Tue Apr 30 06:57:06 UTC 2024 I: starting to build dnaclust/trixie/armhf on jenkins on '2024-04-30 06:56' Tue Apr 30 06:57:06 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_16/4671/console.log Tue Apr 30 06:57:06 UTC 2024 I: Downloading source for trixie/dnaclust=3-7 --2024-04-30 06:57:06-- 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% 307M=0s 2024-04-30 06:57:06 (307 MB/s) - ‘dnaclust_3-7.dsc’ saved [1977/1977] Tue Apr 30 06:57:06 UTC 2024 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 Apr 30 06:57:06 UTC 2024 I: Checking whether the package is not for us Tue Apr 30 06:57:06 UTC 2024 I: Starting 1st build on remote node virt32b-armhf-rb.debian.net. Tue Apr 30 06:57:06 UTC 2024 I: Preparing to do remote build '1' on virt32b-armhf-rb.debian.net. Tue Apr 30 06:59:13 UTC 2024 I: Deleting $TMPDIR on virt32b-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Apr 29 18:57:12 -12 2024 I: pbuilder-time-stamp: 1714460232 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 gpgv: Signature made Fri Aug 9 09:22:11 2019 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tillea@rki.de" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./dnaclust_3-7.dsc: no acceptable signature found 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/6100/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='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='1b4268fa3e924eb380bc8af36ddcea12' 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='6100' 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.KUryA65T/pbuilderrc_k0ir --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.KUryA65T/b1 --logfile b1/build.log dnaclust_3-7.dsc' SUDO_GID='112' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt32b 6.1.0-20-armmp-lpae #1 SMP Debian 6.1.85-1 (2024-04-11) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 26 11:24 /bin -> usr/bin I: user script /srv/workspace/pbuilder/6100/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: armhf 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 ... 19470 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} libsub-override-perl{a} libtool{a} libuchardet0{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 29.7 MB of archives. After unpacking 235 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf libmagic1t64 armhf 1:5.45-3 [98.1 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-3 [42.0 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.21-14+b1 [157 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-3 [1088 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.39.3-6 [81.2 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.7-2 [33.3 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.12.0-3 [1367 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian trixie/main armhf libelf1t64 armhf 0.191-1+b1 [183 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-4+b1 [9070 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.9.14+dfsg-1.3+b3 [598 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.21-14+b1 [1230 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf debhelper all 13.15.3 [901 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf libboost1.83-dev armhf 1.83.0-2+b2 [10.6 MB] Get: 32 http://deb.debian.org/debian trixie/main armhf libboost-dev armhf 1.83.0.2+b2 [3832 B] Get: 33 http://deb.debian.org/debian trixie/main armhf libboost-program-options1.83.0 armhf 1.83.0-2+b2 [326 kB] Get: 34 http://deb.debian.org/debian trixie/main armhf libboost-program-options1.83-dev armhf 1.83.0-2+b2 [370 kB] Get: 35 http://deb.debian.org/debian trixie/main armhf libboost-program-options-dev armhf 1.83.0.2+b2 [3604 B] Get: 36 http://deb.debian.org/debian trixie/main armhf rename all 2.02-1 [21.8 kB] Fetched 29.7 MB in 1s (35.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19470 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_armhf.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:armhf. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_armhf.deb ... Unpacking libmagic1t64:armhf (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_armhf.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_armhf.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-3_armhf.deb ... Unpacking groff-base (1.23.0-3) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.39.3-6_armhf.deb ... Unpacking bsdextrautils (2.39.3-6) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../08-libpipeline1_1.5.7-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.0-3_armhf.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_armhf.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... 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%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... 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 libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:armhf. Preparing to unpack .../22-libelf1t64_0.191-1+b1_armhf.deb ... Unpacking libelf1t64:armhf (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b2_armhf.deb ... Unpacking dwz (0.15-1+b2) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../24-libicu72_72.1-4+b1_armhf.deb ... Unpacking libicu72:armhf (72.1-4+b1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.3+b3_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-14+b1_armhf.deb ... Unpacking gettext (0.21-14+b1) ... 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_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package libboost1.83-dev:armhf. Preparing to unpack .../30-libboost1.83-dev_1.83.0-2+b2_armhf.deb ... Unpacking libboost1.83-dev:armhf (1.83.0-2+b2) ... Selecting previously unselected package libboost-dev:armhf. Preparing to unpack .../31-libboost-dev_1.83.0.2+b2_armhf.deb ... Unpacking libboost-dev:armhf (1.83.0.2+b2) ... Selecting previously unselected package libboost-program-options1.83.0:armhf. Preparing to unpack .../32-libboost-program-options1.83.0_1.83.0-2+b2_armhf.deb ... Unpacking libboost-program-options1.83.0:armhf (1.83.0-2+b2) ... Selecting previously unselected package libboost-program-options1.83-dev:armhf. Preparing to unpack .../33-libboost-program-options1.83-dev_1.83.0-2+b2_armhf.deb ... Unpacking libboost-program-options1.83-dev:armhf (1.83.0-2+b2) ... Selecting previously unselected package libboost-program-options-dev:armhf. Preparing to unpack .../34-libboost-program-options-dev_1.83.0.2+b2_armhf.deb ... Unpacking libboost-program-options-dev:armhf (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:armhf (1.5.7-2) ... Setting up libboost-program-options1.83.0:armhf (1.83.0-2+b2) ... Setting up libboost1.83-dev:armhf (1.83.0-2+b2) ... Setting up libicu72:armhf (72.1-4+b1) ... Setting up bsdextrautils (2.39.3-6) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libmagic1t64:armhf (1:5.45-3) ... Setting up libboost-program-options1.83-dev:armhf (1.83.0-2+b2) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... 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) ... Setting up libelf1t64:armhf (0.191-1+b1) ... Setting up autotools-dev (20220109.1) ... Setting up libboost-program-options-dev:armhf (1.83.0.2+b2) ... Setting up autopoint (0.21-14) ... Setting up autoconf (2.71-3) ... Setting up dwz (0.15-1+b2) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:armhf (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libboost-dev:armhf (1.83.0.2+b2) ... Setting up libxml2:armhf (2.9.14+dfsg-1.3+b3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.15.3) ... Processing triggers for libc-bin (2.37-18) ... 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 (1.33-1). 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 armhf fakeroot debian/rules clean dh clean dh_auto_clean make -j3 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 build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j3 "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 -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 -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 -Wall -pedantic -std=c++98 -O2 fastaselect.cpp 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.") | ^~~~~~~~~~~~~~~~~~~~ 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/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/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/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/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.") | ^~~~~~~~~~~~~~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/dnaclust-3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -std=c++98 -O2 fastasort.cpp -o fastasort.o /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; | ^~~~~~~~~~~~~~~~~~ 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/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.") | ^~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/dnaclust-3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -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 -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 fakeroot debian/rules binary dh binary dh_testroot 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: debian/dnaclust/usr/bin/dnaclust contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'dnaclust' in '../dnaclust_3-7_armhf.deb'. dpkg-deb: building package 'dnaclust-dbgsym' in '../dnaclust-dbgsym_3-7_armhf.deb'. dpkg-genbuildinfo --build=binary -O../dnaclust_3-7_armhf.buildinfo dpkg-genchanges --build=binary -O../dnaclust_3-7_armhf.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/6100 and its subdirectories I: Current time: Mon Apr 29 18:59:01 -12 2024 I: pbuilder-time-stamp: 1714460341 Tue Apr 30 06:59:16 UTC 2024 I: 1st build successful. Starting 2nd build on remote node virt64z-armhf-rb.debian.net. Tue Apr 30 06:59:16 UTC 2024 I: Preparing to do remote build '2' on virt64z-armhf-rb.debian.net. Tue Apr 30 07:01:05 UTC 2024 I: Deleting $TMPDIR on virt64z-armhf-rb.debian.net. Tue Apr 30 07:01:08 UTC 2024 I: dnaclust_3-7_armhf.changes: Format: 1.8 Date: Thu, 08 Aug 2019 13:08:28 +0100 Source: dnaclust Binary: dnaclust dnaclust-dbgsym Architecture: armhf 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: dde28226cfd02df46ad12265c35ae864314c1aa2 1127160 dnaclust-dbgsym_3-7_armhf.deb 47d3948a9545ee7a1fef5e2d875c23afb26aed5a 5180 dnaclust_3-7_armhf.buildinfo cf0d2325190903b3970cb15e87edb898f9e412e5 103844 dnaclust_3-7_armhf.deb Checksums-Sha256: cc968c31ad4ca39b65a2189450b2939f7fd547ad971952046d922f25937caa60 1127160 dnaclust-dbgsym_3-7_armhf.deb 13d0330da3c96ed54fb0be4662dfe5d61a252ea845afb8ad2cc1e20b576d2b03 5180 dnaclust_3-7_armhf.buildinfo f914bbf87c9b7828144b770a414f07208adc3d6d7ec4ee2e5da0e90404cf6e3a 103844 dnaclust_3-7_armhf.deb Files: 0ec9db38217ca48c87642cc3a27f63e9 1127160 debug optional dnaclust-dbgsym_3-7_armhf.deb 9ead9935580adaf7b762cefb4e2b76cf 5180 science optional dnaclust_3-7_armhf.buildinfo 687b929b9b109d323136556431bc65f9 103844 science optional dnaclust_3-7_armhf.deb Tue Apr 30 07:01:09 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-armhf_16-4671.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.KUryA65T/dnaclust_3-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.KUryA65T/dnaclust_3-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.KUryA65T/dnaclust_3-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.KUryA65T/b1/dnaclust_3-7_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.KUryA65T/b2/dnaclust_3-7_armhf.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.457s) 0.457s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.034s) 0.034s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 859ms CPU time consumed: 859ms Tue Apr 30 07:01:10 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Tue Apr 30 07:01:10 UTC 2024 I: dnaclust from trixie built successfully and reproducibly on armhf. Tue Apr 30 07:01:12 UTC 2024 I: Submitting .buildinfo files to external archives: Tue Apr 30 07:01:12 UTC 2024 I: Submitting 8.0K b1/dnaclust_3-7_armhf.buildinfo.asc Tue Apr 30 07:01:13 UTC 2024 I: Submitting 8.0K b2/dnaclust_3-7_armhf.buildinfo.asc Tue Apr 30 07:01:15 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Apr 30 07:01:15 UTC 2024 I: Done submitting .buildinfo files. Tue Apr 30 07:01:15 UTC 2024 I: Removing signed dnaclust_3-7_armhf.buildinfo.asc files: removed './b1/dnaclust_3-7_armhf.buildinfo.asc' removed './b2/dnaclust_3-7_armhf.buildinfo.asc'