragma message: C++03 support was deprecated in Boost.SmartPtr 1.82 and will be removed in Boost.SmartPtr 1.84. Please open an issue in https://github.com/boostorg/smart_ptr if you want it retained.' 19 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.SmartPtr 1.82 and will be removed in Boost.SmartPtr 1.84. Please open an issue in https://github.com/boostorg/smart_ptr if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ dnaclust.cpp: In function 'void makeCluster()': dnaclust.cpp:1337:12: warning: variable 'num_threads_to_use' set but not used [-Wunused-but-set-variable] 1337 | size_t num_threads_to_use = num_threads; | ^~~~~~~~~~~~~~~~~~ dnaclust.cpp:1443:11: warning: variable 'num_threads_to_use' set but not used [-Wunused-but-set-variable] 1443 | int num_threads_to_use = num_threads; | ^~~~~~~~~~~~~~~~~~ dnaclust.cpp: In function 'int main(int, char**)': dnaclust.cpp:1945:11: warning: variable 'num_threads_to_use' set but not used [-Wunused-but-set-variable] 1945 | int num_threads_to_use = num_threads; | ^~~~~~~~~~~~~~~~~~ dnaclust.cpp:2135:14: warning: variable 'num_threads_to_use' set but not used [-Wunused-but-set-variable] 2135 | size_t num_threads_to_use = num_threads; | ^~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/dnaclust-3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -std=c++98 -O2 -Wl,-z,relro -Wl,-z,now fastasort.o fasta.o -lboost_program_options -o fastasort g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/dnaclust-3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -std=c++98 -O2 -Wl,-z,relro -Wl,-z,now fastaselect.o fasta.o -lboost_program_options -o fastaselect g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/dnaclust-3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -std=c++98 -O2 -Wl,-z,relro -Wl,-z,now dnaclust.o fasta.o -lboost_program_options -o dnaclust -lpthread make[1]: Leaving directory '/build/reproducible-path/dnaclust-3' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/dnaclust/ debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/dnaclust-3' dh_install prename 's/\.sh//' /build/reproducible-path/dnaclust-3/debian/dnaclust/usr/bin/* make[1]: Leaving directory '/build/reproducible-path/dnaclust-3' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz dh_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'dnaclust-dbgsym' in '../dnaclust-dbgsym_3-7_arm64.deb'. dpkg-deb: building package 'dnaclust' in '../dnaclust_3-7_arm64.deb'. dpkg-genbuildinfo --build=binary -O../dnaclust_3-7_arm64.buildinfo dpkg-genchanges --build=binary -O../dnaclust_3-7_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/600495/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/600495/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/600495 and its subdirectories I: Current time: Mon Apr 13 20:27:12 +14 2026 I: pbuilder-time-stamp: 1776061632 + false + set +x Mon Apr 13 06:27:12 UTC 2026 I: Signing ./b2/dnaclust_3-7_arm64.buildinfo as dnaclust_3-7_arm64.buildinfo.asc Mon Apr 13 06:27:12 UTC 2026 I: Signed ./b2/dnaclust_3-7_arm64.buildinfo as ./b2/dnaclust_3-7_arm64.buildinfo.asc Mon Apr 13 06:27:12 UTC 2026 - build #2 for dnaclust/trixie/arm64 on codethink03-arm64 done. Starting cleanup. All cleanup done. Mon Apr 13 06:27:12 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-QsmwtgUB, removing. /srv/reproducible-results/rbuild-debian/r-b-build.evYOjC59: total 52 drwxr-xr-x 2 jenkins jenkins 4096 Mar 11 00:03 b1 drwxr-xr-x 2 jenkins jenkins 4096 Mar 11 00:04 b2 -rw-r--r-- 1 jenkins jenkins 1977 Aug 9 2019 dnaclust_3-7.dsc -rw------- 1 jenkins jenkins 37589 Mar 11 00:03 rbuildlog.OYj7LcN /srv/reproducible-results/rbuild-debian/r-b-build.evYOjC59/b1: total 1368 -rw-r--r-- 1 jenkins jenkins 34219 Mar 11 00:03 build.log -rw-r--r-- 1 jenkins jenkins 1172676 Mar 11 00:03 dnaclust-dbgsym_3-7_arm64.deb -rw-r--r-- 1 jenkins jenkins 36972 Mar 11 00:03 dnaclust_3-7.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 1977 Mar 11 00:03 dnaclust_3-7.dsc -rw-r--r-- 1 jenkins jenkins 5052 Mar 11 00:03 dnaclust_3-7_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 5934 Mar 11 00:03 dnaclust_3-7_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1578 Mar 11 00:03 dnaclust_3-7_arm64.changes -rw-r--r-- 1 jenkins jenkins 107344 Mar 11 00:03 dnaclust_3-7_arm64.deb -rw-r--r-- 1 jenkins jenkins 1430 Mar 11 00:03 dnaclust_3-7_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.evYOjC59/b2: total 1360 -rw-r--r-- 1 jenkins jenkins 36157 Mar 11 00:04 build.log -rw-r--r-- 1 jenkins jenkins 1172676 Mar 11 00:04 dnaclust-dbgsym_3-7_arm64.deb -rw-r--r-- 1 jenkins jenkins 36972 Mar 11 00:04 dnaclust_3-7.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 1977 Mar 11 00:04 dnaclust_3-7.dsc -rw-r--r-- 1 jenkins jenkins 5052 Mar 11 00:04 dnaclust_3-7_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 5934 Mar 11 00:04 dnaclust_3-7_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1578 Mar 11 00:04 dnaclust_3-7_arm64.changes -rw-r--r-- 1 jenkins jenkins 107344 Mar 11 00:04 dnaclust_3-7_arm64.deb -rw-r--r-- 1 jenkins jenkins 1430 Mar 11 00:04 dnaclust_3-7_source.changes Tue Mar 11 00:04:16 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Tue Mar 11 00:04:17 UTC 2025 I: dnaclust_3-7_arm64.changes: Format: 1.8 Date: Thu, 08 Aug 2019 13:08:28 +0100 Source: dnaclust Binary: dnaclust dnaclust-dbgsym Architecture: arm64 Version: 3-7 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Saira Hussain Description: dnaclust - tool for clustering millions of short DNA sequences Changes: dnaclust (3-7) unstable; urgency=medium . * Team upload. . [ Saira Hussain ] * Add autopkgtests . [ Andreas Tille ] * debhelper-compat 12 * Standards-Version: 4.4.0 * Secure URI in copyright format * Remove trailing whitespace in debian/changelog * Remove trailing whitespace in debian/control * Use secure URI in debian/watch. Checksums-Sha1: 3f020b858a1bcd64c3ac4250a6d359b3b130f086 1172676 dnaclust-dbgsym_3-7_arm64.deb 36cfccbe1854a33309bc0dafb1a57fbc147937c0 5052 dnaclust_3-7_arm64.buildinfo ade534187e3820e1323189195a6f0c87108bf5d7 107344 dnaclust_3-7_arm64.deb Checksums-Sha256: 57d0173e82752cd44351acb7fa9f39353f0d9ea5ef8771e07589a247414a49af 1172676 dnaclust-dbgsym_3-7_arm64.deb 348c326ea3469afe9daa4ca951519db2a934d4a8dc3d9e0d8fc58380312a24a1 5052 dnaclust_3-7_arm64.buildinfo 9143f58169b4acb2e741ce644c79c211fb3b6f1174cf7d83719f05787ad07726 107344 dnaclust_3-7_arm64.deb Files: 46c7aaee3a916f3630879cea734e1df1 1172676 debug optional dnaclust-dbgsym_3-7_arm64.deb 6b78bdf2a802979ca4b237e62a5830b1 5052 science optional dnaclust_3-7_arm64.buildinfo 80fe8ef35cefe40cb47aaa1a76920290 107344 science optional dnaclust_3-7_arm64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/dnaclust_3-7.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/dnaclust_3-7.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/dnaclust_3-7.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/dnaclust_3-7.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/trixie/arm64/dnaclust_3-7_arm64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/dnaclust_3-7.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-03-11 00:03:00.109938736 +0000 +++ b2/build.log 2025-03-11 00:04:16.686481326 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Mar 10 12:02:14 -12 2025 -I: pbuilder-time-stamp: 1741651334 +I: Current time: Mon Apr 13 20:26:00 +14 2026 +I: pbuilder-time-stamp: 1776061560 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -27,52 +27,84 @@ dpkg-source: info: applying build_with_gcc6.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/246141/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/600495/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Apr 13 06:26 /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/600495/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/600495/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-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=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='5fb4c56ea91f4bd585633640c2ede2f6' - 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='246141' - PS1='# ' - PS2='> ' + INVOCATION_ID=b72a26f5248b48a8a57a2e6c4a5ab658 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=600495 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.evYOjC59/pbuilderrc_xNk3 --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.evYOjC59/b1 --logfile b1/build.log dnaclust_3-7.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.evYOjC59/pbuilderrc_RMqL --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.evYOjC59/b2 --logfile b2/build.log dnaclust_3-7.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/246141/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/600495/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -150,7 +182,7 @@ Get: 34 http://deb.debian.org/debian trixie/main arm64 libboost-program-options1.83-dev arm64 1.83.0-4.1 [369 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libboost-program-options-dev arm64 1.83.0.2+b2 [3600 B] Get: 36 http://deb.debian.org/debian trixie/main arm64 rename all 2.02-1 [21.8 kB] -Fetched 31.4 MB in 0s (178 MB/s) +Fetched 31.4 MB in 0s (85.4 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (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 ... 19914 files and directories currently installed.) @@ -315,7 +347,11 @@ fakeroot is already the newest version (1.37-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/reproducible-path/dnaclust-3/ && 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 > ../dnaclust_3-7_source.changes +I: user script /srv/workspace/pbuilder/600495/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/600495/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/dnaclust-3/ && 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 > ../dnaclust_3-7_source.changes dpkg-buildpackage: info: source package dnaclust dpkg-buildpackage: info: source version 3-7 dpkg-buildpackage: info: source distribution unstable @@ -347,7 +383,7 @@ from /usr/include/boost/program_options/value_semantic.hpp:12, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, - from fastaselect.cpp:8: + from fastasort.cpp:8: /usr/include/boost/any/fwd.hpp:34:1: note: '#pragma message: C++03 support is deprecated in Boost.Any 1.82 and will be removed in Boost.Any 1.84.' 34 | BOOST_PRAGMA_MESSAGE("C++03 support is deprecated in Boost.Any 1.82 and will be removed in Boost.Any 1.84.") | ^~~~~~~~~~~~~~~~~~~~ @@ -359,7 +395,7 @@ from /usr/include/boost/program_options/value_semantic.hpp:12, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, - from fastasort.cpp:8: + from fastaselect.cpp:8: /usr/include/boost/any/fwd.hpp:34:1: note: '#pragma message: C++03 support is deprecated in Boost.Any 1.82 and will be removed in Boost.Any 1.84.' 34 | BOOST_PRAGMA_MESSAGE("C++03 support is deprecated in Boost.Any 1.82 and will be removed in Boost.Any 1.84.") | ^~~~~~~~~~~~~~~~~~~~ @@ -375,21 +411,6 @@ /usr/include/boost/function/detail/requires_cxx11.hpp:18:1: note: '#pragma message: C++03 support was deprecated in Boost.Function 1.82 and will be removed in Boost.Function 1.84. Please open an issue in https://github.com/boostorg/function if you want it retained.' 18 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.Function 1.82 and will be removed in Boost.Function 1.84. Please open an issue in https://github.com/boostorg/function if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/function/detail/requires_cxx11.hpp:18:1: note: '#pragma message: C++03 support was deprecated in Boost.Function 1.82 and will be removed in Boost.Function 1.84. Please open an issue in https://github.com/boostorg/function if you want it retained.' - 18 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.Function 1.82 and will be removed in Boost.Function 1.84. Please open an issue in https://github.com/boostorg/function if you want it retained.") - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/bind/detail/requires_cxx11.hpp:18:1: note: '#pragma message: C++03 support was deprecated in Boost.Bind 1.82 and will be removed in Boost.Bind 1.84. Please open an issue in https://github.com/boostorg/bind if you want it retained.' - 18 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.Bind 1.82 and will be removed in Boost.Bind 1.84. Please open an issue in https://github.com/boostorg/bind if you want it retained.") - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/bind/detail/requires_cxx11.hpp:18:1: note: '#pragma message: C++03 support was deprecated in Boost.Bind 1.82 and will be removed in Boost.Bind 1.84. Please open an issue in https://github.com/boostorg/bind if you want it retained.' - 18 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.Bind 1.82 and will be removed in Boost.Bind 1.84. Please open an issue in https://github.com/boostorg/bind if you want it retained.") - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/lexical_cast.hpp:40:1: note: '#pragma message: C++03 support is deprecated in Boost.LexicalCast 1.82 and will be removed in Boost.LexicalCast 1.84.' - 40 | BOOST_PRAGMA_MESSAGE("C++03 support is deprecated in Boost.LexicalCast 1.82 and will be removed in Boost.LexicalCast 1.84.") - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/lexical_cast.hpp:40:1: note: '#pragma message: C++03 support is deprecated in Boost.LexicalCast 1.82 and will be removed in Boost.LexicalCast 1.84.' - 40 | BOOST_PRAGMA_MESSAGE("C++03 support is deprecated in Boost.LexicalCast 1.82 and will be removed in Boost.LexicalCast 1.84.") - | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/any/fwd.hpp:20, from /usr/include/boost/any.hpp:22, from /usr/include/boost/program_options/value_semantic.hpp:12, @@ -402,9 +423,24 @@ /usr/include/boost/type_index.hpp:39:1: note: '#pragma message: C++03 support is deprecated in Boost.TypeIndex 1.82 and will be removed in Boost.TypeIndex 1.84.' 39 | BOOST_PRAGMA_MESSAGE("C++03 support is deprecated in Boost.TypeIndex 1.82 and will be removed in Boost.TypeIndex 1.84.") | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/function/detail/requires_cxx11.hpp:18:1: note: '#pragma message: C++03 support was deprecated in Boost.Function 1.82 and will be removed in Boost.Function 1.84. Please open an issue in https://github.com/boostorg/function if you want it retained.' + 18 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.Function 1.82 and will be removed in Boost.Function 1.84. Please open an issue in https://github.com/boostorg/function if you want it retained.") + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/bind/detail/requires_cxx11.hpp:18:1: note: '#pragma message: C++03 support was deprecated in Boost.Bind 1.82 and will be removed in Boost.Bind 1.84. Please open an issue in https://github.com/boostorg/bind if you want it retained.' + 18 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.Bind 1.82 and will be removed in Boost.Bind 1.84. Please open an issue in https://github.com/boostorg/bind if you want it retained.") + | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/container_hash/detail/requires_cxx11.hpp:18:1: note: '#pragma message: C++03 support was deprecated in Boost.ContainerHash 1.82 and will be removed in Boost.ContainerHash 1.84. Please open an issue in https://github.com/boostorg/container_hash if you want it retained.' 18 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.ContainerHash 1.82 and will be removed in Boost.ContainerHash 1.84. Please open an issue in https://github.com/boostorg/container_hash if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/bind/detail/requires_cxx11.hpp:18:1: note: '#pragma message: C++03 support was deprecated in Boost.Bind 1.82 and will be removed in Boost.Bind 1.84. Please open an issue in https://github.com/boostorg/bind if you want it retained.' + 18 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.Bind 1.82 and will be removed in Boost.Bind 1.84. Please open an issue in https://github.com/boostorg/bind if you want it retained.") + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/lexical_cast.hpp:40:1: note: '#pragma message: C++03 support is deprecated in Boost.LexicalCast 1.82 and will be removed in Boost.LexicalCast 1.84.' + 40 | BOOST_PRAGMA_MESSAGE("C++03 support is deprecated in Boost.LexicalCast 1.82 and will be removed in Boost.LexicalCast 1.84.") + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/lexical_cast.hpp:40:1: note: '#pragma message: C++03 support is deprecated in Boost.LexicalCast 1.82 and will be removed in Boost.LexicalCast 1.84.' + 40 | BOOST_PRAGMA_MESSAGE("C++03 support is deprecated in Boost.LexicalCast 1.82 and will be removed in Boost.LexicalCast 1.84.") + | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/function/detail/requires_cxx11.hpp:18:1: note: '#pragma message: C++03 support was deprecated in Boost.Function 1.82 and will be removed in Boost.Function 1.84. Please open an issue in https://github.com/boostorg/function if you want it retained.' 18 | BOOST_PRAGMA_MESSAGE("C++03 support was deprecated in Boost.Function 1.82 and will be removed in Boost.Function 1.84. Please open an issue in https://github.com/boostorg/function if you want it retained.") | ^~~~~~~~~~~~~~~~~~~~ @@ -471,8 +507,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'dnaclust' in '../dnaclust_3-7_arm64.deb'. dpkg-deb: building package 'dnaclust-dbgsym' in '../dnaclust-dbgsym_3-7_arm64.deb'. +dpkg-deb: building package 'dnaclust' in '../dnaclust_3-7_arm64.deb'. dpkg-genbuildinfo --build=binary -O../dnaclust_3-7_arm64.buildinfo dpkg-genchanges --build=binary -O../dnaclust_3-7_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -480,12 +516,14 @@ 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/600495/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/600495/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/246141 and its subdirectories -I: Current time: Mon Mar 10 12:02:59 -12 2025 -I: pbuilder-time-stamp: 1741651379 +I: removing directory /srv/workspace/pbuilder/600495 and its subdirectories +I: Current time: Mon Apr 13 20:27:12 +14 2026 +I: pbuilder-time-stamp: 1776061632 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/dnaclust_3-7.diff: 78.0% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/dnaclust_3-7.diff.gz b2/build.log: 81.2% -- replaced with stdout Compressing the 1st log... b1/build.log: 82.1% -- replaced with stdout Tue Mar 11 00:04:18 UTC 2025 I: diffoscope 289 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_dnaclust_trixie_arm64_1741651458 + touch /var/log/reproducible-builds/diffoscope_stamp_dnaclust_trixie_arm64_1741651458 + RESULT=0 + systemd-run '--description=diffoscope on dnaclust/3-7 in trixie/arm64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-arm64_8-53077 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.evYOjC59 --run-session -c jenkins-reproducible-trixie-diffoscope-4bac8521-1e71-482d-8754-dc2105cbb38d -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.evYOjC59/dbd-tmp-18xIw14 ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.evYOjC59/dnaclust_3-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.evYOjC59/dnaclust_3-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.evYOjC59/dnaclust_3-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.evYOjC59/b1/dnaclust_3-7_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.evYOjC59/b2/dnaclust_3-7_arm64.changes' + false + set +x Running as unit: rb-diffoscope-arm64_8-53077.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.evYOjC59/dnaclust_3-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.evYOjC59/dnaclust_3-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.evYOjC59/dnaclust_3-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.evYOjC59/b1/dnaclust_3-7_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.evYOjC59/b2/dnaclust_3-7_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call 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: 236ms CPU time consumed: 237ms _ _ _ __| |_ __ __ _ ___| |_ _ ___| |_ / _` | '_ \ / _` |/ __| | | | / __| __| | (_| | | | | (_| | (__| | |_| \__ \ |_ \__,_|_| |_|\__,_|\___|_|\__,_|___/\__| Tue Mar 11 00:04:19 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists. Tue Mar 11 00:04:19 UTC 2025 I: dnaclust from trixie built successfully and reproducibly on arm64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-03-11 00:04:19] INFO: Starting at 2025-03-11 00:04:19.776899 [2025-03-11 00:04:19] INFO: Generating the pages of 1 package(s) [2025-03-11 00:04:20] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/arm64/dnaclust didn't produce a buildlog, even though it has been built. [2025-03-11 00:04:20] INFO: Finished at 2025-03-11 00:04:20.336639, took: 0:00:00.559746 Tue Mar 11 00:04:20 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/arm64/dnaclust.html Tue Mar 11 00:04:20 UTC 2025 I: Submitting .buildinfo files to external archives: Tue Mar 11 00:04:20 UTC 2025 I: Submitting 8.0K b1/dnaclust_3-7_arm64.buildinfo.asc https://buildinfo.debian.net/36cfccbe1854a33309bc0dafb1a57fbc147937c0/dnaclust_3-7_arm64 Tue Mar 11 00:04:21 UTC 2025 I: Submitting 8.0K b2/dnaclust_3-7_arm64.buildinfo.asc https://buildinfo.debian.net/135cd1c4f5e402405bc0f3c388a70aa5612eb777/dnaclust_3-7_arm64 Tue Mar 11 00:04:23 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Mar 11 00:04:23 UTC 2025 I: Done submitting .buildinfo files. Tue Mar 11 00:04:23 UTC 2025 I: Removing signed dnaclust_3-7_arm64.buildinfo.asc files: removed './b1/dnaclust_3-7_arm64.buildinfo.asc' removed './b2/dnaclust_3-7_arm64.buildinfo.asc' 1741651463 arm64 trixie dnaclust Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/dnaclust_3-7.rbuild.log: 78.0% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/dnaclust_3-7.rbuild.log.gz [2025-03-11 00:04:23] INFO: Starting at 2025-03-11 00:04:23.337684 [2025-03-11 00:04:23] INFO: Generating the pages of 1 package(s) [2025-03-11 00:04:23] INFO: Finished at 2025-03-11 00:04:23.963272, took: 0:00:00.625595 All cleanup done. Tue Mar 11 00:04:24 UTC 2025 - total duration: 0h 2m 26s. Tue Mar 11 00:04:24 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-i49Kxmxk, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 2min 30.647s CPU time consumed: 7.544s