Tue Apr 23 14:16:24 UTC 2024 I: starting to build clonalframeml/trixie/armhf on jenkins on '2024-04-23 14:15' Tue Apr 23 14:16:24 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_12/2622/console.log Tue Apr 23 14:16:24 UTC 2024 I: Downloading source for trixie/clonalframeml=1.13-1 --2024-04-23 14:16:25-- http://deb.debian.org/debian/pool/main/c/clonalframeml/clonalframeml_1.13-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2019 (2.0K) [text/prs.lines.tag] Saving to: ‘clonalframeml_1.13-1.dsc’ 0K . 100% 221M=0s 2024-04-23 14:16:25 (221 MB/s) - ‘clonalframeml_1.13-1.dsc’ saved [2019/2019] Tue Apr 23 14:16:25 UTC 2024 I: clonalframeml_1.13-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: clonalframeml Binary: clonalframeml Architecture: any Version: 1.13-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/xavierdidelot/ClonalFrameML Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/clonalframeml Vcs-Git: https://salsa.debian.org/med-team/clonalframeml.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13) Package-List: clonalframeml deb science optional arch=any Checksums-Sha1: 034b97be56ade035680b9e4ee773c92d7e686c87 113209 clonalframeml_1.13.orig.tar.gz e9cad3beba3cf119dce7940f9ef5d2372c8ce00f 5344 clonalframeml_1.13-1.debian.tar.xz Checksums-Sha256: 6056109380c695020afa0c26f4ce49dcb9267f1a8f26dfb42629bfa63ac25e6e 113209 clonalframeml_1.13.orig.tar.gz 2f982b33620b13e1fb75f0aebf208f8f9b628f54c7635f4250375d7bccd7d88a 5344 clonalframeml_1.13-1.debian.tar.xz Files: 997e1702db1777b52b4c1ab083b4876d 113209 clonalframeml_1.13.orig.tar.gz 9ebd3a4d5e02de37bd17c12fa5b5139a 5344 clonalframeml_1.13-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmW7jggRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHKBw/+IdIvSm0TEMnfPGJBlqgAHC/k3JkAB2+H 3K03rqaDwQKd89TeBjyQ0xli10NKFLdJ4h/+oqz4csQf6A5xiEOQsw17wfpIdJr/ bF56eh83099V62bNpvRjIHV3iWKHxbDYy6Xa7IZYTbsyOXYBEEkrpuiokWIe7PQQ CXxB0KhbHCpXq33o4MiiFrQpuVQpISVa7EHmivE9ylceAdtBPg75PrYnYI+S4Pgl VOw44TMQg7lO3uuvp04Qx+RAbKEKAYt+C/50929aokZzaLWiHuEom+/B+ElWy5Va N7ipR1UnpFCZ7eeCAzRJoh3Ov3ycGmpVtAcYsrP/KFJbrdqzwDDpEWM8HpVLj2hA VnhCStxZRbpbHBOYWTnAPcU24f8MZFVLhdaIVgXhPDAlM6rpOF+ul66NZUi72O0r RHXm0pey1MpL4Wh2HI/i5dsu0oHUPA65gY2OlHdB7ZpfZg91qD8WVYt6SdBLsDII PuihIytbBNibSzDcGIElSeCkNrUSpdJbUNQTCeZ0yCCPlWAsYsMFmqithZYHoh7H OaXCPDYifXWaDwDVZWjaOs9iW3O4U+UnOrjVG2n3kBDNbk//cQ7OQLSYcj5RHjG3 OwZdWAffaHsbIgMEWB36VA4OGE5Zyb/FPlFdmLGLMxzRx8NAG0JW+u3mEUVcjXhV Lo34CN3AiGo= =uEMc -----END PGP SIGNATURE----- Tue Apr 23 14:16:25 UTC 2024 I: Checking whether the package is not for us Tue Apr 23 14:16:25 UTC 2024 I: Starting 1st build on remote node virt64a-armhf-rb.debian.net. Tue Apr 23 14:16:25 UTC 2024 I: Preparing to do remote build '1' on virt64a-armhf-rb.debian.net. Tue Apr 23 14:19:17 UTC 2024 I: Deleting $TMPDIR on virt64a-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Apr 23 02:16:32 -12 2024 I: pbuilder-time-stamp: 1713881792 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 [clonalframeml_1.13-1.dsc] I: copying [./clonalframeml_1.13.orig.tar.gz] I: copying [./clonalframeml_1.13-1.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Feb 1 12:26:48 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./clonalframeml_1.13-1.dsc: no acceptable signature found dpkg-source: info: extracting clonalframeml in clonalframeml-1.13 dpkg-source: info: unpacking clonalframeml_1.13.orig.tar.gz dpkg-source: info: unpacking clonalframeml_1.13-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying cross.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/27619/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='3a6d040e63cf433284ef4b3da48b0616' 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='27619' 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.DLyTFTZF/pbuilderrc_SGgB --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.DLyTFTZF/b1 --logfile b1/build.log clonalframeml_1.13-1.dsc' SUDO_GID='114' SUDO_UID='108' 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 virt64a 6.1.0-20-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 23 11:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/27619/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 (= 13) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19635 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. 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} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{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, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 18.3 MB of archives. After unpacking 68.5 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 1:5.45-2+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf libmagic1 armhf 1:5.45-2+b1 [97.9 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-2+b1 [42.2 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 libelf1 armhf 0.190-1+b1 [171 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1 [101 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+b2 [599 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] Fetched 18.3 MB in 1s (34.5 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 ... 19635 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%3a5.45-2+b1_armhf.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../02-libmagic1_1%3a5.45-2+b1_armhf.deb ... Unpacking libmagic1:armhf (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-2+b1_armhf.deb ... Unpacking file (1:5.45-2+b1) ... 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 libelf1:armhf. Preparing to unpack .../22-libelf1_0.190-1+b1_armhf.deb ... Unpacking libelf1:armhf (0.190-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1_armhf.deb ... Unpacking dwz (0.15-1) ... 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+b2_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.3+b2) ... 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) ... Setting up libpipeline1:armhf (1.5.7-2) ... Setting up libicu72:armhf (72.1-4+b1) ... Setting up bsdextrautils (2.39.3-6) ... Setting up libmagic-mgc (1:5.45-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libmagic1:armhf (1:5.45-2+b1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-2+b1) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-14) ... Setting up autoconf (2.71-3) ... 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 libelf1:armhf (0.190-1+b1) ... Setting up libxml2:armhf (2.9.14+dfsg-1.3+b2) ... 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 dwz (0.15-1) ... 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 (2.37-15) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/clonalframeml-1.13/ && 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 > ../clonalframeml_1.13-1_source.changes dpkg-buildpackage: info: source package clonalframeml dpkg-buildpackage: info: source version 1.13-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src cd src && make -j3 clean make[1]: Entering directory '/build/reproducible-path/clonalframeml-1.13/src' rm -f main.o make[1]: Leaving directory '/build/reproducible-path/clonalframeml-1.13/src' dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src debian/rules binary dh binary --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src dh_auto_configure -O--sourcedirectory=src debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/clonalframeml-1.13' # upstream is querying Git for a revision which is not possible here # that's why we are using the Debian revision echo '#define ClonalFrameML_GITRevision "v1.13-1"' > src/version.h dh_auto_build cd src && make -j3 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/clonalframeml-1.13/src' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalframeml-1.13=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -c -o main.o main.cpp In file included from /usr/include/c++/13/vector:72, from myutils/newick.h:11, from main.h:23, from main.cpp:19: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘std::vector ClonalFrameBaumWelch::maximize_likelihood(const std::vector&)’ at main.h:223:23: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘std::vector ClonalFrameBaumWelch::maximize_likelihood(const std::vector&)’ at main.h:224:23: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘std::vector ClonalFrameBaumWelch::maximize_likelihood(const std::vector&)’ at main.h:225:23: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘std::vector ClonalFrameBaumWelch::maximize_likelihood(const std::vector&)’ at main.h:243:24: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘ClonalFrameBaumWelch::ClonalFrameBaumWelch(const marginal_tree&, const myutils::Matrix&, const std::vector&, const std::vector&, double, const std::vector&, std::vector >&, const std::vector&, const std::vector&, int, bool, bool)’ at main.h:195:27: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘ClonalFrameBaumWelchRhoPerBranch::ClonalFrameBaumWelchRhoPerBranch(const marginal_tree&, const myutils::Matrix&, const std::vector&, const std::vector&, double, const std::vector&, std::vector >&, const std::vector&, const std::vector&, int, bool, bool)’ at main.h:313:27: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void ClonalFrameBaumWelchRhoPerBranch::maximize_likelihood(const std::vector&)’ at main.h:339:23: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘void ClonalFrameBaumWelchRhoPerBranch::maximize_likelihood(const std::vector&)’ at main.h:341:23: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void ClonalFrameBaumWelchRhoPerBranch::maximize_likelihood(const std::vector&)’ at main.h:342:23: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘void ClonalFrameBaumWelchRhoPerBranch::maximize_likelihood(const std::vector&)’ at main.h:344:23: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘myutils::RTRV myutils::ArgumentWizard::function_get_vector(T, std::string&) [with T = double]’ at myutils/argumentwizard.h:199:18, inlined from ‘void myutils::ArgumentWizard::read_data(std::string&)’ at myutils/argumentwizard.h:231:23: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘marginal_tree convert_unrooted_NewickTree_to_marginal_tree(myutils::NewickTree&, std::vector >&, std::vector >&)’ at main.cpp:847:25: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘marginal_tree convert_rooted_NewickTree_to_marginal_tree(myutils::NewickTree&, std::vector >&, std::vector >&)’ at main.cpp:667:25: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘int main(int, const char**)’ at main.cpp:165:23: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘int main(int, const char**)’ at main.cpp:175:21: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘int main(int, const char**)’ at main.cpp:189:28: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘int main(int, const char**)’ at main.cpp:236:24: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o ClonalFrameML main.o make[2]: Leaving directory '/build/reproducible-path/clonalframeml-1.13/src' make[1]: Leaving directory '/build/reproducible-path/clonalframeml-1.13' dh_auto_test -O--sourcedirectory=src create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src dh_auto_install --destdir=debian/clonalframeml/ -O--sourcedirectory=src dh_install -O--sourcedirectory=src dh_installdocs -O--sourcedirectory=src dh_installchangelogs -O--sourcedirectory=src debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/clonalframeml-1.13' dh_installexamples chmod -x debian/clonalframeml/usr/share/doc/clonalframeml/examples/* make[1]: Leaving directory '/build/reproducible-path/clonalframeml-1.13' dh_installman -O--sourcedirectory=src dh_installsystemduser -O--sourcedirectory=src dh_perl -O--sourcedirectory=src dh_link -O--sourcedirectory=src dh_strip_nondeterminism -O--sourcedirectory=src dh_compress -O--sourcedirectory=src dh_fixperms -O--sourcedirectory=src dh_missing -O--sourcedirectory=src dh_dwz -a -O--sourcedirectory=src dh_strip -a -O--sourcedirectory=src dh_makeshlibs -a -O--sourcedirectory=src dh_shlibdeps -a -O--sourcedirectory=src dpkg-shlibdeps: warning: debian/clonalframeml/usr/bin/ClonalFrameML contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src dpkg-deb: building package 'clonalframeml' in '../clonalframeml_1.13-1_armhf.deb'. dpkg-deb: building package 'clonalframeml-dbgsym' in '../clonalframeml-dbgsym_1.13-1_armhf.deb'. dpkg-genbuildinfo --build=binary -O../clonalframeml_1.13-1_armhf.buildinfo dpkg-genchanges --build=binary -O../clonalframeml_1.13-1_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: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/27619 and its subdirectories I: Current time: Tue Apr 23 02:19:10 -12 2024 I: pbuilder-time-stamp: 1713881950 Tue Apr 23 14:19:19 UTC 2024 I: 1st build successful. Starting 2nd build on remote node virt32b-armhf-rb.debian.net. Tue Apr 23 14:19:19 UTC 2024 I: Preparing to do remote build '2' on virt32b-armhf-rb.debian.net. Tue Apr 23 14:22:19 UTC 2024 I: Deleting $TMPDIR on virt32b-armhf-rb.debian.net. Tue Apr 23 14:22:21 UTC 2024 I: clonalframeml_1.13-1_armhf.changes: Format: 1.8 Date: Thu, 01 Feb 2024 13:23:35 +0100 Source: clonalframeml Binary: clonalframeml clonalframeml-dbgsym Architecture: armhf Version: 1.13-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: clonalframeml - Efficient Inference of Recombination in Whole Bacterial Genomes Closes: 1044020 Changes: clonalframeml (1.13-1) unstable; urgency=medium . * New upstream version . [ Komolehin Israel Timilehin ] * Add autopkgtest * Add real world example . [ Andreas Tille ] * Standards-Version: 4.6.2 (routine-update) * Fix clean target Closes: #1044020 Checksums-Sha1: 56569b93b483fa3ade1d74838cf2262c48982c1a 886064 clonalframeml-dbgsym_1.13-1_armhf.deb 5e5b34a45aa20d5ea5e2623418ef421835f8024e 5324 clonalframeml_1.13-1_armhf.buildinfo 9215a49e626e0790e413522a14a287942690b3bf 88392 clonalframeml_1.13-1_armhf.deb Checksums-Sha256: cb208e2aefa9b1f7b932c76dfc20301086dbee0dfdd81667a560c0e98fec135f 886064 clonalframeml-dbgsym_1.13-1_armhf.deb 06e06c1445f67183e65f5d508c4bb070768c61487c1d6e225782f380684ca943 5324 clonalframeml_1.13-1_armhf.buildinfo ceb475e3f486621dd9f87ce5e41182f7f34f8afaf87a26fcbfcc5af549b073d3 88392 clonalframeml_1.13-1_armhf.deb Files: 59fb7ac2ca13eb4098eda9984af55eec 886064 debug optional clonalframeml-dbgsym_1.13-1_armhf.deb c79ad6578c4c3049c908743526633790 5324 science optional clonalframeml_1.13-1_armhf.buildinfo 1f3082f02809e5d7e89f3ce76bafafd2 88392 science optional clonalframeml_1.13-1_armhf.deb Tue Apr 23 14:22:22 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-armhf_12-2622.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.DLyTFTZF/clonalframeml_1.13-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.DLyTFTZF/clonalframeml_1.13-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.DLyTFTZF/clonalframeml_1.13-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.DLyTFTZF/b1/clonalframeml_1.13-1_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.DLyTFTZF/b2/clonalframeml_1.13-1_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: 0.337s) 0.337s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.027s) 0.027s 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: 639ms CPU time consumed: 639ms Tue Apr 23 14:22:23 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Tue Apr 23 14:22:23 UTC 2024 I: clonalframeml from trixie built successfully and reproducibly on armhf. Tue Apr 23 14:22:24 UTC 2024 I: Submitting .buildinfo files to external archives: Tue Apr 23 14:22:24 UTC 2024 I: Submitting 8.0K b1/clonalframeml_1.13-1_armhf.buildinfo.asc Tue Apr 23 14:22:26 UTC 2024 I: Submitting 8.0K b2/clonalframeml_1.13-1_armhf.buildinfo.asc Tue Apr 23 14:22:27 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Apr 23 14:22:27 UTC 2024 I: Done submitting .buildinfo files. Tue Apr 23 14:22:27 UTC 2024 I: Removing signed clonalframeml_1.13-1_armhf.buildinfo.asc files: removed './b1/clonalframeml_1.13-1_armhf.buildinfo.asc' removed './b2/clonalframeml_1.13-1_armhf.buildinfo.asc'