Running as unit: rb-build-amd64_22-58969.service; invocation ID: cc08d4dc8017492bb78cc5cc53861455 ==================================================================================== Thu Sep 18 07:01:24 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_22) on jenkins, called using "ionos5-amd64 ionos11-amd64" as arguments. Thu Sep 18 07:01:24 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-NzOysqnM" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Sep 18 07:01:24 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos5-amd64.debian.net is marked as down. Thu Sep 18 07:01:24 UTC 2025 - checking via ssh if ionos5-amd64.debian.net is up. removed '/tmp/read-only-fs-test-MyGeFN' Thu Sep 18 07:01:25 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos11-amd64.debian.net is marked as down. Thu Sep 18 07:01:25 UTC 2025 - checking via ssh if ionos11-amd64.debian.net is up. removed '/tmp/read-only-fs-test-GGoIK8' ok, let's check if phylonium is building anywhere yet… ok, phylonium is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of phylonium in unstable on amd64 on jenkins now. 1st build will be done on ionos5-amd64.debian.net. 2nd build will be done on ionos11-amd64.debian.net. ============================================================================= Thu Sep 18 07:01:48 UTC 2025 I: starting to build phylonium/unstable/amd64 on jenkins on '2025-09-18 07:01' Thu Sep 18 07:01:48 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_22/58969/console.log 1758178908 amd64 unstable phylonium Thu Sep 18 07:01:48 UTC 2025 I: Downloading source for unstable/phylonium=1.7-3 --2025-09-18 07:01:48-- http://deb.debian.org/debian/pool/main/p/phylonium/phylonium_1.7-3.dsc Connecting to 46.16.76.132:3128... 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% 245M=0s 2025-09-18 07:01:48 (245 MB/s) - ‘phylonium_1.7-3.dsc’ saved [2297/2297] --2025-09-18 07:01:48-- http://deb.debian.org/debian/pool/main/p/phylonium/phylonium_1.7-3.dsc Connecting to 46.16.76.132:3128... 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% 245M=0s 2025-09-18 07:01:48 (245 MB/s) - ‘phylonium_1.7-3.dsc’ saved [2297/2297] Thu Sep 18 07:01:48 UTC 2025 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----- Thu Sep 18 07:01:48 UTC 2025 I: Checking whether the package is not for us Thu Sep 18 07:01:48 UTC 2025 I: Starting 1st build on remote node ionos5-amd64.debian.net. Thu Sep 18 07:01:48 UTC 2025 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Thu Sep 18 07:01:48 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos5-amd64.debian.net is marked as down. Thu Sep 18 07:01:48 UTC 2025 - checking via ssh if ionos5-amd64.debian.net is up. removed '/tmp/read-only-fs-test-ykFDAg' ==================================================================================== Wed Oct 21 13:24:49 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos5-amd64, called using "1 phylonium unstable /srv/reproducible-results/rbuild-debian/r-b-build.MqVGIXEM 1.7-3" as arguments. Wed Oct 21 13:24:49 UTC 2026 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-4LpuehM0" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Oct 21 13:24:49 UTC 2026 I: Downloading source for unstable/phylonium=1.7-3 Reading package lists... NOTICE: 'phylonium' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/phylonium.git Please use: git clone https://salsa.debian.org/med-team/phylonium.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 44.5 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main phylonium 1.7-3 (dsc) [2297 B] Get:2 http://deb.debian.org/debian unstable/main phylonium 1.7-3 (tar) [44.1 MB] Get:3 http://deb.debian.org/debian unstable/main phylonium 1.7-3 (tar) [424 kB] Get:4 http://deb.debian.org/debian unstable/main phylonium 1.7-3 (diff) [5924 B] Fetched 44.5 MB in 1s (77.4 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'phylonium' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/phylonium.git Please use: git clone https://salsa.debian.org/med-team/phylonium.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 44.5 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main phylonium 1.7-3 (dsc) [2297 B] Get:2 http://deb.debian.org/debian unstable/main phylonium 1.7-3 (tar) [44.1 MB] Get:3 http://deb.debian.org/debian unstable/main phylonium 1.7-3 (tar) [424 kB] Get:4 http://deb.debian.org/debian unstable/main phylonium 1.7-3 (diff) [5924 B] Fetched 44.5 MB in 1s (77.4 MB/s) Download complete and in download only mode ============================================================================= Building phylonium in unstable on amd64 on ionos5-amd64 now. Date: Wed Oct 21 13:24:50 UTC 2026 Date UTC: Wed Oct 21 13:24:50 UTC 2026 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Wed Oct 21 01:24:50 -12 2026 I: pbuilder-time-stamp: 1792589090 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 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/1362235/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='2fa902259de24d499e610f7fc2d1d01e' 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='1362235' 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.MqVGIXEM/pbuilderrc_g53s --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.MqVGIXEM/b1 --logfile b1/build.log phylonium_1.7-3.dsc' SUDO_GID='110' SUDO_HOME='/var/lib/jenkins' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1362235/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), 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 ... 19917 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} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{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, 31 newly installed, 0 to remove and 0 not upgraded. Need to get 11.3 MB of archives. After unpacking 42.9 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libdivsufsort3 amd64 2.0.1-6+b1 [45.9 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libdivsufsort-dev amd64 2.0.1-6+b1 [19.1 kB] Fetched 11.3 MB in 4s (2926 kB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41.1-3_amd64.deb ... Unpacking bsdextrautils (2.41.1-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.20-1_amd64.deb ... Unpacking m4 (1.4.20-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.26_all.deb ... Unpacking libdebhelper-perl (13.26) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-5_all.deb ... Unpacking libtool (2.5.4-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_21_all.deb ... Unpacking dh-autoreconf (21) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.15.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.15.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.15.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../21-libelf1t64_0.193-3_amd64.deb ... Unpacking libelf1t64:amd64 (0.193-3) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.16-2_amd64.deb ... Unpacking dwz (0.16-2) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../23-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2-16:amd64. Preparing to unpack .../24-libxml2-16_2.14.5+dfsg-0.2_amd64.deb ... Unpacking libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.23.1-2+b1_amd64.deb ... Unpacking gettext (0.23.1-2+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. 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Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.26) ... Processing triggers for libc-bin (2.41-12) ... 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 amd64 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 '$(top_srcdir)/src/esa.cxx' is in a subdirectory, test/Makefile.am:7: but option 'subdir-objects' is disabled automake: warning: possible forward-incompatibility. automake: At least one source file is in a subdirectory, but the 'subdir-objects' automake: automake option hasn't been enabled. For now, the corresponding output automake: object file(s) will be placed in the top-level directory. However, this automake: behavior may change in a future Automake major version, with object automake: files being placed in the same subdirectory as the corresponding sources. automake: You are advised to start using 'subdir-objects' option throughout your automake: project, to avoid future incompatibility. test/Makefile.am:7: warning: source file '$(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 -- ./configure --build=x86_64-linux-gnu --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/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 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 xargs -n works... 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 or later... 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 -j42 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 -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 -fcf-protection -c -o libpfasta_a-pfasta.o `test -f 'pfasta.c' || echo './'`pfasta.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fcf-protection -c -o revseqcmp.o revseqcmp.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -mpopcnt -mssse3 -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 -fcf-protection -c -o librevseqcmp_ssse3_a-revseqcmp_ssse3.o `test -f 'revseqcmp_ssse3.c' || echo './'`revseqcmp_ssse3.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -mpopcnt -mavx2 -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 -fcf-protection -c -o librevseqcmp_avx2_a-revseqcmp_avx2.o `test -f 'revseqcmp_avx2.c' || echo './'`revseqcmp_avx2.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fcf-protection -c -o seqcmp.o seqcmp.c ar cr libcompat.a gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -mpopcnt -msse2 -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 -fcf-protection -c -o libseqcmp_sse2_a-seqcmp_sse2.o `test -f 'seqcmp_sse2.c' || echo './'`seqcmp_sse2.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -mpopcnt -mavx2 -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 -fcf-protection -c -o libseqcmp_avx2_a-seqcmp_avx2.o `test -f 'seqcmp_avx2.c' || echo './'`seqcmp_avx2.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -mpopcnt -mavx512bw -mavx512vl -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 -fcf-protection -c -o libseqcmp_avx512_a-seqcmp_avx512.o `test -f 'seqcmp_avx512.c' || echo './'`seqcmp_avx512.c ranlib libcompat.a rm -f librevseqcmp_ssse3.a ar cr librevseqcmp_ssse3.a librevseqcmp_ssse3_a-revseqcmp_ssse3.o ranlib librevseqcmp_ssse3.a rm -f libseqcmp_sse2.a ar cr libseqcmp_sse2.a libseqcmp_sse2_a-seqcmp_sse2.o ranlib libseqcmp_sse2.a rm -f libpfasta.a ar cr libpfasta.a libpfasta_a-pfasta.o ranlib libpfasta.a rm -f libseqcmp_avx512.a rm -f librevseqcmp_avx2.a ar cr libseqcmp_avx512.a libseqcmp_avx512_a-seqcmp_avx512.o ar cr librevseqcmp_avx2.a librevseqcmp_avx2_a-revseqcmp_avx2.o ranlib libseqcmp_avx512.a ranlib librevseqcmp_avx2.a rm -f libseqcmp_avx2.a ar cr libseqcmp_avx2.a libseqcmp_avx2_a-seqcmp_avx2.o ranlib libseqcmp_avx2.a rm -f librevseqcmp.a ar cr librevseqcmp.a revseqcmp.o librevseqcmp_ssse3.a librevseqcmp_avx2.a ranlib librevseqcmp.a rm -f libseqcmp.a ar cr libseqcmp.a seqcmp.o libseqcmp_sse2.a libseqcmp_avx2.a libseqcmp_avx512.a ranlib libseqcmp.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 -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 -fcf-protection -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 -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 -fcf-protection -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 -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 -fcf-protection -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 -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 -fcf-protection -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 -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 -fcf-protection -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 -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 -fcf-protection -c -o phylonium-evo_model.o `test -f 'evo_model.cxx' || echo './'`evo_model.cxx esa.cxx: In constructor 'esa::esa(const sequence&)': esa.cxx:69:55: warning: narrowing conversion of '(((& seq)->sequence::size() * 2) + 1)' from 'long unsigned int' to 'saidx64_t' {aka 'long int'} [-Wnarrowing] 69 | esa::esa(const sequence &seq) : m_size{seq.size() * 2 + 1} | ~~~~~~~~~~~~~~~^~~ 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 -fcf-protection -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 ../libs/librevseqcmp_avx2.a ../libs/librevseqcmp_ssse3.a ../libs/libseqcmp_avx2.a ../libs/libseqcmp_sse2.a ../libs/libseqcmp_avx512.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 -j42 check "TESTSUITEFLAGS=-j42 --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 -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 -fcf-protection -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 -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 -fcf-protection -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 -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 -fcf-protection -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 -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 -fcf-protection -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 -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 -fcf-protection -c -o unittests-sequence.o `test -f '../src/sequence.cxx' || echo './'`../src/sequence.cxx g++ -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++17 -Wall -Wextra -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 -fcf-protection -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 -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 -fcf-protection -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 -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 -fcf-protection -c -o unittests-Tsequence.o `test -f 'Tsequence.cxx' || echo './'`Tsequence.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 ../src/esa.cxx: In constructor 'esa::esa(const sequence&)': ../src/esa.cxx:69:55: warning: narrowing conversion of '(((& seq)->sequence::size() * 2) + 1)' from 'long unsigned int' to 'saidx64_t' {aka 'long int'} [-Wnarrowing] 69 | esa::esa(const sequence &seq) : m_size{seq.size() * 2 + 1} | ~~~~~~~~~~~~~~~^~~ 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 -fcf-protection -Wl,-z,relro -Wl,-z,now -o simf simf-simf.o -ldivsufsort64 -lm 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 -fcf-protection -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 ../libs/librevseqcmp_avx2.a ../libs/librevseqcmp_ssse3.a ../libs/libseqcmp_avx2.a ../libs/libseqcmp_sse2.a ../libs/libseqcmp_avx512.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 -j42 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 dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'phylonium' in '../phylonium_1.7-3_amd64.deb'. dpkg-deb: building package 'phylonium-dbgsym' in '../phylonium-dbgsym_1.7-3_amd64.deb'. dpkg-genbuildinfo --build=binary -O../phylonium_1.7-3_amd64.buildinfo dpkg-genchanges --build=binary -O../phylonium_1.7-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1362235 and its subdirectories I: Current time: Wed Oct 21 01:29:29 -12 2026 I: pbuilder-time-stamp: 1792589369 Wed Oct 21 13:29:29 UTC 2026 I: Signing ./b1/phylonium_1.7-3_amd64.buildinfo as phylonium_1.7-3_amd64.buildinfo.asc Wed Oct 21 13:29:29 UTC 2026 I: Signed ./b1/phylonium_1.7-3_amd64.buildinfo as ./b1/phylonium_1.7-3_amd64.buildinfo.asc Wed Oct 21 13:29:29 UTC 2026 - build #1 for phylonium/unstable/amd64 on ionos5-amd64 done. Starting cleanup. All cleanup done. Wed Oct 21 13:29:29 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-4LpuehM0, removing. /srv/reproducible-results/rbuild-debian/r-b-build.MqVGIXEM: total 16 drwxrwxr-x 2 jenkins jenkins 4096 Sep 18 07:06 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 18 07:01 b2 -rw-rw-r-- 1 jenkins jenkins 2297 Mar 29 2024 phylonium_1.7-3.dsc -rw------- 1 jenkins jenkins 3401 Sep 18 07:01 rbuildlog.PcgFtwF /srv/reproducible-results/rbuild-debian/r-b-build.MqVGIXEM/b1: total 912 -rw-r--r-- 1 jenkins jenkins 40860 Sep 18 07:06 build.log -rw-r--r-- 1 jenkins jenkins 549040 Sep 18 07:06 phylonium-dbgsym_1.7-3_amd64.deb -rw-r--r-- 1 jenkins jenkins 5924 Sep 18 07:06 phylonium_1.7-3.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2297 Sep 18 07:06 phylonium_1.7-3.dsc -rw-r--r-- 1 jenkins jenkins 4913 Sep 18 07:06 phylonium_1.7-3_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 5795 Sep 18 07:06 phylonium_1.7-3_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1442 Sep 18 07:06 phylonium_1.7-3_amd64.changes -rw-r--r-- 1 jenkins jenkins 300272 Sep 18 07:06 phylonium_1.7-3_amd64.deb -rw-r--r-- 1 jenkins jenkins 1289 Sep 18 07:06 phylonium_1.7-3_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.MqVGIXEM/b2: total 0 Thu Sep 18 07:06:29 UTC 2025 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Oct 21 01:24:50 -12 2026 I: pbuilder-time-stamp: 1792589090 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 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/1362235/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='2fa902259de24d499e610f7fc2d1d01e' 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='1362235' 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.MqVGIXEM/pbuilderrc_g53s --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.MqVGIXEM/b1 --logfile b1/build.log phylonium_1.7-3.dsc' SUDO_GID='110' SUDO_HOME='/var/lib/jenkins' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1362235/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), 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 ... 19917 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} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{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, 31 newly installed, 0 to remove and 0 not upgraded. Need to get 11.3 MB of archives. After unpacking 42.9 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libdivsufsort3 amd64 2.0.1-6+b1 [45.9 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libdivsufsort-dev amd64 2.0.1-6+b1 [19.1 kB] Fetched 11.3 MB in 4s (2926 kB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41.1-3_amd64.deb ... Unpacking bsdextrautils (2.41.1-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... 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Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.26) ... Processing triggers for libc-bin (2.41-12) ... 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 amd64 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 incompatibility. 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 -- ./configure --build=x86_64-linux-gnu --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/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 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 xargs -n works... 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 or later... 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 -j42 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 -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 -fcf-protection -c -o libpfasta_a-pfasta.o `test -f 'pfasta.c' || echo './'`pfasta.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fcf-protection -c -o revseqcmp.o revseqcmp.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -mpopcnt -mssse3 -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 -fcf-protection -c -o librevseqcmp_ssse3_a-revseqcmp_ssse3.o `test -f 'revseqcmp_ssse3.c' || echo './'`revseqcmp_ssse3.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -mpopcnt -mavx2 -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 -fcf-protection -c -o librevseqcmp_avx2_a-revseqcmp_avx2.o `test -f 'revseqcmp_avx2.c' || echo './'`revseqcmp_avx2.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fcf-protection -c -o seqcmp.o seqcmp.c ar cr libcompat.a gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -mpopcnt -msse2 -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 -fcf-protection -c -o libseqcmp_sse2_a-seqcmp_sse2.o `test -f 'seqcmp_sse2.c' || echo './'`seqcmp_sse2.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -mpopcnt -mavx2 -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 -fcf-protection -c -o libseqcmp_avx2_a-seqcmp_avx2.o `test -f 'seqcmp_avx2.c' || echo './'`seqcmp_avx2.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -mpopcnt -mavx512bw -mavx512vl -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 -fcf-protection -c -o libseqcmp_avx512_a-seqcmp_avx512.o `test -f 'seqcmp_avx512.c' || echo './'`seqcmp_avx512.c ranlib libcompat.a rm -f librevseqcmp_ssse3.a ar cr librevseqcmp_ssse3.a librevseqcmp_ssse3_a-revseqcmp_ssse3.o ranlib librevseqcmp_ssse3.a rm -f libseqcmp_sse2.a ar cr libseqcmp_sse2.a libseqcmp_sse2_a-seqcmp_sse2.o ranlib libseqcmp_sse2.a rm -f libpfasta.a ar cr libpfasta.a libpfasta_a-pfasta.o ranlib libpfasta.a rm -f libseqcmp_avx512.a rm -f librevseqcmp_avx2.a ar cr libseqcmp_avx512.a libseqcmp_avx512_a-seqcmp_avx512.o ar cr librevseqcmp_avx2.a librevseqcmp_avx2_a-revseqcmp_avx2.o ranlib libseqcmp_avx512.a ranlib librevseqcmp_avx2.a rm -f libseqcmp_avx2.a ar cr libseqcmp_avx2.a libseqcmp_avx2_a-seqcmp_avx2.o ranlib libseqcmp_avx2.a rm -f librevseqcmp.a ar cr librevseqcmp.a revseqcmp.o librevseqcmp_ssse3.a librevseqcmp_avx2.a ranlib librevseqcmp.a rm -f libseqcmp.a ar cr libseqcmp.a seqcmp.o libseqcmp_sse2.a libseqcmp_avx2.a libseqcmp_avx512.a ranlib libseqcmp.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 -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 -fcf-protection -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 -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 -fcf-protection -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 -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 -fcf-protection -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 -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 -fcf-protection -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 -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 -fcf-protection -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 -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 -fcf-protection -c -o phylonium-evo_model.o `test -f 'evo_model.cxx' || echo './'`evo_model.cxx esa.cxx: In constructor 'esa::esa(const sequence&)': esa.cxx:69:55: warning: narrowing conversion of '(((& seq)->sequence::size() * 2) + 1)' from 'long unsigned int' to 'saidx64_t' {aka 'long int'} [-Wnarrowing] 69 | esa::esa(const sequence &seq) : m_size{seq.size() * 2 + 1} | ~~~~~~~~~~~~~~~^~~ 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 -fcf-protection -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 ../libs/librevseqcmp_avx2.a ../libs/librevseqcmp_ssse3.a ../libs/libseqcmp_avx2.a ../libs/libseqcmp_sse2.a ../libs/libseqcmp_avx512.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 -j42 check "TESTSUITEFLAGS=-j42 --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 -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 -fcf-protection -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 -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 -fcf-protection -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 -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 -fcf-protection -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 -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 -fcf-protection -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 -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 -fcf-protection -c -o unittests-sequence.o `test -f '../src/sequence.cxx' || echo './'`../src/sequence.cxx g++ -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++17 -Wall -Wextra -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 -fcf-protection -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 -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 -fcf-protection -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 -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 -fcf-protection -c -o unittests-Tsequence.o `test -f 'Tsequence.cxx' || echo './'`Tsequence.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 ../src/esa.cxx: In constructor 'esa::esa(const sequence&)': ../src/esa.cxx:69:55: warning: narrowing conversion of '(((& seq)->sequence::size() * 2) + 1)' from 'long unsigned int' to 'saidx64_t' {aka 'long int'} [-Wnarrowing] 69 | esa::esa(const sequence &seq) : m_size{seq.size() * 2 + 1} | ~~~~~~~~~~~~~~~^~~ 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 -fcf-protection -Wl,-z,relro -Wl,-z,now -o simf simf-simf.o -ldivsufsort64 -lm 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 -fcf-protection -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 ../libs/librevseqcmp_avx2.a ../libs/librevseqcmp_ssse3.a ../libs/libseqcmp_avx2.a ../libs/libseqcmp_sse2.a ../libs/libseqcmp_avx512.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 -j42 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 dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'phylonium' in '../phylonium_1.7-3_amd64.deb'. dpkg-deb: building package 'phylonium-dbgsym' in '../phylonium-dbgsym_1.7-3_amd64.deb'. dpkg-genbuildinfo --build=binary -O../phylonium_1.7-3_amd64.buildinfo dpkg-genchanges --build=binary -O../phylonium_1.7-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1362235 and its subdirectories I: Current time: Wed Oct 21 01:29:29 -12 2026 I: pbuilder-time-stamp: 1792589369 Thu Sep 18 07:06:30 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Thu Sep 18 07:06:30 UTC 2025 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Thu Sep 18 07:06:30 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos11-amd64.debian.net is marked as down. Thu Sep 18 07:06:30 UTC 2025 - checking via ssh if ionos11-amd64.debian.net is up. removed '/tmp/read-only-fs-test-O4iTlt' ==================================================================================== Thu Sep 18 07:06:30 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos11-amd64, called using "2 phylonium unstable /srv/reproducible-results/rbuild-debian/r-b-build.MqVGIXEM 1.7-3" as arguments. Thu Sep 18 07:06:30 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-PzTegntt" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Sep 18 07:06:30 UTC 2025 I: Downloading source for unstable/phylonium=1.7-3 Reading package lists... NOTICE: 'phylonium' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/phylonium.git Please use: git clone https://salsa.debian.org/med-team/phylonium.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 44.5 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main phylonium 1.7-3 (dsc) [2297 B] Get:2 http://deb.debian.org/debian unstable/main phylonium 1.7-3 (tar) [44.1 MB] Get:3 http://deb.debian.org/debian unstable/main phylonium 1.7-3 (tar) [424 kB] Get:4 http://deb.debian.org/debian unstable/main phylonium 1.7-3 (diff) [5924 B] Fetched 44.5 MB in 0s (104 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'phylonium' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/phylonium.git Please use: git clone https://salsa.debian.org/med-team/phylonium.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 44.5 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main phylonium 1.7-3 (dsc) [2297 B] Get:2 http://deb.debian.org/debian unstable/main phylonium 1.7-3 (tar) [44.1 MB] Get:3 http://deb.debian.org/debian unstable/main phylonium 1.7-3 (tar) [424 kB] Get:4 http://deb.debian.org/debian unstable/main phylonium 1.7-3 (diff) [5924 B] Fetched 44.5 MB in 0s (104 MB/s) Download complete and in download only mode ============================================================================= Re-Building phylonium in unstable on amd64 on ionos11-amd64 now. Date: Thu Sep 18 07:06:31 UTC 2025 Date UTC: Thu Sep 18 07:06:31 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.MqVGIXEM + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.MqVGIXEM/pbuilderrc_eO62 + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' phylonium = debian-installer -o phylonium = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' phylonium = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.MqVGIXEM/pbuilderrc_eO62 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.MqVGIXEM/b2 --logfile b2/build.log phylonium_1.7-3.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Thu Sep 18 21:06:31 +14 2025 I: pbuilder-time-stamp: 1758179191 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 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/3509668/tmp/hooks/D01_modify_environment starting debug: Running on ionos11-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Sep 18 07:06 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/3509668/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3509668/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.3.3(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=d30c35d0c2ad4d54a7afe0ed414401b4 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=3509668 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.MqVGIXEM/pbuilderrc_eO62 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.MqVGIXEM/b2 --logfile b2/build.log phylonium_1.7-3.dsc' SUDO_GID=111 SUDO_HOME=/var/lib/jenkins SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3509668/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), 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 ... 19917 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} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{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, 31 newly installed, 0 to remove and 0 not upgraded. Need to get 11.3 MB of archives. After unpacking 42.9 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libdivsufsort3 amd64 2.0.1-6+b1 [45.9 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libdivsufsort-dev amd64 2.0.1-6+b1 [19.1 kB] Fetched 11.3 MB in 1s (19.0 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41.1-3_amd64.deb ... Unpacking bsdextrautils (2.41.1-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.20-1_amd64.deb ... Unpacking m4 (1.4.20-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.26_all.deb ... Unpacking libdebhelper-perl (13.26) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-5_all.deb ... Unpacking libtool (2.5.4-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_21_all.deb ... Unpacking dh-autoreconf (21) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.15.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.15.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.15.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../21-libelf1t64_0.193-3_amd64.deb ... Unpacking libelf1t64:amd64 (0.193-3) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.16-2_amd64.deb ... Unpacking dwz (0.16-2) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../23-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2-16:amd64. Preparing to unpack .../24-libxml2-16_2.14.5+dfsg-0.2_amd64.deb ... Unpacking libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.23.1-2+b1_amd64.deb ... Unpacking gettext (0.23.1-2+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-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 .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.26_all.deb ... Unpacking debhelper (13.26) ... Selecting previously unselected package libdivsufsort3:amd64. Preparing to unpack .../29-libdivsufsort3_2.0.1-6+b1_amd64.deb ... Unpacking libdivsufsort3:amd64 (2.0.1-6+b1) ... Selecting previously unselected package libdivsufsort-dev:amd64. Preparing to unpack .../30-libdivsufsort-dev_2.0.1-6+b1_amd64.deb ... Unpacking libdivsufsort-dev:amd64 (2.0.1-6+b1) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up bsdextrautils (2.41.1-3) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Setting up libdebhelper-perl (13.26) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-1) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.193-3) ... Setting up autotools-dev (20240727.1) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up autoconf (2.72-3.1) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up libdivsufsort3:amd64 (2.0.1-6+b1) ... Setting up libdivsufsort-dev:amd64 (2.0.1-6+b1) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.26) ... Processing triggers for libc-bin (2.41-12) ... 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: user script /srv/workspace/pbuilder/3509668/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/3509668/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/phylonium-1.7/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../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 amd64 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 '$(top_srcdir)/src/esa.cxx' is in a subdirectory, test/Makefile.am:7: but option 'subdir-objects' is disabled automake: warning: possible forward-incompatibility. automake: At least one source file is in a subdirectory, but the 'subdir-objects' automake: automake option hasn't been enabled. For now, the corresponding output automake: object file(s) will be placed in the top-level directory. However, this automake: behavior may change in a future Automake major version, with object automake: files being placed in the same subdirectory as the corresponding sources. automake: You are advised to start using 'subdir-objects' option throughout your automake: project, to avoid future incompatibility. test/Makefile.am:7: warning: source file '$(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 -- ./configure --build=x86_64-linux-gnu --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/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 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 xargs -n works... 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 or later... 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 -j40 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 -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 -fcf-protection -c -o libpfasta_a-pfasta.o `test -f 'pfasta.c' || echo './'`pfasta.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fcf-protection -c -o revseqcmp.o revseqcmp.c ar cr libcompat.a gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -mpopcnt -mssse3 -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 -fcf-protection -c -o librevseqcmp_ssse3_a-revseqcmp_ssse3.o `test -f 'revseqcmp_ssse3.c' || echo './'`revseqcmp_ssse3.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -mpopcnt -mavx2 -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 -fcf-protection -c -o librevseqcmp_avx2_a-revseqcmp_avx2.o `test -f 'revseqcmp_avx2.c' || echo './'`revseqcmp_avx2.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fcf-protection -c -o seqcmp.o seqcmp.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -mpopcnt -msse2 -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 -fcf-protection -c -o libseqcmp_sse2_a-seqcmp_sse2.o `test -f 'seqcmp_sse2.c' || echo './'`seqcmp_sse2.c ranlib libcompat.a gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -mpopcnt -mavx2 -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 -fcf-protection -c -o libseqcmp_avx2_a-seqcmp_avx2.o `test -f 'seqcmp_avx2.c' || echo './'`seqcmp_avx2.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -mpopcnt -mavx512bw -mavx512vl -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 -fcf-protection -c -o libseqcmp_avx512_a-seqcmp_avx512.o `test -f 'seqcmp_avx512.c' || echo './'`seqcmp_avx512.c rm -f librevseqcmp_ssse3.a ar cr librevseqcmp_ssse3.a librevseqcmp_ssse3_a-revseqcmp_ssse3.o rm -f libseqcmp_sse2.a ar cr libseqcmp_sse2.a libseqcmp_sse2_a-seqcmp_sse2.o ranlib librevseqcmp_ssse3.a ranlib libseqcmp_sse2.a rm -f libpfasta.a ar cr libpfasta.a libpfasta_a-pfasta.o ranlib libpfasta.a rm -f libseqcmp_avx512.a ar cr libseqcmp_avx512.a libseqcmp_avx512_a-seqcmp_avx512.o ranlib libseqcmp_avx512.a rm -f librevseqcmp_avx2.a ar cr librevseqcmp_avx2.a librevseqcmp_avx2_a-revseqcmp_avx2.o ranlib librevseqcmp_avx2.a rm -f librevseqcmp.a ar cr librevseqcmp.a revseqcmp.o librevseqcmp_ssse3.a librevseqcmp_avx2.a ranlib librevseqcmp.a rm -f libseqcmp_avx2.a ar cr libseqcmp_avx2.a libseqcmp_avx2_a-seqcmp_avx2.o ranlib libseqcmp_avx2.a rm -f libseqcmp.a ar cr libseqcmp.a seqcmp.o libseqcmp_sse2.a libseqcmp_avx2.a libseqcmp_avx512.a ranlib libseqcmp.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 -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 -fcf-protection -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 -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 -fcf-protection -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 -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 -fcf-protection -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 -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 -fcf-protection -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 -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 -fcf-protection -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 -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 -fcf-protection -c -o phylonium-evo_model.o `test -f 'evo_model.cxx' || echo './'`evo_model.cxx esa.cxx: In constructor 'esa::esa(const sequence&)': esa.cxx:69:55: warning: narrowing conversion of '(((& seq)->sequence::size() * 2) + 1)' from 'long unsigned int' to 'saidx64_t' {aka 'long int'} [-Wnarrowing] 69 | esa::esa(const sequence &seq) : m_size{seq.size() * 2 + 1} | ~~~~~~~~~~~~~~~^~~ 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 -fcf-protection -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 ../libs/librevseqcmp_avx2.a ../libs/librevseqcmp_ssse3.a ../libs/libseqcmp_avx2.a ../libs/libseqcmp_sse2.a ../libs/libseqcmp_avx512.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 -j40 check "TESTSUITEFLAGS=-j40 --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 -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 -fcf-protection -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 -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 -fcf-protection -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 -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 -fcf-protection -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 -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 -fcf-protection -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 -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 -fcf-protection -c -o unittests-sequence.o `test -f '../src/sequence.cxx' || echo './'`../src/sequence.cxx g++ -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++17 -Wall -Wextra -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 -fcf-protection -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 -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 -fcf-protection -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 -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 -fcf-protection -c -o unittests-Tsequence.o `test -f 'Tsequence.cxx' || echo './'`Tsequence.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 ../src/esa.cxx: In constructor 'esa::esa(const sequence&)': ../src/esa.cxx:69:55: warning: narrowing conversion of '(((& seq)->sequence::size() * 2) + 1)' from 'long unsigned int' to 'saidx64_t' {aka 'long int'} [-Wnarrowing] 69 | esa::esa(const sequence &seq) : m_size{seq.size() * 2 + 1} | ~~~~~~~~~~~~~~~^~~ 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 -fcf-protection -Wl,-z,relro -Wl,-z,now -o simf simf-simf.o -ldivsufsort64 -lm 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 -fcf-protection -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 ../libs/librevseqcmp_avx2.a ../libs/librevseqcmp_ssse3.a ../libs/libseqcmp_avx2.a ../libs/libseqcmp_sse2.a ../libs/libseqcmp_avx512.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 -j40 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 dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'phylonium' in '../phylonium_1.7-3_amd64.deb'. dpkg-deb: building package 'phylonium-dbgsym' in '../phylonium-dbgsym_1.7-3_amd64.deb'. dpkg-genbuildinfo --build=binary -O../phylonium_1.7-3_amd64.buildinfo dpkg-genchanges --build=binary -O../phylonium_1.7-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3509668/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3509668/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3509668 and its subdirectories I: Current time: Thu Sep 18 21:08:19 +14 2025 I: pbuilder-time-stamp: 1758179299 + false + set +x Thu Sep 18 07:08:19 UTC 2025 I: Signing ./b2/phylonium_1.7-3_amd64.buildinfo as phylonium_1.7-3_amd64.buildinfo.asc Thu Sep 18 07:08:19 UTC 2025 I: Signed ./b2/phylonium_1.7-3_amd64.buildinfo as ./b2/phylonium_1.7-3_amd64.buildinfo.asc Thu Sep 18 07:08:19 UTC 2025 - build #2 for phylonium/unstable/amd64 on ionos11-amd64 done. Starting cleanup. All cleanup done. Thu Sep 18 07:08:19 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-PzTegntt, removing. /srv/reproducible-results/rbuild-debian/r-b-build.MqVGIXEM: total 56 drwxrwxr-x 2 jenkins jenkins 4096 Sep 18 07:06 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 18 07:08 b2 -rw-rw-r-- 1 jenkins jenkins 2297 Mar 29 2024 phylonium_1.7-3.dsc -rw------- 1 jenkins jenkins 44549 Sep 18 07:06 rbuildlog.PcgFtwF /srv/reproducible-results/rbuild-debian/r-b-build.MqVGIXEM/b1: total 920 -rw-r--r-- 1 jenkins jenkins 40860 Sep 18 07:06 build.log -rw-r--r-- 1 jenkins jenkins 549040 Sep 18 07:06 phylonium-dbgsym_1.7-3_amd64.deb -rw-r--r-- 1 jenkins jenkins 5924 Sep 18 07:06 phylonium_1.7-3.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2297 Sep 18 07:06 phylonium_1.7-3.dsc -rw-r--r-- 1 jenkins jenkins 4913 Sep 18 07:06 phylonium_1.7-3_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 5795 Sep 18 07:06 phylonium_1.7-3_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1442 Sep 18 07:06 phylonium_1.7-3_amd64.changes -rw-r--r-- 1 jenkins jenkins 300272 Sep 18 07:06 phylonium_1.7-3_amd64.deb -rw-r--r-- 1 jenkins jenkins 1289 Sep 18 07:06 phylonium_1.7-3_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.MqVGIXEM/b2: total 916 -rw-rw-r-- 1 jenkins jenkins 42787 Sep 18 07:08 build.log -rw-r--r-- 1 jenkins jenkins 549040 Sep 18 07:08 phylonium-dbgsym_1.7-3_amd64.deb -rw-r--r-- 1 jenkins jenkins 5924 Sep 18 07:08 phylonium_1.7-3.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2297 Sep 18 07:08 phylonium_1.7-3.dsc -rw-rw-r-- 1 jenkins jenkins 4913 Sep 18 07:08 phylonium_1.7-3_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 5795 Sep 18 07:08 phylonium_1.7-3_amd64.buildinfo.asc -rw-rw-r-- 1 jenkins jenkins 1442 Sep 18 07:08 phylonium_1.7-3_amd64.changes -rw-r--r-- 1 jenkins jenkins 300272 Sep 18 07:08 phylonium_1.7-3_amd64.deb -rw-rw-r-- 1 jenkins jenkins 1289 Sep 18 07:08 phylonium_1.7-3_source.changes Thu Sep 18 07:08:19 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Thu Sep 18 07:08:19 UTC 2025 I: phylonium_1.7-3_amd64.changes: Format: 1.8 Date: Fri, 29 Mar 2024 12:36:56 +0100 Source: phylonium Binary: phylonium phylonium-dbgsym Architecture: amd64 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: ba042e0140eaca4d96114cd737facc33fcb273f4 549040 phylonium-dbgsym_1.7-3_amd64.deb 3e298d4820deea5aa9c91c6b1ad8564ca7aaea64 4913 phylonium_1.7-3_amd64.buildinfo 6f47fa4a3efb2242d15b36b4218d1f2e906a36ad 300272 phylonium_1.7-3_amd64.deb Checksums-Sha256: d345aa2afabbf2947100bd9ef957e0e26677bc463ee7bbe26b587a60297c3f7d 549040 phylonium-dbgsym_1.7-3_amd64.deb 2a7a4266338f2ef28c25c3d55435bb0b39095db1ce8b877572aeadcf95a60c36 4913 phylonium_1.7-3_amd64.buildinfo 389f9107faa5001defa8829d98e2e7cf2e9429d72240e4b7d47059d6514fc36f 300272 phylonium_1.7-3_amd64.deb Files: 20132a72c717ea5f58e65b7727b72634 549040 debug optional phylonium-dbgsym_1.7-3_amd64.deb e364b30e118c0bc3b98fa8e858941116 4913 science optional phylonium_1.7-3_amd64.buildinfo 3a1e807e0e932009082a2429ed6b5abf 300272 science optional phylonium_1.7-3_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/phylonium_1.7-3.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/phylonium_1.7-3.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/phylonium_1.7-3.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/phylonium_1.7-3.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/amd64/phylonium_1.7-3_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/phylonium_1.7-3.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-09-18 07:06:29.934265343 +0000 +++ b2/build.log 2025-09-18 07:08:19.742405257 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Oct 21 01:24:50 -12 2026 -I: pbuilder-time-stamp: 1792589090 +I: Current time: Thu Sep 18 21:06:31 +14 2025 +I: pbuilder-time-stamp: 1758179191 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -26,53 +26,85 @@ 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/1362235/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3509668/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Sep 18 07:06 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3509668/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3509668/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='2fa902259de24d499e610f7fc2d1d01e' - 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='1362235' - PS1='# ' - PS2='> ' + INVOCATION_ID=d30c35d0c2ad4d54a7afe0ed414401b4 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3509668 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.MqVGIXEM/pbuilderrc_g53s --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.MqVGIXEM/b1 --logfile b1/build.log phylonium_1.7-3.dsc' - SUDO_GID='110' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.MqVGIXEM/pbuilderrc_eO62 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.MqVGIXEM/b2 --logfile b2/build.log phylonium_1.7-3.dsc' + SUDO_GID=111 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos5-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1362235/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3509668/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -141,7 +173,7 @@ Get: 29 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libdivsufsort3 amd64 2.0.1-6+b1 [45.9 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libdivsufsort-dev amd64 2.0.1-6+b1 [19.1 kB] -Fetched 11.3 MB in 4s (2926 kB/s) +Fetched 11.3 MB in 1s (19.0 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) @@ -280,7 +312,11 @@ 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 +I: user script /srv/workspace/pbuilder/3509668/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3509668/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/phylonium-1.7/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../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 @@ -403,7 +439,7 @@ config.status: executing depfiles commands make[1]: Leaving directory '/build/reproducible-path/phylonium-1.7' dh_auto_build - make -j42 + make -j40 make[1]: Entering directory '/build/reproducible-path/phylonium-1.7' make all-recursive make[2]: Entering directory '/build/reproducible-path/phylonium-1.7' @@ -412,35 +448,35 @@ rm -f libcompat.a gcc -DHAVE_CONFIG_H -I. -I.. -I../opt -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 -fcf-protection -c -o libpfasta_a-pfasta.o `test -f 'pfasta.c' || echo './'`pfasta.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fcf-protection -c -o revseqcmp.o revseqcmp.c +ar cr libcompat.a gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -mpopcnt -mssse3 -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 -fcf-protection -c -o librevseqcmp_ssse3_a-revseqcmp_ssse3.o `test -f 'revseqcmp_ssse3.c' || echo './'`revseqcmp_ssse3.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -mpopcnt -mavx2 -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 -fcf-protection -c -o librevseqcmp_avx2_a-revseqcmp_avx2.o `test -f 'revseqcmp_avx2.c' || echo './'`revseqcmp_avx2.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fcf-protection -c -o seqcmp.o seqcmp.c -ar cr libcompat.a gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -mpopcnt -msse2 -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 -fcf-protection -c -o libseqcmp_sse2_a-seqcmp_sse2.o `test -f 'seqcmp_sse2.c' || echo './'`seqcmp_sse2.c +ranlib libcompat.a gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -mpopcnt -mavx2 -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 -fcf-protection -c -o libseqcmp_avx2_a-seqcmp_avx2.o `test -f 'seqcmp_avx2.c' || echo './'`seqcmp_avx2.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -mpopcnt -mavx512bw -mavx512vl -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 -fcf-protection -c -o libseqcmp_avx512_a-seqcmp_avx512.o `test -f 'seqcmp_avx512.c' || echo './'`seqcmp_avx512.c -ranlib libcompat.a rm -f librevseqcmp_ssse3.a ar cr librevseqcmp_ssse3.a librevseqcmp_ssse3_a-revseqcmp_ssse3.o -ranlib librevseqcmp_ssse3.a rm -f libseqcmp_sse2.a ar cr libseqcmp_sse2.a libseqcmp_sse2_a-seqcmp_sse2.o +ranlib librevseqcmp_ssse3.a ranlib libseqcmp_sse2.a rm -f libpfasta.a ar cr libpfasta.a libpfasta_a-pfasta.o ranlib libpfasta.a rm -f libseqcmp_avx512.a -rm -f librevseqcmp_avx2.a ar cr libseqcmp_avx512.a libseqcmp_avx512_a-seqcmp_avx512.o -ar cr librevseqcmp_avx2.a librevseqcmp_avx2_a-revseqcmp_avx2.o ranlib libseqcmp_avx512.a +rm -f librevseqcmp_avx2.a +ar cr librevseqcmp_avx2.a librevseqcmp_avx2_a-revseqcmp_avx2.o ranlib librevseqcmp_avx2.a -rm -f libseqcmp_avx2.a -ar cr libseqcmp_avx2.a libseqcmp_avx2_a-seqcmp_avx2.o -ranlib libseqcmp_avx2.a rm -f librevseqcmp.a ar cr librevseqcmp.a revseqcmp.o librevseqcmp_ssse3.a librevseqcmp_avx2.a ranlib librevseqcmp.a +rm -f libseqcmp_avx2.a +ar cr libseqcmp_avx2.a libseqcmp_avx2_a-seqcmp_avx2.o +ranlib libseqcmp_avx2.a rm -f libseqcmp.a ar cr libseqcmp.a seqcmp.o libseqcmp_sse2.a libseqcmp_avx2.a libseqcmp_avx512.a ranlib libseqcmp.a @@ -469,7 +505,7 @@ make[2]: Leaving directory '/build/reproducible-path/phylonium-1.7' make[1]: Leaving directory '/build/reproducible-path/phylonium-1.7' dh_auto_test - make -j42 check "TESTSUITEFLAGS=-j42 --verbose" VERBOSE=1 + make -j40 check "TESTSUITEFLAGS=-j40 --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' @@ -540,7 +576,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/phylonium/ - make -j42 install DESTDIR=/build/reproducible-path/phylonium-1.7/debian/phylonium AM_UPDATE_INFO_DIR=no + make -j40 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' @@ -602,12 +638,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3509668/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3509668/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/1362235 and its subdirectories -I: Current time: Wed Oct 21 01:29:29 -12 2026 -I: pbuilder-time-stamp: 1792589369 +I: removing directory /srv/workspace/pbuilder/3509668 and its subdirectories +I: Current time: Thu Sep 18 21:08:19 +14 2025 +I: pbuilder-time-stamp: 1758179299 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/phylonium_1.7-3.diff: 73.6% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/phylonium_1.7-3.diff.gz b2/build.log: 80.0% -- replaced with stdout Compressing the 1st log... b1/build.log: 80.7% -- replaced with stdout Thu Sep 18 07:08:20 UTC 2025 I: diffoscope 306 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_phylonium_unstable_amd64_1758179300 + touch /var/log/reproducible-builds/diffoscope_stamp_phylonium_unstable_amd64_1758179300 + RESULT=0 + systemd-run '--description=diffoscope on phylonium/1.7-3 in unstable/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_22-58969 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.MqVGIXEM --run-session -c jenkins-reproducible-unstable-diffoscope-93be59e5-9843-4d8c-b0e5-580b7b69f3cc -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.MqVGIXEM/dbd-tmp-tPx4XOT ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.MqVGIXEM/phylonium_1.7-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.MqVGIXEM/phylonium_1.7-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.MqVGIXEM/phylonium_1.7-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.MqVGIXEM/b1/phylonium_1.7-3_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.MqVGIXEM/b2/phylonium_1.7-3_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_22-58969.service; invocation ID: bf2dc6c17d8c4e70a931c499b661c7af # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.MqVGIXEM/phylonium_1.7-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.MqVGIXEM/phylonium_1.7-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.MqVGIXEM/phylonium_1.7-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.MqVGIXEM/b1/phylonium_1.7-3_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.MqVGIXEM/b2/phylonium_1.7-3_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 215ms CPU time consumed: 177ms Memory peak: 17.5M (swap: 0B) _ _ _ _ __ | |__ _ _| | ___ _ __ (_)_ _ _ __ ___ | '_ \| '_ \| | | | |/ _ \| '_ \| | | | | '_ ` _ \ | |_) | | | | |_| | | (_) | | | | | |_| | | | | | | | .__/|_| |_|\__, |_|\___/|_| |_|_|\__,_|_| |_| |_| |_| |___/ Thu Sep 18 07:08:21 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Thu Sep 18 07:08:21 UTC 2025 I: phylonium from unstable built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-09-18 07:08:21] INFO: Starting at 2025-09-18 07:08:21.560107 [2025-09-18 07:08:21] INFO: Generating the pages of 1 package(s) [2025-09-18 07:08:21] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/amd64/phylonium didn't produce a buildlog, even though it has been built. [2025-09-18 07:08:21] INFO: Finished at 2025-09-18 07:08:21.794954, took: 0:00:00.234849 Thu Sep 18 07:08:21 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/phylonium.html Thu Sep 18 07:08:21 UTC 2025 I: Removing signed phylonium_1.7-3_amd64.buildinfo.asc files: removed './b1/phylonium_1.7-3_amd64.buildinfo.asc' removed './b2/phylonium_1.7-3_amd64.buildinfo.asc' 1758179301 amd64 unstable phylonium Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/phylonium_1.7-3.rbuild.log: 77.0% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/phylonium_1.7-3.rbuild.log.gz [2025-09-18 07:08:22] INFO: Starting at 2025-09-18 07:08:22.110895 [2025-09-18 07:08:22] INFO: Generating the pages of 1 package(s) [2025-09-18 07:08:22] INFO: Finished at 2025-09-18 07:08:22.339100, took: 0:00:00.228208 All cleanup done. Thu Sep 18 07:08:22 UTC 2025 - total duration: 0h 6m 57s. Thu Sep 18 07:08:22 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-NzOysqnM, removing. Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 6min 57.592s CPU time consumed: 3.049s Memory peak: 40.3M (swap: 0B)