Tue Apr 2 04:29:27 UTC 2024 I: starting to build phylonium/unstable/armhf on jenkins on '2024-04-02 04:29' Tue Apr 2 04:29:27 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_34/3321/console.log Tue Apr 2 04:29:27 UTC 2024 I: Downloading source for unstable/phylonium=1.7-3 --2024-04-02 04:29:27-- http://deb.debian.org/debian/pool/main/p/phylonium/phylonium_1.7-3.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2297 (2.2K) [text/prs.lines.tag] Saving to: ‘phylonium_1.7-3.dsc’ 0K .. 100% 291M=0s 2024-04-02 04:29:27 (291 MB/s) - ‘phylonium_1.7-3.dsc’ saved [2297/2297] Tue Apr 2 04:29:27 UTC 2024 I: phylonium_1.7-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: phylonium Binary: phylonium Architecture: any Version: 1.7-3 Maintainer: Debian Med Packaging Team Uploaders: Fabian Klötzl , Andreas Tille Homepage: https://github.com/EvolBioInf/phylonium Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/phylonium Vcs-Git: https://salsa.debian.org/med-team/phylonium.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libdivsufsort-dev Package-List: phylonium deb science optional arch=any Checksums-Sha1: 7245812e1aa646235d2c3238a87b19c1f9d045dd 44071659 phylonium_1.7.orig-debian-tests-data.tar.gz 452d117b87b8473e2cc710feb5caa32581fad424 424468 phylonium_1.7.orig.tar.gz 40249113861b8b8fbe5b1d6989f9d06d1e988e5b 5924 phylonium_1.7-3.debian.tar.xz Checksums-Sha256: 004b12f29d12ff61334ff18919db62d3557aba3b72eaa1c2a3c7e1091cd0197b 44071659 phylonium_1.7.orig-debian-tests-data.tar.gz 4a19798ecff468e905a3ed2f6a859f65f6d163151cbbc78095e11b4c20a8e9bf 424468 phylonium_1.7.orig.tar.gz f36155776f3a0e3ffad80f084fb31a3a2cbba9db91abf586ec2bcbee9c46dc0d 5924 phylonium_1.7-3.debian.tar.xz Files: 21a3be06d87270c5bc287173f53b1a94 44071659 phylonium_1.7.orig-debian-tests-data.tar.gz 73b8346f68f8cfeafc342a9aca9862c5 424468 phylonium_1.7.orig.tar.gz aeeb8785f7f7ee928865caa95e8ff481 5924 phylonium_1.7-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmYGqJcACgkQPCZ2P2xn 5uJexQ/9FbUoipFxmf2xlWO0SpT8h3BqrwqfELHMccBFmrSEXcuzNTV+3SSYdmlq GafqedX7LySMeW4/sjmH5v5NwEnuE909ejC9K5JGk9sbTiYyKQ/sW58vp7r0UxqM ZsGPcuH/ezaVE0w600nBtEC/gjbJeS3cylKR39SCit8Ts+LUSVAmOZ0USnB7jwcz M+eGGtpkrp3FuOlgGnOvaAWFWQ7QLhni+ECMhJ9g72ZIIak6iP3Dn8b8NB05bKoC OpwaB9ygDSv1ihbMdc4mJ0Nju58FXRKi1Spvg6X20Q2TM2Lf7xUizGQfPwkaS9Fd xug2HkHZokbPBot3xl0D5Cwed0WdjT66fcc7u6n/PP28BfhZhgAeux/RJ2npi+Xb TqPfJMLaQ171hIzJUagZ4pgrnDI2txL0RDUJDYO2UX69wrBePtsP8qAY7qpDy91q 0Is61ACIf5qhRWZ+HzKCvWJMpWFOmyBK/ydr98rX0jlJmfo54CWhKbsP8WT5TkVF HJ3FfBzRGFeE/6XnXORgfFE/Pm3+Rs9PHBlOx+1c1hRYrZarrifDEQ7/IUYQgg2s WelWaMmk5wkRTtzj44aITF+JQP6BpJUE/ZRIRf6OnpZQC497g8T5SRoT109e7e1m LIKlcZjBgjP1JqNDE3XksMd0FUwU/ZVujlaNiaM04VmKdqcwRqE= =GlHW -----END PGP SIGNATURE----- Tue Apr 2 04:29:27 UTC 2024 I: Checking whether the package is not for us Tue Apr 2 04:29:27 UTC 2024 I: Starting 1st build on remote node virt32z-armhf-rb.debian.net. Tue Apr 2 04:29:27 UTC 2024 I: Preparing to do remote build '1' on virt32z-armhf-rb.debian.net. Tue Apr 2 04:32:07 UTC 2024 I: Deleting $TMPDIR on virt32z-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Apr 1 16:29:42 -12 2024 I: pbuilder-time-stamp: 1712032182 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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 [phylonium_1.7-3.dsc] I: copying [./phylonium_1.7.orig-debian-tests-data.tar.gz] I: copying [./phylonium_1.7.orig.tar.gz] I: copying [./phylonium_1.7-3.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Mar 29 11:40:07 2024 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./phylonium_1.7-3.dsc: no acceptable signature found dpkg-source: info: extracting phylonium in phylonium-1.7 dpkg-source: info: unpacking phylonium_1.7.orig.tar.gz dpkg-source: info: unpacking phylonium_1.7.orig-debian-tests-data.tar.gz dpkg-source: info: unpacking phylonium_1.7-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 32-bits.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/22545/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='unstable' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='47e39a88b1384577a59a12b5a71fe0dd' 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='22545' 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.pmTwQvzA/pbuilderrc_uyIM --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.pmTwQvzA/b1 --logfile b1/build.log phylonium_1.7-3.dsc' SUDO_GID='110' SUDO_UID='103' 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 virt32z 6.1.0-18-armmp-lpae #1 SMP Debian 6.1.76-1 (2024-02-01) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 28 07:43 /bin -> usr/bin I: user script /srv/workspace/pbuilder/22545/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), libdivsufsort-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19467 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libdivsufsort-dev; however: Package libdivsufsort-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} 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} libdivsufsort-dev{a} libdivsufsort3{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} 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, 32 newly installed, 0 to remove and 0 not upgraded. Need to get 18.4 MB of archives. After unpacking 68.9 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main armhf sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian unstable/main armhf libmagic-mgc armhf 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main armhf libmagic1t64 armhf 1:5.45-3 [98.1 kB] Get: 4 http://deb.debian.org/debian unstable/main armhf file armhf 1:5.45-3 [42.0 kB] Get: 5 http://deb.debian.org/debian unstable/main armhf gettext-base armhf 0.21-14+b1 [157 kB] Get: 6 http://deb.debian.org/debian unstable/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 7 http://deb.debian.org/debian unstable/main armhf groff-base armhf 1.23.0-3+b1 [1091 kB] Get: 8 http://deb.debian.org/debian unstable/main armhf bsdextrautils armhf 2.39.3-11 [82.5 kB] Get: 9 http://deb.debian.org/debian unstable/main armhf libpipeline1 armhf 1.5.7-2 [33.3 kB] Get: 10 http://deb.debian.org/debian unstable/main armhf man-db armhf 2.12.0-4 [1373 kB] Get: 11 http://deb.debian.org/debian unstable/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 12 http://deb.debian.org/debian unstable/main armhf autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian unstable/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main armhf autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian unstable/main armhf libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian unstable/main armhf libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian unstable/main armhf dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main armhf libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian unstable/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian unstable/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian unstable/main armhf libelf1t64 armhf 0.191-1 [183 kB] Get: 24 http://deb.debian.org/debian unstable/main armhf dwz armhf 0.15-1+b1 [106 kB] Get: 25 http://deb.debian.org/debian unstable/main armhf libicu72 armhf 72.1-4+b1 [9070 kB] Get: 26 http://deb.debian.org/debian unstable/main armhf libxml2 armhf 2.9.14+dfsg-1.3+b2 [599 kB] Get: 27 http://deb.debian.org/debian unstable/main armhf gettext armhf 0.21-14+b1 [1230 kB] Get: 28 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main armhf debhelper all 13.15.3 [901 kB] Get: 31 http://deb.debian.org/debian unstable/main armhf libdivsufsort3 armhf 2.0.1-6 [44.8 kB] Get: 32 http://deb.debian.org/debian unstable/main armhf libdivsufsort-dev armhf 2.0.1-6 [18.8 kB] Fetched 18.4 MB in 0s (83.1 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 ... 19467 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+b1_armhf.deb ... Unpacking groff-base (1.23.0-3+b1) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.39.3-11_armhf.deb ... Unpacking bsdextrautils (2.39.3-11) ... 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_2.12.0-4_armhf.deb ... Unpacking man-db (2.12.0-4) ... 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_armhf.deb ... Unpacking libelf1t64:armhf (0.191-1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_armhf.deb ... Unpacking dwz (0.15-1+b1) ... 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) ... Selecting previously unselected package libdivsufsort3:armhf. Preparing to unpack .../30-libdivsufsort3_2.0.1-6_armhf.deb ... Unpacking libdivsufsort3:armhf (2.0.1-6) ... Selecting previously unselected package libdivsufsort-dev:armhf. Preparing to unpack .../31-libdivsufsort-dev_2.0.1-6_armhf.deb ... Unpacking libdivsufsort-dev:armhf (2.0.1-6) ... Setting up libpipeline1:armhf (1.5.7-2) ... Setting up libicu72:armhf (72.1-4+b1) ... Setting up bsdextrautils (2.39.3-11) ... 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 gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:armhf (0.191-1) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-14) ... Setting up autoconf (2.71-3) ... Setting up dwz (0.15-1+b1) ... 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 libdivsufsort3:armhf (2.0.1-6) ... Setting up libxml2:armhf (2.9.14+dfsg-1.3+b2) ... Setting up libdivsufsort-dev:armhf (2.0.1-6) ... 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+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.0-4) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.15.3) ... Processing triggers for libc-bin (2.37-15.1) ... 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/phylonium-1.7/ && 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 > ../phylonium_1.7-3_source.changes dpkg-buildpackage: info: source package phylonium dpkg-buildpackage: info: source version 1.7-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf configure.ac:11: installing './ar-lib' configure.ac:6: installing './compile' configure.ac:3: installing './install-sh' configure.ac:3: installing './missing' parallel-tests: installing './test-driver' libs/Makefile.am: installing './depcomp' test/Makefile.am:7: warning: source file '$(top_srcdir)/src/esa.cxx' is in a subdirectory, test/Makefile.am:7: but option 'subdir-objects' is disabled automake: warning: possible forward-incompatibility. automake: At least one source file is in a subdirectory, but the 'subdir-objects' automake: automake option hasn't been enabled. For now, the corresponding output automake: object file(s) will be placed in the top-level directory. However, this automake: behavior may change in a future Automake major version, with object automake: files being placed in the same subdirectory as the corresponding sources. automake: You are advised to start using 'subdir-objects' option throughout your automake: project, to avoid future incompatibilities. test/Makefile.am:7: warning: source file '$(top_srcdir)/src/evo_model.cxx' is in a subdirectory, test/Makefile.am:7: but option 'subdir-objects' is disabled test/Makefile.am:7: warning: source file '$(top_srcdir)/src/process.cxx' is in a subdirectory, test/Makefile.am:7: but option 'subdir-objects' is disabled test/Makefile.am:7: warning: source file '$(top_srcdir)/src/sequence.cxx' is in a subdirectory, test/Makefile.am:7: but option 'subdir-objects' is disabled debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/phylonium-1.7' dh_auto_configure -- --disable-x86simd ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --disable-x86simd checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking whether make sets $(MAKE)... (cached) yes checking how to run the C preprocessor... gcc -E checking for ranlib... ranlib checking for ar... ar checking the archiver (ar) interface... ar checking for g++ option to support OpenMP... -fopenmp checking whether g++ supports C++17 features with -std=gnu++17... yes checking for gcc option to support OpenMP... -fopenmp checking for __attribute__((ifunc))... yes checking for cos in -lm... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for divsufsort64.h... yes checking for divsufsort64 in -ldivsufsort64... yes checking for limits.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for stdint.h... (cached) yes checking for inttypes.h... (cached) yes checking for err.h... yes checking for errno.h... yes checking for fcntl.h... yes checking for inline... inline checking for size_t... yes checking for ssize_t... yes checking for int32_t... yes checking for uint8_t... yes checking for _Bool... yes checking for stdbool.h that conforms to C99... yes checking for floor... yes checking for pow... yes checking for sqrt... yes checking for strdup... yes checking for strerror... yes checking for strtoul... yes checking for strtod... yes checking for reallocarray... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating libs/Makefile config.status: creating Makefile config.status: creating man/phylonium.1 config.status: creating src/Makefile config.status: creating test/Makefile config.status: creating config.h config.status: executing depfiles commands make[1]: Leaving directory '/build/reproducible-path/phylonium-1.7' dh_auto_build make -j3 make[1]: Entering directory '/build/reproducible-path/phylonium-1.7' make all-recursive make[2]: Entering directory '/build/reproducible-path/phylonium-1.7' Making all in libs make[3]: Entering directory '/build/reproducible-path/phylonium-1.7/libs' rm -f libcompat.a gcc -DHAVE_CONFIG_H -I. -I.. -I../opt -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libpfasta_a-pfasta.o `test -f 'pfasta.c' || echo './'`pfasta.c gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o revseqcmp.o revseqcmp.c ar cru libcompat.a ar: `u' modifier ignored since `D' is the default (see `U') ranlib libcompat.a gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o seqcmp.o seqcmp.c rm -f librevseqcmp.a rm -f libseqcmp.a ar cru librevseqcmp.a revseqcmp.o ar cru libseqcmp.a seqcmp.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib librevseqcmp.a ar: `u' modifier ignored since `D' is the default (see `U') ranlib libseqcmp.a rm -f libpfasta.a ar cru libpfasta.a libpfasta_a-pfasta.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libpfasta.a make[3]: Leaving directory '/build/reproducible-path/phylonium-1.7/libs' Making all in src make[3]: Entering directory '/build/reproducible-path/phylonium-1.7/src' g++ -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -fopenmp -Wall -Wextra -I../libs -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -fopenmp -O2 -ggdb -g -O2 -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o phylonium-phylonium.o `test -f 'phylonium.cxx' || echo './'`phylonium.cxx g++ -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -fopenmp -Wall -Wextra -I../libs -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -fopenmp -O2 -ggdb -g -O2 -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o phylonium-io.o `test -f 'io.cxx' || echo './'`io.cxx g++ -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -fopenmp -Wall -Wextra -I../libs -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -fopenmp -O2 -ggdb -g -O2 -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o phylonium-sequence.o `test -f 'sequence.cxx' || echo './'`sequence.cxx g++ -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -fopenmp -Wall -Wextra -I../libs -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -fopenmp -O2 -ggdb -g -O2 -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o phylonium-esa.o `test -f 'esa.cxx' || echo './'`esa.cxx g++ -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -fopenmp -Wall -Wextra -I../libs -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -fopenmp -O2 -ggdb -g -O2 -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o phylonium-process.o `test -f 'process.cxx' || echo './'`process.cxx g++ -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -fopenmp -Wall -Wextra -I../libs -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -fopenmp -O2 -ggdb -g -O2 -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o phylonium-evo_model.o `test -f 'evo_model.cxx' || echo './'`evo_model.cxx g++ -std=gnu++17 -fopenmp -O2 -ggdb -g -O2 -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o phylonium phylonium-phylonium.o phylonium-io.o phylonium-sequence.o phylonium-esa.o phylonium-process.o phylonium-evo_model.o ../libs/libcompat.a ../libs/libpfasta.a ../libs/librevseqcmp.a ../libs/libseqcmp.a -ldivsufsort64 -lm make[3]: Leaving directory '/build/reproducible-path/phylonium-1.7/src' Making all in test make[3]: Entering directory '/build/reproducible-path/phylonium-1.7/test' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/phylonium-1.7/test' Making all in . make[3]: Entering directory '/build/reproducible-path/phylonium-1.7' make[3]: Leaving directory '/build/reproducible-path/phylonium-1.7' make[2]: Leaving directory '/build/reproducible-path/phylonium-1.7' make[1]: Leaving directory '/build/reproducible-path/phylonium-1.7' dh_auto_test make -j3 check "TESTSUITEFLAGS=-j3 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/phylonium-1.7' Making check in libs make[2]: Entering directory '/build/reproducible-path/phylonium-1.7/libs' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/phylonium-1.7/libs' Making check in src make[2]: Entering directory '/build/reproducible-path/phylonium-1.7/src' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/phylonium-1.7/src' Making check in test make[2]: Entering directory '/build/reproducible-path/phylonium-1.7/test' make simf unittests make[3]: Entering directory '/build/reproducible-path/phylonium-1.7/test' g++ -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -std=c++17 -Wall -Wextra -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o simf-simf.o `test -f 'simf.cxx' || echo './'`simf.cxx g++ -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++17 -Wall -Wextra -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o unittests-esa.o `test -f '../src/esa.cxx' || echo './'`../src/esa.cxx g++ -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++17 -Wall -Wextra -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o unittests-evo_model.o `test -f '../src/evo_model.cxx' || echo './'`../src/evo_model.cxx g++ -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++17 -Wall -Wextra -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o unittests-process.o `test -f '../src/process.cxx' || echo './'`../src/process.cxx g++ -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++17 -Wall -Wextra -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o unittests-sequence.o `test -f '../src/sequence.cxx' || echo './'`../src/sequence.cxx ../src/process.cxx:433: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 433 | #pragma omp parallel for num_threads(THREADS) | ../src/process.cxx:445: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 445 | #pragma omp critical | ../src/process.cxx:448: warning: ignoring '#pragma omp atomic' [-Wunknown-pragmas] 448 | #pragma omp atomic | ../src/process.cxx:454: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 454 | #pragma omp critical | ../src/process.cxx:524: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 524 | #pragma omp parallel for num_threads(THREADS) | ../src/process.cxx:531: warning: ignoring '#pragma omp atomic' [-Wunknown-pragmas] 531 | #pragma omp atomic | ../src/process.cxx:539: warning: ignoring '#pragma omp atomic' [-Wunknown-pragmas] 539 | #pragma omp atomic read | ../src/process.cxx:545: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 545 | #pragma omp critical | In file included from /usr/include/c++/13/vector:72, from /usr/include/c++/13/functional:64, from simf.cxx:10: /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>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++17 -Wall -Wextra -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o unittests-Tmain.o `test -f 'Tmain.cxx' || echo './'`Tmain.cxx g++ -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++17 -Wall -Wextra -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o unittests-Tprocess.o `test -f 'Tprocess.cxx' || echo './'`Tprocess.cxx g++ -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++17 -Wall -Wextra -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o unittests-Tsequence.o `test -f 'Tsequence.cxx' || echo './'`Tsequence.cxx g++ -std=gnu++17 -ggdb -g -O2 -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o simf simf-simf.o -ldivsufsort64 -lm In file included from /usr/include/c++/13/functional:67, from catch.hpp:3481, from Tmain.cxx:3: /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter&):: >]': /usr/include/c++/13/bits/stl_algo.h:1792:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1792 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&):: >]': /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1812 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 In file included from /usr/include/c++/13/bits/stl_algo.h:61: /usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Distance = int; _Tp = pair; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&):: >]': /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&):: >]': /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from catch.hpp:564: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Catch::SectionEndInfo&}; _Tp = Catch::SectionEndInfo; _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 = Catch::SectionEndInfo; _Alloc = std::allocator]', inlined from 'virtual void Catch::RunContext::sectionEndedEarly(const Catch::SectionEndInfo&)' at catch.hpp:12870:39: /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 = {unsigned int, const Catch::TestCase*}; _Tp = std::pair; _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 = {unsigned int, const Catch::TestCase*}; _Tp = std::pair; _Alloc = std::allocator >]', inlined from 'std::vector Catch::sortTests(const IConfig&, const std::vector&)' at catch.hpp:14235:47: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&):: >]', inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >; _Compare = Catch::sortTests(const IConfig&, const std::vector&)::]' at /usr/include/c++/13/bits/stl_algo.h:4894:18, inlined from 'std::vector Catch::sortTests(const IConfig&, const std::vector&)' at catch.hpp:14238:26: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&):: >]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&):: >]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >; _Compare = Catch::sortTests(const IConfig&, const std::vector&)::]' at /usr/include/c++/13/bits/stl_algo.h:4894:18, inlined from 'std::vector Catch::sortTests(const IConfig&, const std::vector&)' at catch.hpp:14238:26: /usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -ggdb -g -O2 -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o unittests unittests-esa.o unittests-evo_model.o unittests-process.o unittests-sequence.o unittests-Tmain.o unittests-Tprocess.o unittests-Tsequence.o ../libs/libcompat.a ../libs/libpfasta.a ../libs/librevseqcmp.a ../libs/libseqcmp.a -ldivsufsort64 -lm make[3]: Leaving directory '/build/reproducible-path/phylonium-1.7/test' make[2]: Leaving directory '/build/reproducible-path/phylonium-1.7/test' Making check in . make[2]: Entering directory '/build/reproducible-path/phylonium-1.7' make check-TESTS make[3]: Entering directory '/build/reproducible-path/phylonium-1.7' make[4]: Entering directory '/build/reproducible-path/phylonium-1.7' PASS: test/unittests PASS: test/simple.sh ============================================================================ Testsuite summary for phylonium 1.7 ============================================================================ # TOTAL: 2 # PASS: 2 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[4]: Leaving directory '/build/reproducible-path/phylonium-1.7' make[3]: Leaving directory '/build/reproducible-path/phylonium-1.7' make[2]: Leaving directory '/build/reproducible-path/phylonium-1.7' make[1]: Leaving directory '/build/reproducible-path/phylonium-1.7' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/phylonium/ make -j3 install DESTDIR=/build/reproducible-path/phylonium-1.7/debian/phylonium AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/phylonium-1.7' Making install in libs make[2]: Entering directory '/build/reproducible-path/phylonium-1.7/libs' make[3]: Entering directory '/build/reproducible-path/phylonium-1.7/libs' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/phylonium-1.7/libs' make[2]: Leaving directory '/build/reproducible-path/phylonium-1.7/libs' Making install in src make[2]: Entering directory '/build/reproducible-path/phylonium-1.7/src' make[3]: Entering directory '/build/reproducible-path/phylonium-1.7/src' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/phylonium-1.7/debian/phylonium/usr/bin' /usr/bin/install -c phylonium '/build/reproducible-path/phylonium-1.7/debian/phylonium/usr/bin' make[3]: Leaving directory '/build/reproducible-path/phylonium-1.7/src' make[2]: Leaving directory '/build/reproducible-path/phylonium-1.7/src' Making install in test make[2]: Entering directory '/build/reproducible-path/phylonium-1.7/test' make[3]: Entering directory '/build/reproducible-path/phylonium-1.7/test' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/phylonium-1.7/test' make[2]: Leaving directory '/build/reproducible-path/phylonium-1.7/test' Making install in . make[2]: Entering directory '/build/reproducible-path/phylonium-1.7' make[3]: Entering directory '/build/reproducible-path/phylonium-1.7' make[3]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/reproducible-path/phylonium-1.7/debian/phylonium/usr/share/doc/phylonium' /usr/bin/mkdir -p '/build/reproducible-path/phylonium-1.7/debian/phylonium/usr/share/man/man1' /usr/bin/install -c -m 644 documentation/manual.pdf '/build/reproducible-path/phylonium-1.7/debian/phylonium/usr/share/doc/phylonium' /usr/bin/install -c -m 644 man/phylonium.1 '/build/reproducible-path/phylonium-1.7/debian/phylonium/usr/share/man/man1' make[3]: Leaving directory '/build/reproducible-path/phylonium-1.7' make[2]: Leaving directory '/build/reproducible-path/phylonium-1.7' make[1]: Leaving directory '/build/reproducible-path/phylonium-1.7' dh_installdocs dh_installdocs: warning: Could not parse doc-base for doc-base Document id; skipping dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: debian/phylonium/usr/bin/phylonium 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 'phylonium' in '../phylonium_1.7-3_armhf.deb'. dpkg-deb: building package 'phylonium-dbgsym' in '../phylonium-dbgsym_1.7-3_armhf.deb'. dpkg-genbuildinfo --build=binary -O../phylonium_1.7-3_armhf.buildinfo dpkg-genchanges --build=binary -O../phylonium_1.7-3_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/22545 and its subdirectories I: Current time: Mon Apr 1 16:32:02 -12 2024 I: pbuilder-time-stamp: 1712032322 Tue Apr 2 04:32:10 UTC 2024 I: 1st build successful. Starting 2nd build on remote node virt64a-armhf-rb.debian.net. Tue Apr 2 04:32:10 UTC 2024 I: Preparing to do remote build '2' on virt64a-armhf-rb.debian.net. Tue Apr 2 04:35:28 UTC 2024 I: Deleting $TMPDIR on virt64a-armhf-rb.debian.net. Tue Apr 2 04:35:31 UTC 2024 I: phylonium_1.7-3_armhf.changes: Format: 1.8 Date: Fri, 29 Mar 2024 12:36:56 +0100 Source: phylonium Binary: phylonium phylonium-dbgsym Architecture: armhf Version: 1.7-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: phylonium - Fast and Accurate Estimation of Evolutionary Distances Closes: 1067920 Changes: phylonium (1.7-3) unstable; urgency=medium . * Team upload. * Cherry-pick patch from upstream (plus an addition from me) to fix the 32-bits build. Closes: #1067920 Checksums-Sha1: 8b357cfc98f2b059c972e0c743fd224e4dca716d 553884 phylonium-dbgsym_1.7-3_armhf.deb e5c9f5b79f9e9d70c815891acb036563bad26920 5070 phylonium_1.7-3_armhf.buildinfo a64c485eb6b120b21d632cd67f3a90f3385ebb35 288096 phylonium_1.7-3_armhf.deb Checksums-Sha256: d7dede30703272d4bd46854980bfb53481c3f0b6fbaf63ea82a7a8326fb272b9 553884 phylonium-dbgsym_1.7-3_armhf.deb 2796b3724bd5aa0144a8a98888c44e45ba489cd89c5ff7c1ea8ebe1e50dcfa01 5070 phylonium_1.7-3_armhf.buildinfo 65c646400c55cb48f4d85b639e97cf5f83346d6e7f46e29bda36f126a0d9a8dc 288096 phylonium_1.7-3_armhf.deb Files: 8c65c93ea235f6aa41a304a0c43fbd03 553884 debug optional phylonium-dbgsym_1.7-3_armhf.deb 753c513eb80baa786cbf8d0df19d05ee 5070 science optional phylonium_1.7-3_armhf.buildinfo 4d3d773af6a2d51ce1f84f0c886ca6ef 288096 science optional phylonium_1.7-3_armhf.deb Tue Apr 2 04:35:32 UTC 2024 I: diffoscope 262 will be used to compare the two builds: Running as unit: rb-diffoscope-armhf_34-3321.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.pmTwQvzA/phylonium_1.7-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.pmTwQvzA/phylonium_1.7-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.pmTwQvzA/phylonium_1.7-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.pmTwQvzA/b1/phylonium_1.7-3_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.pmTwQvzA/b2/phylonium_1.7-3_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: 0.434s) 0.434s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.029s) 0.029s 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: 809ms CPU time consumed: 810ms Tue Apr 2 04:35:33 UTC 2024 I: diffoscope 262 found no differences in the changes files, and a .buildinfo file also exists. Tue Apr 2 04:35:33 UTC 2024 I: phylonium from unstable built successfully and reproducibly on armhf. Tue Apr 2 04:35:35 UTC 2024 I: Submitting .buildinfo files to external archives: Tue Apr 2 04:35:35 UTC 2024 I: Submitting 8.0K b1/phylonium_1.7-3_armhf.buildinfo.asc Tue Apr 2 04:35:36 UTC 2024 I: Submitting 8.0K b2/phylonium_1.7-3_armhf.buildinfo.asc Tue Apr 2 04:35:36 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Apr 2 04:35:36 UTC 2024 I: Done submitting .buildinfo files. Tue Apr 2 04:35:36 UTC 2024 I: Removing signed phylonium_1.7-3_armhf.buildinfo.asc files: removed './b1/phylonium_1.7-3_armhf.buildinfo.asc' removed './b2/phylonium_1.7-3_armhf.buildinfo.asc'